Starting phenix.real_space_refine on Sat Mar 7 13:20:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uix_20790/03_2026/6uix_20790.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uix_20790/03_2026/6uix_20790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uix_20790/03_2026/6uix_20790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uix_20790/03_2026/6uix_20790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uix_20790/03_2026/6uix_20790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uix_20790/03_2026/6uix_20790.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 154 5.16 5 C 28776 2.51 5 N 8030 2.21 5 O 7238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44198 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "C" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "E" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "F" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "I" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "J" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "K" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "L" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "M" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "N" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "O" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "P" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "Q" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "R" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "S" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "T" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "U" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "V" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2009 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 15, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Time building chain proxies: 10.36, per 1000 atoms: 0.23 Number of scatterers: 44198 At special positions: 0 Unit cell: (148.77, 146.718, 189.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 154 16.00 O 7238 8.00 N 8030 7.00 C 28776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.02 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.02 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.02 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.02 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.02 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.02 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.02 Simple disulfide: pdb=" SG CYS L 46 " - pdb=" SG CYS L 130 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 162 " distance=2.02 Simple disulfide: pdb=" SG CYS M 46 " - pdb=" SG CYS M 130 " distance=2.03 Simple disulfide: pdb=" SG CYS M 48 " - pdb=" SG CYS M 162 " distance=2.02 Simple disulfide: pdb=" SG CYS N 46 " - pdb=" SG CYS N 130 " distance=2.03 Simple disulfide: pdb=" SG CYS N 48 " - pdb=" SG CYS N 162 " distance=2.02 Simple disulfide: pdb=" SG CYS O 46 " - pdb=" SG CYS O 130 " distance=2.03 Simple disulfide: pdb=" SG CYS O 48 " - pdb=" SG CYS O 162 " distance=2.02 Simple disulfide: pdb=" SG CYS P 46 " - pdb=" SG CYS P 130 " distance=2.03 Simple disulfide: pdb=" SG CYS P 48 " - pdb=" SG CYS P 162 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 46 " - pdb=" SG CYS Q 130 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 48 " - pdb=" SG CYS Q 162 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 130 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 162 " distance=2.02 Simple disulfide: pdb=" SG CYS S 46 " - pdb=" SG CYS S 130 " distance=2.03 Simple disulfide: pdb=" SG CYS S 48 " - pdb=" SG CYS S 162 " distance=2.02 Simple disulfide: pdb=" SG CYS T 46 " - pdb=" SG CYS T 130 " distance=2.03 Simple disulfide: pdb=" SG CYS T 48 " - pdb=" SG CYS T 162 " distance=2.02 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 130 " distance=2.03 Simple disulfide: pdb=" SG CYS U 48 " - pdb=" SG CYS U 162 " distance=2.02 Simple disulfide: pdb=" SG CYS V 46 " - pdb=" SG CYS V 130 " distance=2.03 Simple disulfide: pdb=" SG CYS V 48 " - pdb=" SG CYS V 162 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 2.1 seconds 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11528 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 22 sheets defined 79.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 32 through 40 Processing helix chain 'A' and resid 52 through 76 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 169 through 209 Processing helix chain 'A' and resid 214 through 251 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 52 through 76 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 169 through 209 Processing helix chain 'B' and resid 214 through 251 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 52 through 76 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.507A pdb=" N VAL C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 169 through 209 Processing helix chain 'C' and resid 214 through 251 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 52 through 76 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 169 through 209 Processing helix chain 'D' and resid 214 through 251 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 52 through 76 Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU E 155 " --> pdb=" O ALA E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 169 through 209 Processing helix chain 'E' and resid 214 through 251 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 306 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 52 through 76 Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 111 Processing helix chain 'F' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 169 through 209 Processing helix chain 'F' and resid 214 through 251 Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 306 Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 52 through 76 Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 111 Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 133 Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 169 through 209 Processing helix chain 'G' and resid 214 through 251 Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 306 Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 52 through 76 Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 111 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG H 124 " --> pdb=" O ILE H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 133 Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 138 through 145 Processing helix chain 'H' and resid 149 through 159 removed outlier: 3.964A pdb=" N GLU H 155 " --> pdb=" O ALA H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 169 through 209 Processing helix chain 'H' and resid 214 through 251 Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 306 Processing helix chain 'I' and resid 33 through 40 Processing helix chain 'I' and resid 52 through 76 Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 77 through 88 removed outlier: 4.327A pdb=" N HIS I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 111 Processing helix chain 'I' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 120 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG I 124 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 133 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 138 through 145 Processing helix chain 'I' and resid 149 through 159 removed outlier: 3.964A pdb=" N GLU I 155 " --> pdb=" O ALA I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 169 through 209 Processing helix chain 'I' and resid 214 through 251 Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 306 Processing helix chain 'J' and resid 33 through 40 Processing helix chain 'J' and resid 52 through 76 Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 111 Processing helix chain 'J' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 133 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 138 through 145 Processing helix chain 'J' and resid 149 through 159 removed outlier: 3.966A pdb=" N GLU J 155 " --> pdb=" O ALA J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 163 Processing helix chain 'J' and resid 169 through 209 Processing helix chain 'J' and resid 214 through 251 Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 297 through 306 Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 52 through 76 Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 111 Processing helix chain 'K' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL K 115 " --> pdb=" O ALA K 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 120 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG K 124 " --> pdb=" O ILE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 133 Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 138 through 145 Processing helix chain 'K' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU K 155 " --> pdb=" O ALA K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 163 Processing helix chain 'K' and resid 169 through 209 Processing helix chain 'K' and resid 214 through 251 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 280 Processing helix chain 'K' and resid 297 through 306 Processing helix chain 'L' and resid 33 through 40 Processing helix chain 'L' and resid 52 through 76 Proline residue: L 64 - end of helix Processing helix chain 'L' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 111 Processing helix chain 'L' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 120 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG L 124 " --> pdb=" O ILE L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 133 Processing helix chain 'L' and resid 134 through 136 No H-bonds generated for 'chain 'L' and resid 134 through 136' Processing helix chain 'L' and resid 138 through 145 Processing helix chain 'L' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU L 155 " --> pdb=" O ALA L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 163 Processing helix chain 'L' and resid 169 through 209 Processing helix chain 'L' and resid 214 through 251 Processing helix chain 'L' and resid 257 through 267 Processing helix chain 'L' and resid 274 through 280 Processing helix chain 'L' and resid 297 through 306 Processing helix chain 'M' and resid 33 through 40 Processing helix chain 'M' and resid 52 through 76 Proline residue: M 64 - end of helix Processing helix chain 'M' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS M 88 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 111 Processing helix chain 'M' and resid 111 through 125 removed outlier: 3.507A pdb=" N VAL M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG M 124 " --> pdb=" O ILE M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 133 Processing helix chain 'M' and resid 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU M 155 " --> pdb=" O ALA M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 163 Processing helix chain 'M' and resid 169 through 209 Processing helix chain 'M' and resid 214 through 251 Processing helix chain 'M' and resid 257 through 267 Processing helix chain 'M' and resid 274 through 280 Processing helix chain 'M' and resid 297 through 306 Processing helix chain 'N' and resid 33 through 40 Processing helix chain 'N' and resid 52 through 76 Proline residue: N 64 - end of helix Processing helix chain 'N' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 111 Processing helix chain 'N' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL N 115 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE N 120 " --> pdb=" O THR N 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG N 124 " --> pdb=" O ILE N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 133 Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 138 through 145 Processing helix chain 'N' and resid 149 through 159 removed outlier: 3.964A pdb=" N GLU N 155 " --> pdb=" O ALA N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 163 Processing helix chain 'N' and resid 169 through 209 Processing helix chain 'N' and resid 214 through 251 Processing helix chain 'N' and resid 257 through 267 Processing helix chain 'N' and resid 274 through 280 Processing helix chain 'N' and resid 297 through 306 Processing helix chain 'O' and resid 33 through 40 Processing helix chain 'O' and resid 52 through 76 Proline residue: O 64 - end of helix Processing helix chain 'O' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 111 Processing helix chain 'O' and resid 111 through 125 removed outlier: 3.507A pdb=" N VAL O 115 " --> pdb=" O ALA O 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE O 120 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG O 124 " --> pdb=" O ILE O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 133 Processing helix chain 'O' and resid 134 through 136 No H-bonds generated for 'chain 'O' and resid 134 through 136' Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 163 Processing helix chain 'O' and resid 169 through 209 Processing helix chain 'O' and resid 214 through 251 Processing helix chain 'O' and resid 257 through 267 Processing helix chain 'O' and resid 274 through 280 Processing helix chain 'O' and resid 297 through 306 Processing helix chain 'P' and resid 33 through 40 Processing helix chain 'P' and resid 52 through 76 Proline residue: P 64 - end of helix Processing helix chain 'P' and resid 77 through 88 removed outlier: 4.325A pdb=" N HIS P 88 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 111 Processing helix chain 'P' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE P 120 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG P 124 " --> pdb=" O ILE P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 133 Processing helix chain 'P' and resid 134 through 136 No H-bonds generated for 'chain 'P' and resid 134 through 136' Processing helix chain 'P' and resid 138 through 145 Processing helix chain 'P' and resid 149 through 159 removed outlier: 3.966A pdb=" N GLU P 155 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 163 Processing helix chain 'P' and resid 169 through 209 Processing helix chain 'P' and resid 214 through 251 Processing helix chain 'P' and resid 257 through 267 Processing helix chain 'P' and resid 274 through 280 Processing helix chain 'P' and resid 297 through 306 Processing helix chain 'Q' and resid 33 through 40 Processing helix chain 'Q' and resid 52 through 76 Proline residue: Q 64 - end of helix Processing helix chain 'Q' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS Q 88 " --> pdb=" O ALA Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 111 Processing helix chain 'Q' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL Q 115 " --> pdb=" O ALA Q 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE Q 120 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG Q 124 " --> pdb=" O ILE Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 133 Processing helix chain 'Q' and resid 134 through 136 No H-bonds generated for 'chain 'Q' and resid 134 through 136' Processing helix chain 'Q' and resid 138 through 145 Processing helix chain 'Q' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU Q 155 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 163 Processing helix chain 'Q' and resid 169 through 209 Processing helix chain 'Q' and resid 214 through 251 Processing helix chain 'Q' and resid 257 through 267 Processing helix chain 'Q' and resid 274 through 280 Processing helix chain 'Q' and resid 297 through 306 Processing helix chain 'R' and resid 33 through 40 Processing helix chain 'R' and resid 52 through 76 Proline residue: R 64 - end of helix Processing helix chain 'R' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 111 Processing helix chain 'R' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG R 124 " --> pdb=" O ILE R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 133 Processing helix chain 'R' and resid 134 through 136 No H-bonds generated for 'chain 'R' and resid 134 through 136' Processing helix chain 'R' and resid 138 through 145 Processing helix chain 'R' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 163 Processing helix chain 'R' and resid 169 through 209 Processing helix chain 'R' and resid 214 through 251 Processing helix chain 'R' and resid 257 through 267 Processing helix chain 'R' and resid 274 through 280 Processing helix chain 'R' and resid 297 through 306 Processing helix chain 'S' and resid 33 through 40 Processing helix chain 'S' and resid 52 through 76 Proline residue: S 64 - end of helix Processing helix chain 'S' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS S 88 " --> pdb=" O ALA S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL S 115 " --> pdb=" O ALA S 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE S 120 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG S 124 " --> pdb=" O ILE S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 133 Processing helix chain 'S' and resid 134 through 136 No H-bonds generated for 'chain 'S' and resid 134 through 136' Processing helix chain 'S' and resid 138 through 145 Processing helix chain 'S' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU S 155 " --> pdb=" O ALA S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 163 Processing helix chain 'S' and resid 169 through 209 Processing helix chain 'S' and resid 214 through 251 Processing helix chain 'S' and resid 257 through 267 Processing helix chain 'S' and resid 274 through 280 Processing helix chain 'S' and resid 297 through 306 Processing helix chain 'T' and resid 33 through 40 Processing helix chain 'T' and resid 52 through 76 Proline residue: T 64 - end of helix Processing helix chain 'T' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS T 88 " --> pdb=" O ALA T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 111 Processing helix chain 'T' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL T 115 " --> pdb=" O ALA T 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE T 120 " --> pdb=" O THR T 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG T 124 " --> pdb=" O ILE T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 133 Processing helix chain 'T' and resid 134 through 136 No H-bonds generated for 'chain 'T' and resid 134 through 136' Processing helix chain 'T' and resid 138 through 145 Processing helix chain 'T' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU T 155 " --> pdb=" O ALA T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 163 Processing helix chain 'T' and resid 169 through 209 Processing helix chain 'T' and resid 214 through 251 Processing helix chain 'T' and resid 257 through 267 Processing helix chain 'T' and resid 274 through 280 Processing helix chain 'T' and resid 297 through 306 Processing helix chain 'U' and resid 33 through 40 Processing helix chain 'U' and resid 52 through 76 Proline residue: U 64 - end of helix Processing helix chain 'U' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS U 88 " --> pdb=" O ALA U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 111 Processing helix chain 'U' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL U 115 " --> pdb=" O ALA U 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE U 120 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG U 124 " --> pdb=" O ILE U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 133 Processing helix chain 'U' and resid 134 through 136 No H-bonds generated for 'chain 'U' and resid 134 through 136' Processing helix chain 'U' and resid 138 through 145 Processing helix chain 'U' and resid 149 through 159 removed outlier: 3.965A pdb=" N GLU U 155 " --> pdb=" O ALA U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 163 Processing helix chain 'U' and resid 169 through 209 Processing helix chain 'U' and resid 214 through 251 Processing helix chain 'U' and resid 257 through 267 Processing helix chain 'U' and resid 274 through 280 Processing helix chain 'U' and resid 297 through 306 Processing helix chain 'V' and resid 33 through 40 Processing helix chain 'V' and resid 52 through 76 Proline residue: V 64 - end of helix Processing helix chain 'V' and resid 77 through 88 removed outlier: 4.326A pdb=" N HIS V 88 " --> pdb=" O ALA V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 111 Processing helix chain 'V' and resid 111 through 125 removed outlier: 3.506A pdb=" N VAL V 115 " --> pdb=" O ALA V 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE V 120 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG V 124 " --> pdb=" O ILE V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 133 Processing helix chain 'V' and resid 134 through 136 No H-bonds generated for 'chain 'V' and resid 134 through 136' Processing helix chain 'V' and resid 138 through 145 Processing helix chain 'V' and resid 149 through 159 removed outlier: 3.966A pdb=" N GLU V 155 " --> pdb=" O ALA V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 163 Processing helix chain 'V' and resid 169 through 209 Processing helix chain 'V' and resid 214 through 251 Processing helix chain 'V' and resid 257 through 267 Processing helix chain 'V' and resid 274 through 280 Processing helix chain 'V' and resid 297 through 306 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA3, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AA4, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AA5, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AA6, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AA7, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AA8, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AA9, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AB1, first strand: chain 'J' and resid 289 through 290 Processing sheet with id=AB2, first strand: chain 'K' and resid 289 through 290 Processing sheet with id=AB3, first strand: chain 'L' and resid 289 through 290 Processing sheet with id=AB4, first strand: chain 'M' and resid 289 through 290 Processing sheet with id=AB5, first strand: chain 'N' and resid 289 through 290 Processing sheet with id=AB6, first strand: chain 'O' and resid 289 through 290 Processing sheet with id=AB7, first strand: chain 'P' and resid 289 through 290 Processing sheet with id=AB8, first strand: chain 'Q' and resid 289 through 290 Processing sheet with id=AB9, first strand: chain 'R' and resid 289 through 290 Processing sheet with id=AC1, first strand: chain 'S' and resid 289 through 290 Processing sheet with id=AC2, first strand: chain 'T' and resid 289 through 290 Processing sheet with id=AC3, first strand: chain 'U' and resid 289 through 290 Processing sheet with id=AC4, first strand: chain 'V' and resid 289 through 290 3389 hydrogen bonds defined for protein. 10035 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: 9.73 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14263 1.34 - 1.46: 10720 1.46 - 1.58: 20249 1.58 - 1.70: 0 1.70 - 1.81: 154 Bond restraints: 45386 Sorted by residual: bond pdb=" CB VAL E 247 " pdb=" CG1 VAL E 247 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.89e+00 bond pdb=" CB VAL Q 247 " pdb=" CG1 VAL Q 247 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.86e+00 bond pdb=" CB VAL N 247 " pdb=" CG1 VAL N 247 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.86e+00 bond pdb=" CB VAL P 247 " pdb=" CG1 VAL P 247 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.85e+00 bond pdb=" CB VAL F 247 " pdb=" CG1 VAL F 247 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.82e+00 ... (remaining 45381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 57529 1.58 - 3.16: 3832 3.16 - 4.73: 591 4.73 - 6.31: 264 6.31 - 7.89: 88 Bond angle restraints: 62304 Sorted by residual: angle pdb=" N GLY V 62 " pdb=" CA GLY V 62 " pdb=" C GLY V 62 " ideal model delta sigma weight residual 112.49 116.69 -4.20 1.21e+00 6.83e-01 1.20e+01 angle pdb=" N GLY D 62 " pdb=" CA GLY D 62 " pdb=" C GLY D 62 " ideal model delta sigma weight residual 112.49 116.68 -4.19 1.21e+00 6.83e-01 1.20e+01 angle pdb=" N GLY K 62 " pdb=" CA GLY K 62 " pdb=" C GLY K 62 " ideal model delta sigma weight residual 112.49 116.68 -4.19 1.21e+00 6.83e-01 1.20e+01 angle pdb=" N GLY G 62 " pdb=" CA GLY G 62 " pdb=" C GLY G 62 " ideal model delta sigma weight residual 112.49 116.66 -4.17 1.21e+00 6.83e-01 1.19e+01 angle pdb=" N GLY R 62 " pdb=" CA GLY R 62 " pdb=" C GLY R 62 " ideal model delta sigma weight residual 112.49 116.66 -4.17 1.21e+00 6.83e-01 1.19e+01 ... (remaining 62299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 23438 15.00 - 30.01: 2301 30.01 - 45.01: 661 45.01 - 60.01: 88 60.01 - 75.01: 44 Dihedral angle restraints: 26532 sinusoidal: 8734 harmonic: 17798 Sorted by residual: dihedral pdb=" CA LEU H 256 " pdb=" C LEU H 256 " pdb=" N ASN H 257 " pdb=" CA ASN H 257 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU S 256 " pdb=" C LEU S 256 " pdb=" N ASN S 257 " pdb=" CA ASN S 257 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU L 256 " pdb=" C LEU L 256 " pdb=" N ASN L 257 " pdb=" CA ASN L 257 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 26529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3791 0.034 - 0.068: 1931 0.068 - 0.102: 1087 0.102 - 0.136: 287 0.136 - 0.169: 142 Chirality restraints: 7238 Sorted by residual: chirality pdb=" CA THR I 234 " pdb=" N THR I 234 " pdb=" C THR I 234 " pdb=" CB THR I 234 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA THR B 234 " pdb=" N THR B 234 " pdb=" C THR B 234 " pdb=" CB THR B 234 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA THR U 234 " pdb=" N THR U 234 " pdb=" C THR U 234 " pdb=" CB THR U 234 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 7235 not shown) Planarity restraints: 7986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 113 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO L 114 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 114 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 114 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 113 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO J 114 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO J 114 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 114 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Q 113 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO Q 114 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO Q 114 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO Q 114 " -0.030 5.00e-02 4.00e+02 ... (remaining 7983 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6203 2.74 - 3.28: 45562 3.28 - 3.82: 79557 3.82 - 4.36: 84921 4.36 - 4.90: 147452 Nonbonded interactions: 363695 Sorted by model distance: nonbonded pdb=" OD1 ASN L 226 " pdb=" OG SER M 239 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASN A 226 " pdb=" OG SER B 239 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASN K 226 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN F 226 " pdb=" OG SER G 239 " model vdw 2.208 3.040 nonbonded pdb=" OG SER L 239 " pdb=" OD1 ASN V 226 " model vdw 2.208 3.040 ... (remaining 363690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 41.660 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.009 0.073 45430 Z= 0.406 Angle : 0.958 7.888 62392 Z= 0.540 Chirality : 0.054 0.169 7238 Planarity : 0.008 0.053 7986 Dihedral : 13.688 75.013 14872 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.08), residues: 6006 helix: -2.20 (0.06), residues: 4444 sheet: None (None), residues: 0 loop : -2.89 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 240 TYR 0.020 0.003 TYR U 214 PHE 0.012 0.002 PHE J 253 TRP 0.009 0.002 TRP B 80 HIS 0.004 0.001 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00876 (45386) covalent geometry : angle 0.95754 (62304) SS BOND : bond 0.00678 ( 44) SS BOND : angle 1.03251 ( 88) hydrogen bonds : bond 0.12798 ( 3389) hydrogen bonds : angle 6.05050 (10035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.717 Fit side-chains revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8726 (t0) cc_final: 0.8514 (t0) REVERT: A 233 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7907 (mtp180) REVERT: D 233 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7872 (mtp180) REVERT: F 228 ASP cc_start: 0.8702 (t0) cc_final: 0.8484 (t0) REVERT: F 233 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7883 (mtp180) REVERT: G 228 ASP cc_start: 0.8602 (t0) cc_final: 0.8347 (t0) REVERT: J 228 ASP cc_start: 0.8735 (t0) cc_final: 0.8443 (t0) REVERT: K 228 ASP cc_start: 0.8596 (t0) cc_final: 0.8344 (t0) REVERT: L 126 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8740 (pm20) REVERT: L 228 ASP cc_start: 0.8643 (t0) cc_final: 0.8393 (t0) REVERT: M 126 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8514 (mp0) REVERT: M 228 ASP cc_start: 0.8757 (t0) cc_final: 0.8463 (t0) REVERT: N 126 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8560 (mp0) REVERT: N 228 ASP cc_start: 0.8620 (t0) cc_final: 0.8407 (t0) REVERT: O 126 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8737 (pm20) REVERT: O 228 ASP cc_start: 0.8561 (t0) cc_final: 0.8265 (t0) REVERT: P 126 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8779 (pm20) REVERT: P 228 ASP cc_start: 0.8616 (t0) cc_final: 0.8379 (t0) REVERT: Q 126 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8547 (mp0) REVERT: Q 228 ASP cc_start: 0.8608 (t0) cc_final: 0.8364 (t0) REVERT: R 126 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8548 (pm20) REVERT: R 228 ASP cc_start: 0.8618 (t0) cc_final: 0.8278 (t0) REVERT: R 232 GLN cc_start: 0.9131 (mm110) cc_final: 0.8923 (mm110) REVERT: S 126 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8580 (mp0) REVERT: S 228 ASP cc_start: 0.8605 (t0) cc_final: 0.8379 (t0) REVERT: T 126 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8603 (mp0) REVERT: T 228 ASP cc_start: 0.8705 (t0) cc_final: 0.8472 (t0) REVERT: U 126 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8555 (mp0) REVERT: U 228 ASP cc_start: 0.8613 (t0) cc_final: 0.8392 (t0) REVERT: V 126 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8454 (mp0) REVERT: V 228 ASP cc_start: 0.8564 (t0) cc_final: 0.8337 (t0) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2494 time to fit residues: 119.4371 Evaluate side-chains 184 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 40.0000 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 273 GLN A 279 ASN B 226 ASN B 273 GLN B 279 ASN C 226 ASN C 273 GLN C 279 ASN D 226 ASN D 273 GLN D 279 ASN E 226 ASN E 273 GLN E 279 ASN F 226 ASN F 273 GLN F 279 ASN G 226 ASN G 273 GLN G 279 ASN H 226 ASN H 273 GLN H 279 ASN I 226 ASN I 273 GLN I 279 ASN J 226 ASN J 273 GLN J 279 ASN K 226 ASN K 273 GLN K 279 ASN L 226 ASN L 273 GLN L 279 ASN M 226 ASN M 273 GLN M 279 ASN N 226 ASN N 273 GLN N 279 ASN O 226 ASN O 273 GLN O 279 ASN P 226 ASN P 273 GLN P 279 ASN Q 226 ASN Q 273 GLN Q 279 ASN R 226 ASN R 273 GLN R 279 ASN S 226 ASN S 273 GLN S 279 ASN T 226 ASN T 273 GLN T 279 ASN U 226 ASN U 273 GLN U 279 ASN V 226 ASN V 273 GLN V 279 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.061790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.045688 restraints weight = 259598.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.047231 restraints weight = 121847.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048291 restraints weight = 76807.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.048761 restraints weight = 57512.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.049272 restraints weight = 49655.271| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 45430 Z= 0.259 Angle : 0.654 6.013 62392 Z= 0.345 Chirality : 0.037 0.141 7238 Planarity : 0.005 0.029 7986 Dihedral : 4.758 18.963 6644 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.44 % Allowed : 16.00 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.10), residues: 6006 helix: 0.20 (0.07), residues: 4510 sheet: None (None), residues: 0 loop : -2.54 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 233 TYR 0.013 0.002 TYR P 223 PHE 0.011 0.001 PHE V 69 TRP 0.013 0.001 TRP S 80 HIS 0.004 0.001 HIS N 78 Details of bonding type rmsd covalent geometry : bond 0.00544 (45386) covalent geometry : angle 0.65349 (62304) SS BOND : bond 0.00342 ( 44) SS BOND : angle 0.84440 ( 88) hydrogen bonds : bond 0.03913 ( 3389) hydrogen bonds : angle 4.40754 (10035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: B 227 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: C 227 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: D 227 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: E 227 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: G 228 ASP cc_start: 0.8635 (t0) cc_final: 0.8402 (t0) REVERT: H 227 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: J 222 GLN cc_start: 0.9009 (mt0) cc_final: 0.8797 (mt0) REVERT: J 227 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: J 228 ASP cc_start: 0.8756 (t0) cc_final: 0.8516 (t0) REVERT: K 227 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: K 228 ASP cc_start: 0.8647 (t0) cc_final: 0.8446 (t0) REVERT: L 126 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8851 (pm20) REVERT: L 228 ASP cc_start: 0.8689 (t0) cc_final: 0.8469 (t0) REVERT: M 126 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8668 (pm20) REVERT: M 228 ASP cc_start: 0.8784 (t0) cc_final: 0.8506 (t0) REVERT: N 126 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8730 (pm20) REVERT: N 228 ASP cc_start: 0.8710 (t0) cc_final: 0.8501 (t0) REVERT: O 126 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8795 (pm20) REVERT: P 126 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8849 (pm20) REVERT: Q 126 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8726 (pm20) REVERT: Q 228 ASP cc_start: 0.8655 (t0) cc_final: 0.8431 (t0) REVERT: R 126 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8661 (pm20) REVERT: S 126 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8721 (pm20) REVERT: T 126 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8862 (pm20) REVERT: T 228 ASP cc_start: 0.8794 (t0) cc_final: 0.8536 (t0) REVERT: U 126 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8795 (pm20) REVERT: U 228 ASP cc_start: 0.8660 (t0) cc_final: 0.8458 (t0) REVERT: V 126 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8719 (pm20) REVERT: V 228 ASP cc_start: 0.8642 (t0) cc_final: 0.8430 (t0) outliers start: 17 outliers final: 9 residues processed: 232 average time/residue: 0.2552 time to fit residues: 103.5136 Evaluate side-chains 205 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 285 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 272 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 502 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 582 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 199 optimal weight: 0.0170 chunk 88 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 461 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 81 ASN C 81 ASN D 81 ASN E 81 ASN F 81 ASN G 81 ASN G 222 GLN H 81 ASN I 81 ASN J 81 ASN K 81 ASN P 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.062565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.046718 restraints weight = 257009.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.048334 restraints weight = 119877.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.049337 restraints weight = 74297.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.050031 restraints weight = 55567.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.050392 restraints weight = 46071.560| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 45430 Z= 0.136 Angle : 0.550 7.108 62392 Z= 0.284 Chirality : 0.035 0.100 7238 Planarity : 0.004 0.024 7986 Dihedral : 4.318 17.193 6644 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.52 % Allowed : 18.08 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.11), residues: 6006 helix: 1.18 (0.08), residues: 4532 sheet: None (None), residues: 0 loop : -2.18 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 233 TYR 0.008 0.001 TYR P 287 PHE 0.013 0.001 PHE N 69 TRP 0.009 0.001 TRP R 80 HIS 0.004 0.001 HIS V 78 Details of bonding type rmsd covalent geometry : bond 0.00285 (45386) covalent geometry : angle 0.54970 (62304) SS BOND : bond 0.00238 ( 44) SS BOND : angle 0.66340 ( 88) hydrogen bonds : bond 0.03401 ( 3389) hydrogen bonds : angle 4.07918 (10035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8062 (tm-30) REVERT: B 227 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: C 229 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 227 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: G 227 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: G 228 ASP cc_start: 0.8552 (t0) cc_final: 0.8247 (t0) REVERT: I 227 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: J 228 ASP cc_start: 0.8693 (t0) cc_final: 0.8388 (t0) REVERT: K 227 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: K 228 ASP cc_start: 0.8532 (t0) cc_final: 0.8327 (t0) REVERT: L 126 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8827 (pm20) REVERT: M 126 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8669 (pm20) REVERT: M 222 GLN cc_start: 0.8913 (mt0) cc_final: 0.8680 (mt0) REVERT: M 228 ASP cc_start: 0.8711 (t0) cc_final: 0.8375 (t0) REVERT: N 126 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8709 (pm20) REVERT: N 228 ASP cc_start: 0.8608 (t0) cc_final: 0.8352 (t0) REVERT: O 126 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8808 (pm20) REVERT: P 126 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8856 (pm20) REVERT: Q 126 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8737 (pm20) REVERT: Q 228 ASP cc_start: 0.8584 (t0) cc_final: 0.8355 (t0) REVERT: R 126 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8780 (pm20) REVERT: R 228 ASP cc_start: 0.8570 (t0) cc_final: 0.8336 (t0) REVERT: R 229 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8403 (tm-30) REVERT: R 232 GLN cc_start: 0.9031 (mm110) cc_final: 0.8742 (mm110) REVERT: S 126 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8740 (pm20) REVERT: T 126 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8857 (pm20) REVERT: T 228 ASP cc_start: 0.8701 (t0) cc_final: 0.8410 (t0) REVERT: U 126 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8800 (pm20) REVERT: U 228 ASP cc_start: 0.8620 (t0) cc_final: 0.8392 (t0) REVERT: U 229 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8141 (tm-30) REVERT: V 126 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8803 (pm20) REVERT: V 228 ASP cc_start: 0.8555 (t0) cc_final: 0.8267 (t0) outliers start: 20 outliers final: 15 residues processed: 232 average time/residue: 0.2373 time to fit residues: 97.2876 Evaluate side-chains 211 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 287 optimal weight: 6.9990 chunk 530 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 389 optimal weight: 40.0000 chunk 72 optimal weight: 7.9990 chunk 593 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 0.0980 chunk 494 optimal weight: 2.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 300 HIS R 232 GLN U 300 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.061912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.045892 restraints weight = 258412.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.047445 restraints weight = 119486.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.048506 restraints weight = 75102.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.049127 restraints weight = 56247.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.049514 restraints weight = 47258.059| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 45430 Z= 0.171 Angle : 0.561 7.499 62392 Z= 0.290 Chirality : 0.035 0.105 7238 Planarity : 0.004 0.023 7986 Dihedral : 4.125 15.252 6644 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.74 % Allowed : 18.88 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.11), residues: 6006 helix: 1.68 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -2.04 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 233 TYR 0.008 0.001 TYR E 223 PHE 0.039 0.001 PHE V 69 TRP 0.008 0.001 TRP P 80 HIS 0.003 0.001 HIS S 78 Details of bonding type rmsd covalent geometry : bond 0.00361 (45386) covalent geometry : angle 0.56036 (62304) SS BOND : bond 0.00299 ( 44) SS BOND : angle 0.66275 ( 88) hydrogen bonds : bond 0.03413 ( 3389) hydrogen bonds : angle 3.94275 (10035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 227 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: A 229 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 227 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: B 229 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8275 (tm-30) REVERT: C 191 LEU cc_start: 0.9748 (tt) cc_final: 0.9538 (pp) REVERT: C 222 GLN cc_start: 0.8907 (mt0) cc_final: 0.8672 (mt0) REVERT: C 227 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: D 227 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: E 227 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: F 227 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: G 227 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: G 228 ASP cc_start: 0.8620 (t0) cc_final: 0.8345 (t0) REVERT: H 227 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: H 229 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8263 (tm-30) REVERT: I 227 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: J 227 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: J 228 ASP cc_start: 0.8744 (t0) cc_final: 0.8436 (t0) REVERT: K 222 GLN cc_start: 0.8886 (mt0) cc_final: 0.8599 (tt0) REVERT: K 227 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: K 228 ASP cc_start: 0.8603 (t0) cc_final: 0.8389 (t0) REVERT: L 126 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8837 (pm20) REVERT: L 228 ASP cc_start: 0.8794 (t0) cc_final: 0.8577 (t0) REVERT: M 126 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8674 (pm20) REVERT: M 228 ASP cc_start: 0.8759 (t0) cc_final: 0.8404 (t0) REVERT: N 126 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8739 (pm20) REVERT: N 228 ASP cc_start: 0.8675 (t0) cc_final: 0.8431 (t0) REVERT: O 126 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8819 (pm20) REVERT: O 227 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: P 126 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8861 (pm20) REVERT: Q 126 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8752 (pm20) REVERT: Q 228 ASP cc_start: 0.8658 (t0) cc_final: 0.8412 (t0) REVERT: R 126 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8801 (pm20) REVERT: S 126 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8732 (pm20) REVERT: T 126 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8888 (pm20) REVERT: T 228 ASP cc_start: 0.8784 (t0) cc_final: 0.8505 (t0) REVERT: U 126 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8802 (pm20) REVERT: U 228 ASP cc_start: 0.8660 (t0) cc_final: 0.8422 (t0) REVERT: V 126 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8812 (pm20) REVERT: V 222 GLN cc_start: 0.9006 (mt0) cc_final: 0.8696 (tt0) REVERT: V 228 ASP cc_start: 0.8659 (t0) cc_final: 0.8403 (t0) outliers start: 67 outliers final: 39 residues processed: 268 average time/residue: 0.2263 time to fit residues: 109.3557 Evaluate side-chains 239 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 232 GLN Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 123 optimal weight: 20.0000 chunk 517 optimal weight: 9.9990 chunk 428 optimal weight: 0.9980 chunk 519 optimal weight: 50.0000 chunk 584 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 340 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 531 optimal weight: 5.9990 chunk 331 optimal weight: 10.0000 chunk 434 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 300 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.061878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.045873 restraints weight = 258414.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.047378 restraints weight = 119496.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.048419 restraints weight = 76621.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.049131 restraints weight = 57429.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.049487 restraints weight = 47487.021| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 45430 Z= 0.165 Angle : 0.560 8.084 62392 Z= 0.286 Chirality : 0.036 0.105 7238 Planarity : 0.003 0.023 7986 Dihedral : 4.028 14.276 6644 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.23 % Allowed : 19.25 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.11), residues: 6006 helix: 1.97 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.93 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 233 TYR 0.007 0.001 TYR P 287 PHE 0.033 0.001 PHE V 69 TRP 0.008 0.001 TRP O 80 HIS 0.003 0.001 HIS S 78 Details of bonding type rmsd covalent geometry : bond 0.00350 (45386) covalent geometry : angle 0.56018 (62304) SS BOND : bond 0.00268 ( 44) SS BOND : angle 0.61810 ( 88) hydrogen bonds : bond 0.03359 ( 3389) hydrogen bonds : angle 3.88126 (10035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 198 time to evaluate : 1.657 Fit side-chains REVERT: A 227 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: A 229 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 227 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: B 229 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8220 (tm-30) REVERT: C 191 LEU cc_start: 0.9754 (tt) cc_final: 0.9547 (pp) REVERT: C 227 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: D 222 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: D 227 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: E 222 GLN cc_start: 0.8998 (mt0) cc_final: 0.8726 (tt0) REVERT: E 227 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: F 222 GLN cc_start: 0.8950 (mt0) cc_final: 0.8582 (tt0) REVERT: G 227 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: G 228 ASP cc_start: 0.8620 (t0) cc_final: 0.8347 (t0) REVERT: H 227 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: H 229 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8198 (tm-30) REVERT: I 227 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: J 222 GLN cc_start: 0.8951 (mt0) cc_final: 0.8740 (tt0) REVERT: J 227 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: J 228 ASP cc_start: 0.8744 (t0) cc_final: 0.8453 (t0) REVERT: K 227 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: K 228 ASP cc_start: 0.8614 (t0) cc_final: 0.8377 (t0) REVERT: L 126 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8839 (pm20) REVERT: L 227 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: L 228 ASP cc_start: 0.8797 (t0) cc_final: 0.8536 (t0) REVERT: M 126 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8677 (pm20) REVERT: M 222 GLN cc_start: 0.8955 (mt0) cc_final: 0.8555 (tt0) REVERT: M 228 ASP cc_start: 0.8787 (t0) cc_final: 0.8437 (t0) REVERT: N 126 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8735 (pm20) REVERT: N 222 GLN cc_start: 0.8975 (mt0) cc_final: 0.8645 (tt0) REVERT: N 228 ASP cc_start: 0.8689 (t0) cc_final: 0.8453 (t0) REVERT: O 126 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8821 (pm20) REVERT: O 227 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: P 126 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8840 (pm20) REVERT: Q 126 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8752 (pm20) REVERT: Q 228 ASP cc_start: 0.8662 (t0) cc_final: 0.8417 (t0) REVERT: R 126 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8772 (pm20) REVERT: R 222 GLN cc_start: 0.8930 (mt0) cc_final: 0.8594 (tt0) REVERT: S 126 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8711 (pm20) REVERT: T 126 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8877 (pm20) REVERT: T 228 ASP cc_start: 0.8781 (t0) cc_final: 0.8492 (t0) REVERT: U 126 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8800 (pm20) REVERT: U 228 ASP cc_start: 0.8660 (t0) cc_final: 0.8417 (t0) REVERT: V 126 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8787 (pm20) REVERT: V 228 ASP cc_start: 0.8652 (t0) cc_final: 0.8390 (t0) outliers start: 86 outliers final: 56 residues processed: 277 average time/residue: 0.2214 time to fit residues: 111.3850 Evaluate side-chains 255 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 33 optimal weight: 50.0000 chunk 473 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 454 optimal weight: 0.5980 chunk 476 optimal weight: 6.9990 chunk 536 optimal weight: 1.9990 chunk 490 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 549 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 135 optimal weight: 110.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.060854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044737 restraints weight = 260359.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.046242 restraints weight = 123426.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.047265 restraints weight = 78324.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.047896 restraints weight = 58967.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.048325 restraints weight = 49519.945| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 45430 Z= 0.230 Angle : 0.606 8.024 62392 Z= 0.310 Chirality : 0.037 0.114 7238 Planarity : 0.004 0.024 7986 Dihedral : 4.028 14.592 6644 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.88 % Allowed : 18.81 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.11), residues: 6006 helix: 2.10 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.93 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 233 TYR 0.008 0.002 TYR H 223 PHE 0.030 0.001 PHE U 69 TRP 0.009 0.001 TRP R 80 HIS 0.004 0.001 HIS S 78 Details of bonding type rmsd covalent geometry : bond 0.00487 (45386) covalent geometry : angle 0.60577 (62304) SS BOND : bond 0.00331 ( 44) SS BOND : angle 0.67104 ( 88) hydrogen bonds : bond 0.03528 ( 3389) hydrogen bonds : angle 3.92058 (10035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 185 time to evaluate : 1.682 Fit side-chains REVERT: A 191 LEU cc_start: 0.9754 (tt) cc_final: 0.9528 (pp) REVERT: A 227 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: A 229 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8170 (tm-30) REVERT: B 227 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: C 222 GLN cc_start: 0.8896 (mt0) cc_final: 0.8536 (tt0) REVERT: C 227 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: D 222 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8715 (tt0) REVERT: D 227 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: D 229 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 222 GLN cc_start: 0.9027 (mt0) cc_final: 0.8760 (tt0) REVERT: E 227 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: F 227 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: G 227 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: G 228 ASP cc_start: 0.8669 (t0) cc_final: 0.8414 (t0) REVERT: G 229 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8447 (tm-30) REVERT: H 227 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: I 227 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: J 222 GLN cc_start: 0.8992 (mt0) cc_final: 0.8657 (tt0) REVERT: J 227 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: J 228 ASP cc_start: 0.8804 (t0) cc_final: 0.8517 (t0) REVERT: K 222 GLN cc_start: 0.8906 (mt0) cc_final: 0.8620 (tt0) REVERT: K 227 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: K 228 ASP cc_start: 0.8687 (t0) cc_final: 0.8425 (t0) REVERT: L 126 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8876 (pm20) REVERT: L 227 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: M 126 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8689 (pm20) REVERT: M 222 GLN cc_start: 0.9005 (mt0) cc_final: 0.8785 (tt0) REVERT: N 126 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8772 (pm20) REVERT: N 222 GLN cc_start: 0.9000 (mt0) cc_final: 0.8740 (tt0) REVERT: N 228 ASP cc_start: 0.8736 (t0) cc_final: 0.8480 (t0) REVERT: O 126 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8839 (pm20) REVERT: P 126 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8844 (pm20) REVERT: Q 126 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8761 (pm20) REVERT: Q 227 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8479 (tm-30) REVERT: R 126 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8698 (pm20) REVERT: R 222 GLN cc_start: 0.8951 (mt0) cc_final: 0.8601 (tt0) REVERT: S 126 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8727 (pm20) REVERT: T 126 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8895 (pm20) REVERT: T 228 ASP cc_start: 0.8831 (t0) cc_final: 0.8548 (t0) REVERT: U 126 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8815 (pm20) REVERT: U 228 ASP cc_start: 0.8709 (t0) cc_final: 0.8466 (t0) REVERT: V 126 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8748 (pm20) REVERT: V 222 GLN cc_start: 0.9059 (mt0) cc_final: 0.8743 (tt0) REVERT: V 228 ASP cc_start: 0.8700 (t0) cc_final: 0.8433 (t0) outliers start: 111 outliers final: 84 residues processed: 291 average time/residue: 0.2117 time to fit residues: 112.7648 Evaluate side-chains 276 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 178 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 227 GLU Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 232 GLN Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 288 optimal weight: 0.9990 chunk 454 optimal weight: 0.9990 chunk 362 optimal weight: 0.0770 chunk 495 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 542 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 568 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN D 81 ASN G 81 ASN K 81 ASN N 246 ASN P 246 ASN T 246 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.061830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.045902 restraints weight = 257655.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.047446 restraints weight = 119863.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.048493 restraints weight = 75411.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.048998 restraints weight = 56489.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.049478 restraints weight = 48592.307| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 45430 Z= 0.121 Angle : 0.560 8.756 62392 Z= 0.280 Chirality : 0.035 0.117 7238 Planarity : 0.003 0.023 7986 Dihedral : 3.930 14.175 6644 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.81 % Allowed : 19.09 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.11), residues: 6006 helix: 2.23 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.77 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 233 TYR 0.008 0.001 TYR G 287 PHE 0.030 0.001 PHE U 69 TRP 0.007 0.001 TRP T 80 HIS 0.002 0.001 HIS L 78 Details of bonding type rmsd covalent geometry : bond 0.00260 (45386) covalent geometry : angle 0.56040 (62304) SS BOND : bond 0.00218 ( 44) SS BOND : angle 0.61497 ( 88) hydrogen bonds : bond 0.03190 ( 3389) hydrogen bonds : angle 3.80107 (10035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 210 time to evaluate : 1.612 Fit side-chains REVERT: A 222 GLN cc_start: 0.8959 (mt0) cc_final: 0.8702 (tt0) REVERT: A 227 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: A 229 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 227 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: C 222 GLN cc_start: 0.8916 (mt0) cc_final: 0.8510 (tt0) REVERT: C 227 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: D 222 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: D 227 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: E 222 GLN cc_start: 0.9025 (mt0) cc_final: 0.8711 (tt0) REVERT: E 227 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: F 222 GLN cc_start: 0.8978 (mt0) cc_final: 0.8561 (tt0) REVERT: F 227 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: G 227 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: G 228 ASP cc_start: 0.8647 (t0) cc_final: 0.8356 (t0) REVERT: H 222 GLN cc_start: 0.8938 (mt0) cc_final: 0.8713 (tt0) REVERT: H 227 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: I 227 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: I 229 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8473 (tm-30) REVERT: J 222 GLN cc_start: 0.8987 (mt0) cc_final: 0.8738 (tt0) REVERT: J 227 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: J 228 ASP cc_start: 0.8752 (t0) cc_final: 0.8459 (t0) REVERT: K 222 GLN cc_start: 0.8927 (mt0) cc_final: 0.8650 (tt0) REVERT: K 227 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: K 228 ASP cc_start: 0.8620 (t0) cc_final: 0.8354 (t0) REVERT: L 126 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8848 (pm20) REVERT: L 227 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: M 126 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8687 (pm20) REVERT: M 222 GLN cc_start: 0.8986 (mt0) cc_final: 0.8762 (tt0) REVERT: N 126 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8730 (pm20) REVERT: N 222 GLN cc_start: 0.9010 (mt0) cc_final: 0.8658 (tt0) REVERT: N 228 ASP cc_start: 0.8717 (t0) cc_final: 0.8448 (t0) REVERT: O 126 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8833 (pm20) REVERT: P 126 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8831 (pm20) REVERT: P 222 GLN cc_start: 0.9017 (mt0) cc_final: 0.8554 (tt0) REVERT: Q 126 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8746 (pm20) REVERT: R 126 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8688 (pm20) REVERT: R 222 GLN cc_start: 0.8972 (mt0) cc_final: 0.8684 (tt0) REVERT: S 126 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8710 (pm20) REVERT: S 222 GLN cc_start: 0.8981 (mt0) cc_final: 0.8625 (tt0) REVERT: T 126 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8874 (pm20) REVERT: T 228 ASP cc_start: 0.8808 (t0) cc_final: 0.8502 (t0) REVERT: U 126 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8796 (pm20) REVERT: U 228 ASP cc_start: 0.8732 (t0) cc_final: 0.8465 (t0) REVERT: V 126 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8766 (pm20) REVERT: V 222 GLN cc_start: 0.9060 (mt0) cc_final: 0.8689 (tt0) REVERT: V 228 ASP cc_start: 0.8681 (t0) cc_final: 0.8398 (t0) outliers start: 108 outliers final: 72 residues processed: 312 average time/residue: 0.2101 time to fit residues: 119.1137 Evaluate side-chains 269 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 184 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 232 GLN Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 75 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 402 optimal weight: 8.9990 chunk 499 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 370 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 81 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.061360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.045259 restraints weight = 261181.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.046787 restraints weight = 122307.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.047811 restraints weight = 77234.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.048490 restraints weight = 58189.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.048829 restraints weight = 48612.601| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 45430 Z= 0.178 Angle : 0.585 8.395 62392 Z= 0.295 Chirality : 0.036 0.158 7238 Planarity : 0.003 0.023 7986 Dihedral : 3.876 14.236 6644 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.12 % Allowed : 19.01 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.11), residues: 6006 helix: 2.31 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.75 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 233 TYR 0.007 0.001 TYR G 287 PHE 0.027 0.001 PHE L 69 TRP 0.007 0.001 TRP C 80 HIS 0.003 0.001 HIS L 78 Details of bonding type rmsd covalent geometry : bond 0.00380 (45386) covalent geometry : angle 0.58450 (62304) SS BOND : bond 0.00275 ( 44) SS BOND : angle 0.61163 ( 88) hydrogen bonds : bond 0.03317 ( 3389) hydrogen bonds : angle 3.79470 (10035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 184 time to evaluate : 1.632 Fit side-chains REVERT: A 222 GLN cc_start: 0.8904 (mt0) cc_final: 0.8675 (tt0) REVERT: A 227 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: A 229 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8167 (tm-30) REVERT: B 227 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: C 227 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: D 222 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: D 227 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: D 229 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8352 (tm-30) REVERT: E 227 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: F 222 GLN cc_start: 0.8961 (mt0) cc_final: 0.8572 (tt0) REVERT: F 227 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: G 227 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: G 228 ASP cc_start: 0.8639 (t0) cc_final: 0.8378 (t0) REVERT: G 229 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8402 (tm-30) REVERT: H 222 GLN cc_start: 0.8949 (mt0) cc_final: 0.8518 (tt0) REVERT: H 227 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: H 229 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8285 (tm-30) REVERT: I 227 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: J 227 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: J 228 ASP cc_start: 0.8745 (t0) cc_final: 0.8459 (t0) REVERT: K 222 GLN cc_start: 0.8876 (mt0) cc_final: 0.8639 (tt0) REVERT: K 227 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: K 228 ASP cc_start: 0.8629 (t0) cc_final: 0.8367 (t0) REVERT: L 126 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8830 (pm20) REVERT: M 126 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8696 (pm20) REVERT: N 126 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8756 (pm20) REVERT: N 222 GLN cc_start: 0.8962 (mt0) cc_final: 0.8696 (tt0) REVERT: N 228 ASP cc_start: 0.8689 (t0) cc_final: 0.8416 (t0) REVERT: O 126 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8834 (pm20) REVERT: P 126 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8837 (pm20) REVERT: P 222 GLN cc_start: 0.8983 (mt0) cc_final: 0.8644 (tt0) REVERT: Q 126 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8756 (pm20) REVERT: Q 227 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: R 126 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8694 (pm20) REVERT: R 222 GLN cc_start: 0.8939 (mt0) cc_final: 0.8622 (tt0) REVERT: S 126 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8724 (pm20) REVERT: T 126 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8900 (pm20) REVERT: T 228 ASP cc_start: 0.8781 (t0) cc_final: 0.8476 (t0) REVERT: U 126 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8811 (pm20) REVERT: U 228 ASP cc_start: 0.8682 (t0) cc_final: 0.8442 (t0) REVERT: V 126 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8789 (pm20) REVERT: V 222 GLN cc_start: 0.9009 (mt0) cc_final: 0.8754 (tt0) REVERT: V 228 ASP cc_start: 0.8659 (t0) cc_final: 0.8393 (t0) outliers start: 120 outliers final: 94 residues processed: 298 average time/residue: 0.2055 time to fit residues: 112.4794 Evaluate side-chains 288 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 181 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 227 GLU Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 232 GLN Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 367 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 549 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 394 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 573 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN J 81 ASN M 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.061613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.045590 restraints weight = 258463.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.047119 restraints weight = 120739.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.048171 restraints weight = 76285.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.048740 restraints weight = 57222.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.049189 restraints weight = 48464.651| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 45430 Z= 0.150 Angle : 0.575 8.757 62392 Z= 0.288 Chirality : 0.036 0.145 7238 Planarity : 0.003 0.022 7986 Dihedral : 3.823 14.174 6644 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.83 % Allowed : 19.35 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.11), residues: 6006 helix: 2.38 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.68 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 233 TYR 0.008 0.001 TYR G 287 PHE 0.027 0.001 PHE L 69 TRP 0.006 0.001 TRP T 80 HIS 0.002 0.000 HIS L 78 Details of bonding type rmsd covalent geometry : bond 0.00321 (45386) covalent geometry : angle 0.57462 (62304) SS BOND : bond 0.00239 ( 44) SS BOND : angle 0.59432 ( 88) hydrogen bonds : bond 0.03215 ( 3389) hydrogen bonds : angle 3.74702 (10035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 188 time to evaluate : 1.919 Fit side-chains REVERT: A 222 GLN cc_start: 0.8944 (mt0) cc_final: 0.8706 (tt0) REVERT: A 227 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: A 229 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8177 (tm-30) REVERT: C 227 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: D 222 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: D 227 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: D 229 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8324 (tm-30) REVERT: E 222 GLN cc_start: 0.9041 (mt0) cc_final: 0.8727 (tt0) REVERT: E 227 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: F 222 GLN cc_start: 0.8988 (mt0) cc_final: 0.8693 (tt0) REVERT: F 227 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: G 227 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: G 228 ASP cc_start: 0.8650 (t0) cc_final: 0.8374 (t0) REVERT: G 229 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8385 (tm-30) REVERT: H 222 GLN cc_start: 0.8955 (mt0) cc_final: 0.8513 (tt0) REVERT: H 227 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: H 229 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8276 (tm-30) REVERT: I 191 LEU cc_start: 0.9736 (tt) cc_final: 0.9507 (pp) REVERT: I 222 GLN cc_start: 0.9003 (tt0) cc_final: 0.8745 (tt0) REVERT: I 227 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: I 229 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8512 (tm-30) REVERT: J 222 GLN cc_start: 0.9040 (tt0) cc_final: 0.8838 (tt0) REVERT: J 227 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: J 228 ASP cc_start: 0.8774 (t0) cc_final: 0.8475 (t0) REVERT: K 222 GLN cc_start: 0.8903 (mt0) cc_final: 0.8630 (tt0) REVERT: K 227 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: K 228 ASP cc_start: 0.8608 (t0) cc_final: 0.8365 (t0) REVERT: L 126 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8841 (pm20) REVERT: M 126 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8713 (pm20) REVERT: N 126 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8743 (pm20) REVERT: N 222 GLN cc_start: 0.8986 (mt0) cc_final: 0.8723 (tt0) REVERT: N 228 ASP cc_start: 0.8716 (t0) cc_final: 0.8454 (t0) REVERT: O 126 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8826 (pm20) REVERT: P 126 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8827 (pm20) REVERT: P 222 GLN cc_start: 0.9005 (mt0) cc_final: 0.8648 (tt0) REVERT: Q 126 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8753 (pm20) REVERT: R 126 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8691 (pm20) REVERT: R 222 GLN cc_start: 0.8963 (mt0) cc_final: 0.8643 (tt0) REVERT: S 126 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8719 (pm20) REVERT: S 222 GLN cc_start: 0.8984 (mt0) cc_final: 0.8653 (tt0) REVERT: T 126 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8895 (pm20) REVERT: T 222 GLN cc_start: 0.9027 (mt0) cc_final: 0.8791 (tt0) REVERT: T 228 ASP cc_start: 0.8812 (t0) cc_final: 0.8503 (t0) REVERT: U 126 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8811 (pm20) REVERT: U 228 ASP cc_start: 0.8720 (t0) cc_final: 0.8474 (t0) REVERT: V 126 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8769 (pm20) REVERT: V 222 GLN cc_start: 0.9045 (mt0) cc_final: 0.8765 (tt0) REVERT: V 228 ASP cc_start: 0.8687 (t0) cc_final: 0.8414 (t0) outliers start: 109 outliers final: 95 residues processed: 294 average time/residue: 0.2158 time to fit residues: 116.1445 Evaluate side-chains 287 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 181 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 167 optimal weight: 20.0000 chunk 232 optimal weight: 1.9990 chunk 499 optimal weight: 3.9990 chunk 574 optimal weight: 9.9990 chunk 119 optimal weight: 50.0000 chunk 347 optimal weight: 7.9990 chunk 588 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.062171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.046220 restraints weight = 259408.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.047750 restraints weight = 119477.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.048820 restraints weight = 75768.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.049337 restraints weight = 56560.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.049806 restraints weight = 48403.442| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 45430 Z= 0.135 Angle : 0.568 9.228 62392 Z= 0.282 Chirality : 0.036 0.141 7238 Planarity : 0.003 0.023 7986 Dihedral : 3.711 13.856 6644 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 19.48 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.11), residues: 6006 helix: 2.50 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.61 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 233 TYR 0.007 0.001 TYR G 287 PHE 0.026 0.001 PHE L 69 TRP 0.006 0.001 TRP A 80 HIS 0.002 0.000 HIS V 78 Details of bonding type rmsd covalent geometry : bond 0.00290 (45386) covalent geometry : angle 0.56817 (62304) SS BOND : bond 0.00230 ( 44) SS BOND : angle 0.58802 ( 88) hydrogen bonds : bond 0.03108 ( 3389) hydrogen bonds : angle 3.67595 (10035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12012 Ramachandran restraints generated. 6006 Oldfield, 0 Emsley, 6006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 205 time to evaluate : 1.533 Fit side-chains REVERT: A 227 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: A 229 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 222 GLN cc_start: 0.8926 (mt0) cc_final: 0.8669 (tt0) REVERT: C 227 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: D 222 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: D 227 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: D 229 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8272 (tm-30) REVERT: E 222 GLN cc_start: 0.8967 (mt0) cc_final: 0.8708 (tt0) REVERT: E 227 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: F 222 GLN cc_start: 0.8932 (mt0) cc_final: 0.8616 (tt0) REVERT: F 227 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: G 222 GLN cc_start: 0.8916 (mt0) cc_final: 0.8589 (tt0) REVERT: G 227 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: G 228 ASP cc_start: 0.8590 (t0) cc_final: 0.8294 (t0) REVERT: H 222 GLN cc_start: 0.8920 (mt0) cc_final: 0.8508 (tt0) REVERT: H 227 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: H 229 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8272 (tm-30) REVERT: I 222 GLN cc_start: 0.8979 (tt0) cc_final: 0.8723 (tt0) REVERT: I 227 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: I 229 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8478 (tm-30) REVERT: J 227 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: J 228 ASP cc_start: 0.8693 (t0) cc_final: 0.8412 (t0) REVERT: K 222 GLN cc_start: 0.8865 (mt0) cc_final: 0.8621 (tt0) REVERT: K 227 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: K 228 ASP cc_start: 0.8564 (t0) cc_final: 0.8326 (t0) REVERT: L 126 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8841 (pm20) REVERT: M 126 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8712 (pm20) REVERT: N 126 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8740 (pm20) REVERT: N 222 GLN cc_start: 0.8950 (mt0) cc_final: 0.8701 (tt0) REVERT: N 228 ASP cc_start: 0.8661 (t0) cc_final: 0.8394 (t0) REVERT: O 126 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8824 (pm20) REVERT: O 222 GLN cc_start: 0.8878 (mt0) cc_final: 0.8678 (tt0) REVERT: P 126 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8826 (pm20) REVERT: P 222 GLN cc_start: 0.8965 (mt0) cc_final: 0.8624 (tt0) REVERT: Q 126 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8754 (pm20) REVERT: Q 227 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: R 126 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8689 (pm20) REVERT: R 222 GLN cc_start: 0.8927 (mt0) cc_final: 0.8665 (tt0) REVERT: S 126 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8726 (pm20) REVERT: S 222 GLN cc_start: 0.8934 (mt0) cc_final: 0.8687 (tt0) REVERT: T 126 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8872 (pm20) REVERT: T 222 GLN cc_start: 0.8968 (mt0) cc_final: 0.8759 (tt0) REVERT: T 228 ASP cc_start: 0.8737 (t0) cc_final: 0.8436 (t0) REVERT: U 126 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8790 (pm20) REVERT: U 228 ASP cc_start: 0.8688 (t0) cc_final: 0.8434 (t0) REVERT: V 126 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8723 (pm20) REVERT: V 222 GLN cc_start: 0.9010 (mt0) cc_final: 0.8750 (tt0) REVERT: V 228 ASP cc_start: 0.8614 (t0) cc_final: 0.8337 (t0) outliers start: 108 outliers final: 95 residues processed: 310 average time/residue: 0.2112 time to fit residues: 118.9593 Evaluate side-chains 288 residues out of total 5148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 181 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 227 GLU Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain S residue 285 TYR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 285 TYR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 285 TYR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 193 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 353 optimal weight: 0.8980 chunk 501 optimal weight: 20.0000 chunk 550 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 527 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.062475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046902 restraints weight = 263459.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.048447 restraints weight = 120411.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.049508 restraints weight = 75370.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.050090 restraints weight = 56589.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.050309 restraints weight = 48198.328| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 45430 Z= 0.129 Angle : 0.571 8.905 62392 Z= 0.282 Chirality : 0.036 0.151 7238 Planarity : 0.003 0.023 7986 Dihedral : 3.698 13.792 6644 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.01 % Allowed : 19.71 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.11), residues: 6006 helix: 2.52 (0.08), residues: 4620 sheet: None (None), residues: 0 loop : -1.54 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 233 TYR 0.007 0.001 TYR K 287 PHE 0.026 0.001 PHE L 69 TRP 0.008 0.001 TRP L 117 HIS 0.002 0.000 HIS V 78 Details of bonding type rmsd covalent geometry : bond 0.00278 (45386) covalent geometry : angle 0.57089 (62304) SS BOND : bond 0.00224 ( 44) SS BOND : angle 0.57837 ( 88) hydrogen bonds : bond 0.03097 ( 3389) hydrogen bonds : angle 3.65535 (10035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6725.36 seconds wall clock time: 118 minutes 7.73 seconds (7087.73 seconds total)