Starting phenix.real_space_refine on Thu Mar 21 09:48:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtd_34250/03_2024/8gtd_34250.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtd_34250/03_2024/8gtd_34250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtd_34250/03_2024/8gtd_34250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtd_34250/03_2024/8gtd_34250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtd_34250/03_2024/8gtd_34250.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtd_34250/03_2024/8gtd_34250.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 14784 2.51 5 N 7392 2.21 5 O 7404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29580 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "M" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "B" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "N" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "C" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "O" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "P" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "Q" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "F" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "R" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "G" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "S" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "H" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "T" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "I" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "U" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "J" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "V" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "K" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "W" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "L" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 867 Chain: "X" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Time building chain proxies: 18.55, per 1000 atoms: 0.63 Number of scatterers: 29580 At special positions: 0 Unit cell: (170.328, 170.328, 148.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 7404 8.00 N 7392 7.00 C 14784 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: 13.06 Conformation dependent library (CDL) restraints added in 9.1 seconds 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 84 sheets defined 46.1% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 347' Processing helix chain 'A' and resid 377 through 394 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 449 removed outlier: 3.588A pdb=" N PHE A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS A 435 " --> pdb=" O PHE A 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP M 27 " --> pdb=" O VAL M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 68 Processing helix chain 'M' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG M 116 " --> pdb=" O THR M 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR M 130 " --> pdb=" O GLU M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 167 Processing helix chain 'B' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 151 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 347' Processing helix chain 'B' and resid 377 through 394 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 408 through 449 removed outlier: 3.589A pdb=" N PHE B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 435 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Proline residue: B 444 - end of helix Processing helix chain 'B' and resid 458 through 464 removed outlier: 4.079A pdb=" N PHE B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 27 removed outlier: 4.431A pdb=" N ASP N 27 " --> pdb=" O VAL N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 68 Processing helix chain 'N' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG N 116 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR N 130 " --> pdb=" O GLU N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 167 Processing helix chain 'C' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 107 through 123 removed outlier: 4.100A pdb=" N GLY C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 151 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA C 345 " --> pdb=" O PRO C 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 340 through 347' Processing helix chain 'C' and resid 377 through 394 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE C 431 " --> pdb=" O GLN C 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS C 435 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Proline residue: C 444 - end of helix Processing helix chain 'C' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE C 498 " --> pdb=" O THR C 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS C 499 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP C 522 " --> pdb=" O GLN C 518 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP O 27 " --> pdb=" O VAL O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 68 Processing helix chain 'O' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG O 116 " --> pdb=" O THR O 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR O 130 " --> pdb=" O GLU O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 167 Processing helix chain 'D' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 88 Processing helix chain 'D' and resid 107 through 123 removed outlier: 4.100A pdb=" N GLY D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 151 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 239 through 241 No H-bonds generated for 'chain 'D' and resid 239 through 241' Processing helix chain 'D' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN D 346 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 340 through 347' Processing helix chain 'D' and resid 377 through 394 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE D 431 " --> pdb=" O GLN D 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS D 435 " --> pdb=" O PHE D 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP D 436 " --> pdb=" O GLU D 432 " (cutoff:3.500A) Proline residue: D 444 - end of helix Processing helix chain 'D' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE D 498 " --> pdb=" O THR D 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS D 499 " --> pdb=" O ARG D 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 502 " --> pdb=" O ILE D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP D 522 " --> pdb=" O GLN D 518 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP P 27 " --> pdb=" O VAL P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 68 Processing helix chain 'P' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG P 116 " --> pdb=" O THR P 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR P 130 " --> pdb=" O GLU P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 167 Processing helix chain 'E' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU E 54 " --> pdb=" O THR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 151 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 239 through 241 No H-bonds generated for 'chain 'E' and resid 239 through 241' Processing helix chain 'E' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU E 304 " --> pdb=" O THR E 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 317 " --> pdb=" O GLU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 347 removed outlier: 4.164A pdb=" N ASP E 344 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA E 345 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 340 through 347' Processing helix chain 'E' and resid 377 through 394 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE E 431 " --> pdb=" O GLN E 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS E 435 " --> pdb=" O PHE E 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP E 436 " --> pdb=" O GLU E 432 " (cutoff:3.500A) Proline residue: E 444 - end of helix Processing helix chain 'E' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA E 464 " --> pdb=" O ASP E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE E 498 " --> pdb=" O THR E 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS E 499 " --> pdb=" O ARG E 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG E 502 " --> pdb=" O ILE E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP E 522 " --> pdb=" O GLN E 518 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP Q 27 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 68 Processing helix chain 'Q' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG Q 116 " --> pdb=" O THR Q 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR Q 130 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 167 Processing helix chain 'F' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU F 54 " --> pdb=" O THR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 88 Processing helix chain 'F' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 151 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 239 through 241 No H-bonds generated for 'chain 'F' and resid 239 through 241' Processing helix chain 'F' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG F 303 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU F 304 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP F 344 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA F 345 " --> pdb=" O PRO F 341 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 347' Processing helix chain 'F' and resid 377 through 394 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE F 431 " --> pdb=" O GLN F 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS F 435 " --> pdb=" O PHE F 431 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP F 436 " --> pdb=" O GLU F 432 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'F' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE F 462 " --> pdb=" O LYS F 458 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA F 464 " --> pdb=" O ASP F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE F 498 " --> pdb=" O THR F 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS F 499 " --> pdb=" O ARG F 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG F 502 " --> pdb=" O ILE F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 27 removed outlier: 4.431A pdb=" N ASP R 27 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 68 Processing helix chain 'R' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG R 116 " --> pdb=" O THR R 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR R 130 " --> pdb=" O GLU R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 167 Processing helix chain 'G' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 88 Processing helix chain 'G' and resid 107 through 123 removed outlier: 4.100A pdb=" N GLY G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 151 Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 239 through 241 No H-bonds generated for 'chain 'G' and resid 239 through 241' Processing helix chain 'G' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG G 303 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU G 304 " --> pdb=" O THR G 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 317 " --> pdb=" O GLU G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP G 344 " --> pdb=" O GLY G 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA G 345 " --> pdb=" O PRO G 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN G 346 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 340 through 347' Processing helix chain 'G' and resid 377 through 394 Processing helix chain 'G' and resid 396 through 401 Processing helix chain 'G' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE G 431 " --> pdb=" O GLN G 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS G 435 " --> pdb=" O PHE G 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Proline residue: G 444 - end of helix Processing helix chain 'G' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE G 462 " --> pdb=" O LYS G 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA G 464 " --> pdb=" O ASP G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP G 480 " --> pdb=" O ASN G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE G 498 " --> pdb=" O THR G 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS G 499 " --> pdb=" O ARG G 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG G 502 " --> pdb=" O ILE G 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP G 522 " --> pdb=" O GLN G 518 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP S 27 " --> pdb=" O VAL S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 68 Processing helix chain 'S' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG S 116 " --> pdb=" O THR S 112 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR S 130 " --> pdb=" O GLU S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 167 Processing helix chain 'H' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU H 54 " --> pdb=" O THR H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 88 Processing helix chain 'H' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY H 111 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 151 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 239 through 241 No H-bonds generated for 'chain 'H' and resid 239 through 241' Processing helix chain 'H' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU H 304 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR H 317 " --> pdb=" O GLU H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP H 344 " --> pdb=" O GLY H 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA H 345 " --> pdb=" O PRO H 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN H 346 " --> pdb=" O GLU H 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 340 through 347' Processing helix chain 'H' and resid 377 through 394 Processing helix chain 'H' and resid 396 through 401 Processing helix chain 'H' and resid 408 through 449 removed outlier: 3.589A pdb=" N PHE H 431 " --> pdb=" O GLN H 427 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS H 435 " --> pdb=" O PHE H 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP H 436 " --> pdb=" O GLU H 432 " (cutoff:3.500A) Proline residue: H 444 - end of helix Processing helix chain 'H' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE H 462 " --> pdb=" O LYS H 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA H 464 " --> pdb=" O ASP H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP H 480 " --> pdb=" O ASN H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE H 498 " --> pdb=" O THR H 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS H 499 " --> pdb=" O ARG H 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG H 502 " --> pdb=" O ILE H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP H 522 " --> pdb=" O GLN H 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP T 27 " --> pdb=" O VAL T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 68 Processing helix chain 'T' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG T 116 " --> pdb=" O THR T 112 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR T 130 " --> pdb=" O GLU T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 147 through 167 Processing helix chain 'I' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU I 54 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 107 through 123 removed outlier: 4.100A pdb=" N GLY I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 151 Processing helix chain 'I' and resid 221 through 225 Processing helix chain 'I' and resid 239 through 241 No H-bonds generated for 'chain 'I' and resid 239 through 241' Processing helix chain 'I' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG I 303 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU I 304 " --> pdb=" O THR I 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR I 317 " --> pdb=" O GLU I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP I 344 " --> pdb=" O GLY I 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA I 345 " --> pdb=" O PRO I 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN I 346 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE I 347 " --> pdb=" O ASP I 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 340 through 347' Processing helix chain 'I' and resid 377 through 394 Processing helix chain 'I' and resid 396 through 401 Processing helix chain 'I' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE I 431 " --> pdb=" O GLN I 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS I 435 " --> pdb=" O PHE I 431 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP I 436 " --> pdb=" O GLU I 432 " (cutoff:3.500A) Proline residue: I 444 - end of helix Processing helix chain 'I' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE I 462 " --> pdb=" O LYS I 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA I 464 " --> pdb=" O ASP I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP I 480 " --> pdb=" O ASN I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE I 498 " --> pdb=" O THR I 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS I 499 " --> pdb=" O ARG I 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP I 522 " --> pdb=" O GLN I 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP U 27 " --> pdb=" O VAL U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 68 Processing helix chain 'U' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG U 116 " --> pdb=" O THR U 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR U 130 " --> pdb=" O GLU U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 167 Processing helix chain 'J' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU J 54 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 88 Processing helix chain 'J' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 151 Processing helix chain 'J' and resid 221 through 225 Processing helix chain 'J' and resid 239 through 241 No H-bonds generated for 'chain 'J' and resid 239 through 241' Processing helix chain 'J' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG J 303 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU J 304 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR J 317 " --> pdb=" O GLU J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP J 344 " --> pdb=" O GLY J 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA J 345 " --> pdb=" O PRO J 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN J 346 " --> pdb=" O GLU J 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE J 347 " --> pdb=" O ASP J 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 340 through 347' Processing helix chain 'J' and resid 377 through 394 Processing helix chain 'J' and resid 396 through 401 Processing helix chain 'J' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE J 431 " --> pdb=" O GLN J 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS J 435 " --> pdb=" O PHE J 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP J 436 " --> pdb=" O GLU J 432 " (cutoff:3.500A) Proline residue: J 444 - end of helix Processing helix chain 'J' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE J 462 " --> pdb=" O LYS J 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA J 464 " --> pdb=" O ASP J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP J 480 " --> pdb=" O ASN J 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE J 498 " --> pdb=" O THR J 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS J 499 " --> pdb=" O ARG J 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG J 502 " --> pdb=" O ILE J 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP J 522 " --> pdb=" O GLN J 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP V 27 " --> pdb=" O VAL V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 68 Processing helix chain 'V' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG V 116 " --> pdb=" O THR V 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR V 130 " --> pdb=" O GLU V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 167 Processing helix chain 'K' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 88 Processing helix chain 'K' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 Processing helix chain 'K' and resid 221 through 225 Processing helix chain 'K' and resid 239 through 241 No H-bonds generated for 'chain 'K' and resid 239 through 241' Processing helix chain 'K' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG K 303 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU K 304 " --> pdb=" O THR K 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR K 317 " --> pdb=" O GLU K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 removed outlier: 4.164A pdb=" N ASP K 344 " --> pdb=" O GLY K 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA K 345 " --> pdb=" O PRO K 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN K 346 " --> pdb=" O GLU K 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE K 347 " --> pdb=" O ASP K 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 340 through 347' Processing helix chain 'K' and resid 377 through 394 Processing helix chain 'K' and resid 396 through 401 Processing helix chain 'K' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE K 431 " --> pdb=" O GLN K 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS K 435 " --> pdb=" O PHE K 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP K 436 " --> pdb=" O GLU K 432 " (cutoff:3.500A) Proline residue: K 444 - end of helix Processing helix chain 'K' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE K 462 " --> pdb=" O LYS K 458 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA K 464 " --> pdb=" O ASP K 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP K 480 " --> pdb=" O ASN K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE K 498 " --> pdb=" O THR K 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS K 499 " --> pdb=" O ARG K 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG K 502 " --> pdb=" O ILE K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP K 522 " --> pdb=" O GLN K 518 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP W 27 " --> pdb=" O VAL W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 68 Processing helix chain 'W' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG W 116 " --> pdb=" O THR W 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR W 130 " --> pdb=" O GLU W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 167 Processing helix chain 'L' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU L 54 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 Processing helix chain 'L' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY L 111 " --> pdb=" O ASP L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 151 Processing helix chain 'L' and resid 221 through 225 Processing helix chain 'L' and resid 239 through 241 No H-bonds generated for 'chain 'L' and resid 239 through 241' Processing helix chain 'L' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG L 303 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU L 304 " --> pdb=" O THR L 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 317 " --> pdb=" O GLU L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP L 344 " --> pdb=" O GLY L 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA L 345 " --> pdb=" O PRO L 341 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN L 346 " --> pdb=" O GLU L 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE L 347 " --> pdb=" O ASP L 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 340 through 347' Processing helix chain 'L' and resid 377 through 394 Processing helix chain 'L' and resid 396 through 401 Processing helix chain 'L' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE L 431 " --> pdb=" O GLN L 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS L 435 " --> pdb=" O PHE L 431 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP L 436 " --> pdb=" O GLU L 432 " (cutoff:3.500A) Proline residue: L 444 - end of helix Processing helix chain 'L' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE L 462 " --> pdb=" O LYS L 458 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA L 464 " --> pdb=" O ASP L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP L 480 " --> pdb=" O ASN L 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE L 498 " --> pdb=" O THR L 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS L 499 " --> pdb=" O ARG L 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 502 " --> pdb=" O ILE L 498 " (cutoff:3.500A) Processing helix chain 'L' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP L 522 " --> pdb=" O GLN L 518 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 27 removed outlier: 4.431A pdb=" N ASP X 27 " --> pdb=" O VAL X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 68 Processing helix chain 'X' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG X 116 " --> pdb=" O THR X 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR X 130 " --> pdb=" O GLU X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG A 94 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE A 154 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA A 253 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 256 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER A 258 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG A 271 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA5, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'M' and resid 80 through 83 Processing sheet with id=AA7, first strand: chain 'M' and resid 137 through 138 removed outlier: 3.617A pdb=" N SER M 137 " --> pdb=" O SER N 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 141 through 142 removed outlier: 3.593A pdb=" N SER X 137 " --> pdb=" O SER M 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG B 94 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE B 154 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA B 253 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B 256 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER B 258 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG B 271 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'N' and resid 80 through 83 Processing sheet with id=AB6, first strand: chain 'N' and resid 137 through 138 removed outlier: 3.588A pdb=" N SER N 137 " --> pdb=" O SER O 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 94 through 96 removed outlier: 3.586A pdb=" N ARG C 94 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE C 154 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 243 through 245 removed outlier: 3.613A pdb=" N ALA C 253 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 256 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER C 258 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG C 271 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AC2, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC3, first strand: chain 'O' and resid 80 through 83 Processing sheet with id=AC4, first strand: chain 'O' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER O 137 " --> pdb=" O SER P 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG D 94 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE D 154 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA D 253 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET D 256 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER D 258 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG D 271 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 327 through 328 Processing sheet with id=AC9, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'P' and resid 80 through 83 Processing sheet with id=AD2, first strand: chain 'P' and resid 137 through 138 removed outlier: 3.597A pdb=" N SER P 137 " --> pdb=" O SER Q 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG E 94 " --> pdb=" O ARG E 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE E 154 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA E 253 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET E 256 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER E 258 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG E 271 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 327 through 328 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'Q' and resid 80 through 83 Processing sheet with id=AD9, first strand: chain 'Q' and resid 137 through 138 removed outlier: 3.595A pdb=" N SER Q 137 " --> pdb=" O SER R 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG F 94 " --> pdb=" O ARG F 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE F 154 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA F 253 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET F 256 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER F 258 " --> pdb=" O ARG F 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG F 271 " --> pdb=" O SER F 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 327 through 328 Processing sheet with id=AE5, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'R' and resid 80 through 83 Processing sheet with id=AE7, first strand: chain 'R' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER R 137 " --> pdb=" O SER S 142 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG G 94 " --> pdb=" O ARG G 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE G 154 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA G 253 " --> pdb=" O GLU G 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET G 256 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER G 258 " --> pdb=" O ARG G 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG G 271 " --> pdb=" O SER G 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 327 through 328 Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AF4, first strand: chain 'S' and resid 80 through 83 Processing sheet with id=AF5, first strand: chain 'S' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER S 137 " --> pdb=" O SER T 142 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG H 94 " --> pdb=" O ARG H 468 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE H 154 " --> pdb=" O ILE H 220 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA H 253 " --> pdb=" O GLU H 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET H 256 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER H 258 " --> pdb=" O ARG H 271 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ARG H 271 " --> pdb=" O SER H 258 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 327 through 328 Processing sheet with id=AG1, first strand: chain 'T' and resid 10 through 12 Processing sheet with id=AG2, first strand: chain 'T' and resid 80 through 83 Processing sheet with id=AG3, first strand: chain 'T' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER T 137 " --> pdb=" O SER U 142 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 94 through 96 removed outlier: 3.586A pdb=" N ARG I 94 " --> pdb=" O ARG I 468 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE I 154 " --> pdb=" O ILE I 220 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 243 through 245 removed outlier: 3.613A pdb=" N ALA I 253 " --> pdb=" O GLU I 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET I 256 " --> pdb=" O LEU I 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER I 258 " --> pdb=" O ARG I 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG I 271 " --> pdb=" O SER I 258 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 327 through 328 Processing sheet with id=AG8, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AG9, first strand: chain 'U' and resid 80 through 83 Processing sheet with id=AH1, first strand: chain 'U' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER U 137 " --> pdb=" O SER V 142 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG J 94 " --> pdb=" O ARG J 468 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE J 154 " --> pdb=" O ILE J 220 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA J 253 " --> pdb=" O GLU J 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET J 256 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER J 258 " --> pdb=" O ARG J 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG J 271 " --> pdb=" O SER J 258 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 327 through 328 Processing sheet with id=AH6, first strand: chain 'V' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'V' and resid 80 through 83 Processing sheet with id=AH8, first strand: chain 'V' and resid 137 through 138 removed outlier: 3.597A pdb=" N SER V 137 " --> pdb=" O SER W 142 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG K 94 " --> pdb=" O ARG K 468 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE K 154 " --> pdb=" O ILE K 220 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA K 253 " --> pdb=" O GLU K 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET K 256 " --> pdb=" O LEU K 273 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER K 258 " --> pdb=" O ARG K 271 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG K 271 " --> pdb=" O SER K 258 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 327 through 328 Processing sheet with id=AI4, first strand: chain 'W' and resid 10 through 12 Processing sheet with id=AI5, first strand: chain 'W' and resid 80 through 83 Processing sheet with id=AI6, first strand: chain 'W' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER W 137 " --> pdb=" O SER X 142 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG L 94 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE L 154 " --> pdb=" O ILE L 220 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA L 253 " --> pdb=" O GLU L 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET L 256 " --> pdb=" O LEU L 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER L 258 " --> pdb=" O ARG L 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG L 271 " --> pdb=" O SER L 258 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 327 through 328 Processing sheet with id=AJ2, first strand: chain 'X' and resid 10 through 12 Processing sheet with id=AJ3, first strand: chain 'X' and resid 80 through 83 2604 hydrogen bonds defined for protein. 7488 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: 14.30 Time building geometry restraints manager: 13.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.22: 1615 1.22 - 1.31: 5849 1.31 - 1.39: 7296 1.39 - 1.48: 7403 1.48 - 1.57: 7369 Bond restraints: 29532 Sorted by residual: bond pdb=" C ILE E 147 " pdb=" O ILE E 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.85e+01 bond pdb=" C ILE K 147 " pdb=" O ILE K 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.85e+01 bond pdb=" C ILE C 147 " pdb=" O ILE C 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.84e+01 bond pdb=" C ILE I 147 " pdb=" O ILE I 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.84e+01 bond pdb=" C ILE G 147 " pdb=" O ILE G 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.80e+01 ... (remaining 29527 not shown) Histogram of bond angle deviations from ideal: 99.95 - 105.10: 233 105.10 - 110.26: 2385 110.26 - 115.41: 4264 115.41 - 120.56: 17494 120.56 - 125.71: 12464 Bond angle restraints: 36840 Sorted by residual: angle pdb=" N ILE P 143 " pdb=" CA ILE P 143 " pdb=" C ILE P 143 " ideal model delta sigma weight residual 110.72 123.10 -12.38 1.01e+00 9.80e-01 1.50e+02 angle pdb=" N ILE V 143 " pdb=" CA ILE V 143 " pdb=" C ILE V 143 " ideal model delta sigma weight residual 110.72 123.08 -12.36 1.01e+00 9.80e-01 1.50e+02 angle pdb=" N ILE X 143 " pdb=" CA ILE X 143 " pdb=" C ILE X 143 " ideal model delta sigma weight residual 110.72 123.08 -12.36 1.01e+00 9.80e-01 1.50e+02 angle pdb=" N ILE R 143 " pdb=" CA ILE R 143 " pdb=" C ILE R 143 " ideal model delta sigma weight residual 110.72 123.08 -12.36 1.01e+00 9.80e-01 1.50e+02 angle pdb=" N ILE W 143 " pdb=" CA ILE W 143 " pdb=" C ILE W 143 " ideal model delta sigma weight residual 110.72 123.07 -12.35 1.01e+00 9.80e-01 1.50e+02 ... (remaining 36835 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.90: 7296 15.90 - 31.78: 48 31.78 - 47.67: 0 47.67 - 63.56: 0 63.56 - 79.45: 12 Dihedral angle restraints: 7356 sinusoidal: 12 harmonic: 7344 Sorted by residual: dihedral pdb=" CA PRO E 130 " pdb=" C PRO E 130 " pdb=" N CYS E 131 " pdb=" CA CYS E 131 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PRO L 130 " pdb=" C PRO L 130 " pdb=" N CYS L 131 " pdb=" CA CYS L 131 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PRO F 130 " pdb=" C PRO F 130 " pdb=" N CYS F 131 " pdb=" CA CYS F 131 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 7353 not shown) Chirality restraints: 0 Planarity restraints: 7356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE H 147 " -0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE H 147 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE H 147 " -0.032 2.00e-02 2.50e+03 pdb=" N ALA H 148 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 147 " 0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE E 147 " -0.087 2.00e-02 2.50e+03 pdb=" O ILE E 147 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA E 148 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 147 " -0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE K 147 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE K 147 " -0.032 2.00e-02 2.50e+03 pdb=" N ALA K 148 " -0.029 2.00e-02 2.50e+03 ... (remaining 7353 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 12788 2.81 - 3.33: 24269 3.33 - 3.85: 35855 3.85 - 4.38: 34622 4.38 - 4.90: 51011 Nonbonded interactions: 158545 Sorted by model distance: nonbonded pdb=" O ASP N 109 " pdb=" O GLU O 41 " model vdw 2.285 3.040 nonbonded pdb=" O GLU M 41 " pdb=" O ASP X 109 " model vdw 2.291 3.040 nonbonded pdb=" O ASP T 109 " pdb=" O GLU U 41 " model vdw 2.296 3.040 nonbonded pdb=" O ASP V 109 " pdb=" O GLU W 41 " model vdw 2.296 3.040 nonbonded pdb=" O ASP P 109 " pdb=" O GLU Q 41 " model vdw 2.296 3.040 ... (remaining 158540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. 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: 0.660 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: 0.020 Extract box with map and model: 5.010 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 93.050 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4289 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 : 0.014 0.108 29532 Z= 1.081 Angle : 2.156 13.358 36840 Z= 1.601 Chirality : 0.000 0.000 0 Planarity : 0.008 0.050 7356 Dihedral : 5.493 79.451 7356 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 1.64 % Allowed : 8.39 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7296 helix: 2.98 (0.09), residues: 2976 sheet: -0.17 (0.18), residues: 804 loop : -2.22 (0.09), residues: 3516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.201 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0238 time to fit residues: 0.7664 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.215 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.111 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0132 time to fit residues: 0.1954 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 50.0000 chunk 545 optimal weight: 50.0000 chunk 302 optimal weight: 40.0000 chunk 186 optimal weight: 0.0470 chunk 368 optimal weight: 50.0000 chunk 291 optimal weight: 40.0000 chunk 564 optimal weight: 50.0000 chunk 218 optimal weight: 20.0000 chunk 343 optimal weight: 0.0170 chunk 420 optimal weight: 40.0000 chunk 653 optimal weight: 50.0000 overall best weight: 20.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4802 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 29532 Z= 0.245 Angle : 0.690 6.349 36840 Z= 0.424 Chirality : 0.000 0.000 0 Planarity : 0.004 0.016 7356 Dihedral : 6.063 26.393 7356 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.10), residues: 7296 helix: 2.69 (0.09), residues: 2868 sheet: -0.69 (0.16), residues: 948 loop : -2.63 (0.10), residues: 3480 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0189 time to fit residues: 0.7163 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.195 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0105 time to fit residues: 0.1572 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 30.0000 chunk 202 optimal weight: 40.0000 chunk 544 optimal weight: 40.0000 chunk 445 optimal weight: 20.0000 chunk 180 optimal weight: 50.0000 chunk 655 optimal weight: 40.0000 chunk 707 optimal weight: 50.0000 chunk 583 optimal weight: 30.0000 chunk 649 optimal weight: 50.0000 chunk 223 optimal weight: 0.8980 chunk 525 optimal weight: 40.0000 overall best weight: 24.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4897 moved from start: 0.8535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 29532 Z= 0.249 Angle : 0.670 6.063 36840 Z= 0.422 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 7356 Dihedral : 5.582 20.162 7356 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.87 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.10), residues: 7296 helix: 2.34 (0.09), residues: 2916 sheet: -0.87 (0.17), residues: 960 loop : -2.65 (0.10), residues: 3420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0188 time to fit residues: 0.7332 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.221 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0105 time to fit residues: 0.1676 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 50.0000 chunk 492 optimal weight: 4.9990 chunk 339 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 312 optimal weight: 0.0670 chunk 439 optimal weight: 20.0000 chunk 657 optimal weight: 9.9990 chunk 695 optimal weight: 40.0000 chunk 343 optimal weight: 0.0670 chunk 623 optimal weight: 20.0000 chunk 187 optimal weight: 50.0000 overall best weight: 7.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4854 moved from start: 0.8805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 29532 Z= 0.104 Angle : 0.417 5.632 36840 Z= 0.249 Chirality : 0.000 0.000 0 Planarity : 0.002 0.010 7356 Dihedral : 4.142 18.277 7356 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.58 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 7296 helix: 3.13 (0.09), residues: 2892 sheet: -0.72 (0.17), residues: 960 loop : -2.42 (0.10), residues: 3444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11812 Ramachandran restraints generated. 5906 Oldfield, 0 Emsley, 5906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11812 Ramachandran restraints generated. 5906 Oldfield, 0 Emsley, 5906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0177 time to fit residues: 0.6705 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.207 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0095 time to fit residues: 0.1488 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 50.0000 chunk 395 optimal weight: 50.0000 chunk 10 optimal weight: 40.0000 chunk 518 optimal weight: 2.9990 chunk 287 optimal weight: 40.0000 chunk 593 optimal weight: 50.0000 chunk 481 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 355 optimal weight: 0.0040 chunk 624 optimal weight: 40.0000 chunk 175 optimal weight: 40.0000 overall best weight: 24.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4922 moved from start: 0.9526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 29532 Z= 0.230 Angle : 0.601 6.089 36840 Z= 0.378 Chirality : 0.000 0.000 0 Planarity : 0.003 0.014 7356 Dihedral : 5.417 21.475 7356 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.16 % Favored : 86.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 7296 helix: 2.21 (0.09), residues: 2916 sheet: -0.72 (0.19), residues: 828 loop : -2.75 (0.10), residues: 3552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0186 time to fit residues: 0.7154 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.211 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0096 time to fit residues: 0.1532 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 50.0000 chunk 626 optimal weight: 30.0000 chunk 137 optimal weight: 50.0000 chunk 408 optimal weight: 10.0000 chunk 171 optimal weight: 50.0000 chunk 696 optimal weight: 50.0000 chunk 578 optimal weight: 30.0000 chunk 322 optimal weight: 40.0000 chunk 57 optimal weight: 8.9990 chunk 230 optimal weight: 30.0000 chunk 365 optimal weight: 50.0000 overall best weight: 21.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4917 moved from start: 0.9950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 29532 Z= 0.197 Angle : 0.525 5.327 36840 Z= 0.326 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 7356 Dihedral : 5.198 19.892 7356 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.50 % Favored : 87.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.10), residues: 7296 helix: 2.21 (0.09), residues: 2856 sheet: -1.39 (0.17), residues: 948 loop : -2.96 (0.10), residues: 3492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0198 time to fit residues: 0.7190 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.195 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0110 time to fit residues: 0.1517 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 chunk 396 optimal weight: 50.0000 chunk 508 optimal weight: 20.0000 chunk 394 optimal weight: 40.0000 chunk 586 optimal weight: 50.0000 chunk 389 optimal weight: 50.0000 chunk 693 optimal weight: 40.0000 chunk 434 optimal weight: 50.0000 chunk 423 optimal weight: 30.0000 chunk 320 optimal weight: 50.0000 overall best weight: 36.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4953 moved from start: 1.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 29532 Z= 0.312 Angle : 0.711 6.670 36840 Z= 0.455 Chirality : 0.000 0.000 0 Planarity : 0.004 0.016 7356 Dihedral : 6.396 25.810 7356 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.49 % Allowed : 16.28 % Favored : 83.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.10), residues: 7296 helix: 1.05 (0.09), residues: 2904 sheet: -1.56 (0.20), residues: 720 loop : -3.48 (0.09), residues: 3672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0186 time to fit residues: 0.7100 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.235 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0107 time to fit residues: 0.1625 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 50.0000 chunk 277 optimal weight: 50.0000 chunk 414 optimal weight: 50.0000 chunk 209 optimal weight: 40.0000 chunk 136 optimal weight: 50.0000 chunk 134 optimal weight: 40.0000 chunk 441 optimal weight: 30.0000 chunk 472 optimal weight: 30.0000 chunk 343 optimal weight: 50.0000 chunk 64 optimal weight: 30.0000 chunk 545 optimal weight: 50.0000 overall best weight: 34.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 moved from start: 1.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 29532 Z= 0.296 Angle : 0.667 5.479 36840 Z= 0.428 Chirality : 0.000 0.000 0 Planarity : 0.004 0.017 7356 Dihedral : 6.296 25.973 7356 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.11 % Favored : 82.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.10), residues: 7296 helix: 0.94 (0.09), residues: 2820 sheet: -2.07 (0.19), residues: 852 loop : -3.80 (0.09), residues: 3624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0191 time to fit residues: 0.7327 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.219 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0104 time to fit residues: 0.1659 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 50.0000 chunk 664 optimal weight: 50.0000 chunk 606 optimal weight: 1.9990 chunk 646 optimal weight: 40.0000 chunk 389 optimal weight: 50.0000 chunk 281 optimal weight: 40.0000 chunk 507 optimal weight: 30.0000 chunk 198 optimal weight: 50.0000 chunk 584 optimal weight: 50.0000 chunk 611 optimal weight: 40.0000 chunk 644 optimal weight: 50.0000 overall best weight: 30.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 moved from start: 1.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 29532 Z= 0.269 Angle : 0.642 5.785 36840 Z= 0.408 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 7356 Dihedral : 6.105 26.234 7356 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.93 % Favored : 81.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.10), residues: 7296 helix: 0.90 (0.09), residues: 2820 sheet: -1.96 (0.21), residues: 732 loop : -3.83 (0.09), residues: 3744 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0198 time to fit residues: 0.7631 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.223 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0103 time to fit residues: 0.1555 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 40.0000 chunk 683 optimal weight: 20.0000 chunk 417 optimal weight: 9.9990 chunk 324 optimal weight: 50.0000 chunk 475 optimal weight: 30.0000 chunk 717 optimal weight: 20.0000 chunk 660 optimal weight: 50.0000 chunk 571 optimal weight: 50.0000 chunk 59 optimal weight: 30.0000 chunk 441 optimal weight: 30.0000 chunk 350 optimal weight: 50.0000 overall best weight: 21.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4940 moved from start: 1.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 29532 Z= 0.202 Angle : 0.542 5.643 36840 Z= 0.339 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.525 27.134 7356 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.66 % Allowed : 15.13 % Favored : 84.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.10), residues: 7296 helix: 1.27 (0.10), residues: 2904 sheet: -2.41 (0.19), residues: 852 loop : -3.89 (0.09), residues: 3540 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.239 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0194 time to fit residues: 0.7407 Evaluate side-chains 12 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.204 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0100 time to fit residues: 0.1456 Evaluate side-chains 1 residues out of total 139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 40.0000 chunk 608 optimal weight: 50.0000 chunk 174 optimal weight: 50.0000 chunk 526 optimal weight: 40.0000 chunk 84 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 572 optimal weight: 40.0000 chunk 239 optimal weight: 40.0000 chunk 587 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 105 optimal weight: 50.0000 overall best weight: 33.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.082984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.075959 restraints weight = 8062.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.074049 restraints weight = 15277.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.073280 restraints weight = 21713.133| |-----------------------------------------------------------------------------| r_work (final): 0.2820 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.078039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.067421 restraints weight = 3648.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.067421 restraints weight = 3555.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.067420 restraints weight = 3555.823| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5029 moved from start: 1.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 29532 Z= 0.296 Angle : 0.668 6.090 36840 Z= 0.428 Chirality : 0.000 0.000 0 Planarity : 0.004 0.017 7356 Dihedral : 6.199 24.771 7356 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.82 % Allowed : 18.91 % Favored : 80.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.10), residues: 7296 helix: 0.84 (0.09), residues: 2832 sheet: -2.06 (0.21), residues: 708 loop : -4.02 (0.09), residues: 3756 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.89 seconds wall clock time: 60 minutes 56.10 seconds (3656.10 seconds total)