Starting phenix.real_space_refine on Wed Aug 27 01:36:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkn_38421/08_2025/8xkn_38421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkn_38421/08_2025/8xkn_38421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xkn_38421/08_2025/8xkn_38421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkn_38421/08_2025/8xkn_38421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xkn_38421/08_2025/8xkn_38421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkn_38421/08_2025/8xkn_38421.map" } resolution = 3.11 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= 0.006 sd= 0.068 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 96 5.16 5 C 29160 2.51 5 N 7416 2.21 5 O 9216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45888 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "C" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "G" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "H" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "I" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "M" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "N" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "O" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "S" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "T" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "U" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1910 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "Y" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Time building chain proxies: 8.42, per 1000 atoms: 0.18 Number of scatterers: 45888 At special positions: 0 Unit cell: (143.65, 141.95, 195.5, 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 96 16.00 O 9216 8.00 N 7416 7.00 C 29160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11040 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 59 sheets defined 4.1% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.064A pdb=" N LEU B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 78 removed outlier: 4.194A pdb=" N LEU C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 78 removed outlier: 4.087A pdb=" N LEU D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 78 removed outlier: 4.012A pdb=" N LEU E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 78 removed outlier: 4.075A pdb=" N LEU F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 78 removed outlier: 4.143A pdb=" N LEU G 73 " --> pdb=" O ASP G 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 78 removed outlier: 4.064A pdb=" N LEU H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 78 removed outlier: 4.185A pdb=" N LEU I 73 " --> pdb=" O ASP I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 78 removed outlier: 4.078A pdb=" N LEU J 73 " --> pdb=" O ASP J 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 78 removed outlier: 4.016A pdb=" N LEU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 78 removed outlier: 4.063A pdb=" N LEU L 73 " --> pdb=" O ASP L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 78 removed outlier: 4.129A pdb=" N LEU M 73 " --> pdb=" O ASP M 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 78 removed outlier: 4.098A pdb=" N LEU N 73 " --> pdb=" O ASP N 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 78 removed outlier: 4.157A pdb=" N LEU O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 78 removed outlier: 4.083A pdb=" N LEU P 73 " --> pdb=" O ASP P 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 78 removed outlier: 4.013A pdb=" N LEU Q 73 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 78 removed outlier: 4.054A pdb=" N LEU R 73 " --> pdb=" O ASP R 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 78 removed outlier: 4.147A pdb=" N LEU S 73 " --> pdb=" O ASP S 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 78 removed outlier: 4.072A pdb=" N LEU T 73 " --> pdb=" O ASP T 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 78 removed outlier: 4.177A pdb=" N LEU U 73 " --> pdb=" O ASP U 69 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 78 removed outlier: 4.040A pdb=" N LEU V 73 " --> pdb=" O ASP V 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 removed outlier: 3.969A pdb=" N LEU W 73 " --> pdb=" O ASP W 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 78 removed outlier: 4.038A pdb=" N LEU X 73 " --> pdb=" O ASP X 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 78 removed outlier: 4.088A pdb=" N LEU Y 73 " --> pdb=" O ASP Y 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'B' and resid 198 through 200 removed outlier: 4.339A pdb=" N ILE B 59 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 50 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARG B 42 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 52 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS B 40 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS B 54 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU B 38 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLU B 56 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 36 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B 58 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN B 34 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN B 60 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 32 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR B 62 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 30 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS B 64 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 97 current: chain 'B' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 123 through 126 current: chain 'C' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 21 through 24 current: chain 'C' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 48 through 65 current: chain 'C' and resid 187 through 200 Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 177 through 180 removed outlier: 3.524A pdb=" N SER B 189 " --> pdb=" O ALA B 179 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 230 through 238 current: chain 'G' and resid 123 through 126 Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 97 current: chain 'C' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 123 through 126 current: chain 'D' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 24 current: chain 'D' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 48 through 65 current: chain 'D' and resid 187 through 200 Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'D' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 82 through 97 current: chain 'D' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 123 through 126 current: chain 'E' and resid 230 through 234 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 105 Processing sheet with id=AB1, first strand: chain 'D' and resid 204 through 209 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 204 through 209 current: chain 'E' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 24 current: chain 'E' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 48 through 65 current: chain 'E' and resid 187 through 191 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 187 through 191 current: chain 'E' and resid 217 through 222 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 85 through 97 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 97 current: chain 'E' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 123 through 126 current: chain 'F' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 21 through 24 current: chain 'F' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 48 through 65 current: chain 'F' and resid 187 through 200 Processing sheet with id=AB3, first strand: chain 'E' and resid 103 through 105 Processing sheet with id=AB4, first strand: chain 'F' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 82 through 97 current: chain 'F' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 123 through 126 current: chain 'G' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 24 current: chain 'G' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 48 through 65 current: chain 'G' and resid 187 through 191 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 187 through 191 current: chain 'G' and resid 217 through 222 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 103 through 105 Processing sheet with id=AB6, first strand: chain 'G' and resid 103 through 105 Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 14 Processing sheet with id=AB8, first strand: chain 'H' and resid 27 through 43 removed outlier: 6.320A pdb=" N LYS H 64 " --> pdb=" O GLN H 28 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA H 30 " --> pdb=" O THR H 62 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR H 62 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE H 32 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN H 60 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN H 34 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU H 58 " --> pdb=" O GLN H 34 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE H 36 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLU H 56 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU H 38 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS H 54 " --> pdb=" O GLU H 38 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS H 40 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE H 52 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ARG H 42 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU H 50 " --> pdb=" O ARG H 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 48 through 65 current: chain 'H' and resid 187 through 200 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 217 through 222 current: chain 'M' and resid 123 through 126 Processing sheet with id=AB9, first strand: chain 'H' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 82 through 97 current: chain 'H' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 123 through 126 current: chain 'I' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 21 through 24 current: chain 'I' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 48 through 65 current: chain 'I' and resid 187 through 200 Processing sheet with id=AC1, first strand: chain 'H' and resid 103 through 105 Processing sheet with id=AC2, first strand: chain 'I' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 82 through 97 current: chain 'I' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 123 through 126 current: chain 'J' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 21 through 24 current: chain 'J' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 48 through 65 current: chain 'J' and resid 187 through 200 Processing sheet with id=AC3, first strand: chain 'I' and resid 103 through 105 Processing sheet with id=AC4, first strand: chain 'J' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 82 through 97 current: chain 'J' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 123 through 126 current: chain 'K' and resid 230 through 235 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AC6, first strand: chain 'J' and resid 204 through 209 removed outlier: 6.319A pdb=" N LYS K 64 " --> pdb=" O GLN K 28 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA K 30 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR K 62 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE K 32 " --> pdb=" O ASN K 60 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN K 60 " --> pdb=" O PHE K 32 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN K 34 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU K 58 " --> pdb=" O GLN K 34 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE K 36 " --> pdb=" O GLU K 56 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU K 56 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU K 38 " --> pdb=" O LYS K 54 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS K 54 " --> pdb=" O GLU K 38 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS K 40 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE K 52 " --> pdb=" O LYS K 40 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG K 42 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU K 50 " --> pdb=" O ARG K 42 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE K 59 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN K 197 " --> pdb=" O TYR K 171 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR K 171 " --> pdb=" O ASN K 197 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 85 through 97 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 85 through 97 current: chain 'K' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 123 through 126 current: chain 'L' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 21 through 24 current: chain 'L' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 48 through 65 current: chain 'L' and resid 187 through 200 Processing sheet with id=AC8, first strand: chain 'K' and resid 103 through 105 Processing sheet with id=AC9, first strand: chain 'K' and resid 177 through 180 removed outlier: 6.423A pdb=" N THR K 177 " --> pdb=" O ASP K 190 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP K 190 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA K 179 " --> pdb=" O TYR K 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 82 through 97 current: chain 'L' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 123 through 126 current: chain 'M' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 21 through 24 current: chain 'M' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 48 through 65 current: chain 'M' and resid 187 through 191 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 187 through 191 current: chain 'M' and resid 217 through 222 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AD3, first strand: chain 'M' and resid 103 through 105 Processing sheet with id=AD4, first strand: chain 'N' and resid 11 through 14 Processing sheet with id=AD5, first strand: chain 'N' and resid 27 through 43 removed outlier: 6.345A pdb=" N LYS N 64 " --> pdb=" O GLN N 28 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA N 30 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR N 62 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE N 32 " --> pdb=" O ASN N 60 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN N 60 " --> pdb=" O PHE N 32 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN N 34 " --> pdb=" O GLU N 58 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU N 58 " --> pdb=" O GLN N 34 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE N 36 " --> pdb=" O GLU N 56 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU N 56 " --> pdb=" O ILE N 36 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU N 38 " --> pdb=" O LYS N 54 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS N 54 " --> pdb=" O GLU N 38 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS N 40 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE N 52 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG N 42 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU N 50 " --> pdb=" O ARG N 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 48 through 65 current: chain 'N' and resid 187 through 200 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 217 through 222 current: chain 'S' and resid 123 through 126 Processing sheet with id=AD6, first strand: chain 'N' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 82 through 97 current: chain 'N' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 123 through 126 current: chain 'O' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 21 through 24 current: chain 'O' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 48 through 65 current: chain 'O' and resid 187 through 200 Processing sheet with id=AD7, first strand: chain 'N' and resid 103 through 105 Processing sheet with id=AD8, first strand: chain 'O' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 82 through 97 current: chain 'O' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 123 through 126 current: chain 'P' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 21 through 24 current: chain 'P' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 48 through 65 current: chain 'P' and resid 187 through 200 Processing sheet with id=AD9, first strand: chain 'O' and resid 103 through 105 Processing sheet with id=AE1, first strand: chain 'P' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 82 through 97 current: chain 'P' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 123 through 126 current: chain 'Q' and resid 230 through 234 No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'P' and resid 103 through 105 Processing sheet with id=AE3, first strand: chain 'P' and resid 204 through 209 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 204 through 209 current: chain 'Q' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 21 through 24 current: chain 'Q' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 48 through 65 current: chain 'Q' and resid 187 through 191 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 187 through 191 current: chain 'Q' and resid 217 through 222 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'Q' and resid 85 through 97 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 85 through 97 current: chain 'Q' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 123 through 126 current: chain 'R' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 21 through 24 current: chain 'R' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 48 through 65 current: chain 'R' and resid 187 through 200 Processing sheet with id=AE5, first strand: chain 'Q' and resid 103 through 105 Processing sheet with id=AE6, first strand: chain 'R' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 82 through 97 current: chain 'R' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 123 through 126 current: chain 'S' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 21 through 24 current: chain 'S' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 48 through 65 current: chain 'S' and resid 187 through 191 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 187 through 191 current: chain 'S' and resid 217 through 222 No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'R' and resid 103 through 105 Processing sheet with id=AE8, first strand: chain 'S' and resid 103 through 105 Processing sheet with id=AE9, first strand: chain 'T' and resid 11 through 14 Processing sheet with id=AF1, first strand: chain 'T' and resid 27 through 43 removed outlier: 6.324A pdb=" N LYS T 64 " --> pdb=" O GLN T 28 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA T 30 " --> pdb=" O THR T 62 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR T 62 " --> pdb=" O ALA T 30 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE T 32 " --> pdb=" O ASN T 60 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN T 60 " --> pdb=" O PHE T 32 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN T 34 " --> pdb=" O GLU T 58 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU T 58 " --> pdb=" O GLN T 34 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE T 36 " --> pdb=" O GLU T 56 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU T 56 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU T 38 " --> pdb=" O LYS T 54 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS T 54 " --> pdb=" O GLU T 38 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS T 40 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE T 52 " --> pdb=" O LYS T 40 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARG T 42 " --> pdb=" O LEU T 50 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU T 50 " --> pdb=" O ARG T 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 48 through 65 current: chain 'T' and resid 187 through 200 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 217 through 222 current: chain 'Y' and resid 123 through 126 Processing sheet with id=AF2, first strand: chain 'T' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 82 through 97 current: chain 'T' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 123 through 126 current: chain 'U' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 21 through 24 current: chain 'U' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 48 through 65 current: chain 'U' and resid 187 through 200 Processing sheet with id=AF3, first strand: chain 'T' and resid 103 through 105 Processing sheet with id=AF4, first strand: chain 'U' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 82 through 97 current: chain 'U' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 123 through 126 current: chain 'V' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 21 through 24 current: chain 'V' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 48 through 65 current: chain 'V' and resid 187 through 200 Processing sheet with id=AF5, first strand: chain 'U' and resid 103 through 105 Processing sheet with id=AF6, first strand: chain 'V' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 82 through 97 current: chain 'V' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 123 through 126 current: chain 'W' and resid 230 through 235 No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'V' and resid 103 through 105 Processing sheet with id=AF8, first strand: chain 'V' and resid 204 through 209 removed outlier: 6.368A pdb=" N LYS W 64 " --> pdb=" O GLN W 28 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA W 30 " --> pdb=" O THR W 62 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR W 62 " --> pdb=" O ALA W 30 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE W 32 " --> pdb=" O ASN W 60 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN W 60 " --> pdb=" O PHE W 32 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN W 34 " --> pdb=" O GLU W 58 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU W 58 " --> pdb=" O GLN W 34 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE W 36 " --> pdb=" O GLU W 56 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLU W 56 " --> pdb=" O ILE W 36 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU W 38 " --> pdb=" O LYS W 54 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS W 54 " --> pdb=" O GLU W 38 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS W 40 " --> pdb=" O ILE W 52 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE W 52 " --> pdb=" O LYS W 40 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG W 42 " --> pdb=" O LEU W 50 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU W 50 " --> pdb=" O ARG W 42 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE W 59 " --> pdb=" O ALA W 222 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN W 197 " --> pdb=" O TYR W 171 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR W 171 " --> pdb=" O ASN W 197 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 85 through 97 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 85 through 97 current: chain 'W' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 123 through 126 current: chain 'X' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 21 through 24 current: chain 'X' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 48 through 65 current: chain 'X' and resid 187 through 200 Processing sheet with id=AG1, first strand: chain 'W' and resid 103 through 105 Processing sheet with id=AG2, first strand: chain 'W' and resid 177 through 180 removed outlier: 6.433A pdb=" N THR W 177 " --> pdb=" O ASP W 190 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP W 190 " --> pdb=" O THR W 177 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA W 179 " --> pdb=" O TYR W 188 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 82 through 97 current: chain 'X' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 123 through 126 current: chain 'Y' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 21 through 24 current: chain 'Y' and resid 48 through 65 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 48 through 65 current: chain 'Y' and resid 187 through 191 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 187 through 191 current: chain 'Y' and resid 217 through 222 No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'X' and resid 103 through 105 Processing sheet with id=AG5, first strand: chain 'Y' and resid 103 through 105 290 hydrogen bonds defined for protein. 840 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: 5.69 Time building geometry restraints manager: 3.59 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: 14916 1.34 - 1.45: 5865 1.45 - 1.57: 25683 1.57 - 1.69: 0 1.69 - 1.80: 192 Bond restraints: 46656 Sorted by residual: bond pdb=" N VAL Y 128 " pdb=" CA VAL Y 128 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.04e+00 bond pdb=" N VAL K 128 " pdb=" CA VAL K 128 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 8.80e+00 bond pdb=" N VAL S 128 " pdb=" CA VAL S 128 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.24e-02 6.50e+03 8.80e+00 bond pdb=" N VAL P 128 " pdb=" CA VAL P 128 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.41e+00 bond pdb=" N ILE H 59 " pdb=" CA ILE H 59 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 7.95e+00 ... (remaining 46651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 62223 2.03 - 4.05: 714 4.05 - 6.08: 71 6.08 - 8.11: 9 8.11 - 10.13: 19 Bond angle restraints: 63036 Sorted by residual: angle pdb=" N VAL B 111 " pdb=" CA VAL B 111 " pdb=" C VAL B 111 " ideal model delta sigma weight residual 113.53 107.89 5.64 9.80e-01 1.04e+00 3.31e+01 angle pdb=" CA ILE V 126 " pdb=" C ILE V 126 " pdb=" O ILE V 126 " ideal model delta sigma weight residual 121.92 117.68 4.24 1.17e+00 7.31e-01 1.31e+01 angle pdb=" C THR L 101 " pdb=" N ASN L 102 " pdb=" CA ASN L 102 " ideal model delta sigma weight residual 122.46 127.55 -5.09 1.41e+00 5.03e-01 1.30e+01 angle pdb=" C THR Q 101 " pdb=" N ASN Q 102 " pdb=" CA ASN Q 102 " ideal model delta sigma weight residual 122.82 127.94 -5.12 1.42e+00 4.96e-01 1.30e+01 angle pdb=" CA THR K 130 " pdb=" CB THR K 130 " pdb=" OG1 THR K 130 " ideal model delta sigma weight residual 109.60 104.37 5.23 1.50e+00 4.44e-01 1.21e+01 ... (remaining 63031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 24848 17.97 - 35.95: 2643 35.95 - 53.92: 758 53.92 - 71.90: 148 71.90 - 89.87: 55 Dihedral angle restraints: 28452 sinusoidal: 11364 harmonic: 17088 Sorted by residual: dihedral pdb=" CA ALA C 9 " pdb=" C ALA C 9 " pdb=" N ASP C 10 " pdb=" CA ASP C 10 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ALA J 25 " pdb=" C ALA J 25 " pdb=" N GLU J 26 " pdb=" CA GLU J 26 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ALA D 25 " pdb=" C ALA D 25 " pdb=" N GLU D 26 " pdb=" CA GLU D 26 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 28449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5386 0.050 - 0.099: 1390 0.099 - 0.149: 405 0.149 - 0.198: 17 0.198 - 0.248: 2 Chirality restraints: 7200 Sorted by residual: chirality pdb=" CA ILE V 126 " pdb=" N ILE V 126 " pdb=" C ILE V 126 " pdb=" CB ILE V 126 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE P 126 " pdb=" N ILE P 126 " pdb=" C ILE P 126 " pdb=" CB ILE P 126 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL V 128 " pdb=" N VAL V 128 " pdb=" C VAL V 128 " pdb=" CB VAL V 128 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 7197 not shown) Planarity restraints: 8100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 195 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO G 196 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 196 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 196 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 195 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO M 196 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO M 196 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 196 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE K 195 " -0.040 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO K 196 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 196 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 196 " -0.033 5.00e-02 4.00e+02 ... (remaining 8097 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1532 2.70 - 3.25: 40970 3.25 - 3.80: 65802 3.80 - 4.35: 89885 4.35 - 4.90: 158131 Nonbonded interactions: 356320 Sorted by model distance: nonbonded pdb=" OE2 GLU F 93 " pdb=" OH TYR F 151 " model vdw 2.145 3.040 nonbonded pdb=" OE2 GLU G 93 " pdb=" OH TYR G 151 " model vdw 2.164 3.040 nonbonded pdb=" OE2 GLU L 93 " pdb=" OH TYR L 151 " model vdw 2.167 3.040 nonbonded pdb=" OE2 GLU R 93 " pdb=" OH TYR R 151 " model vdw 2.173 3.040 nonbonded pdb=" OE2 GLU S 93 " pdb=" OH TYR S 151 " model vdw 2.175 3.040 ... (remaining 356315 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'G' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'H' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = (chain 'L' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'M' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'N' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = (chain 'R' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'S' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'T' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = (chain 'X' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'Y' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.860 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.005 0.040 46656 Z= 0.217 Angle : 0.605 10.133 63036 Z= 0.339 Chirality : 0.047 0.248 7200 Planarity : 0.004 0.061 8100 Dihedral : 16.553 89.870 17412 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.32 % Allowed : 22.27 % Favored : 77.41 % 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 aren not related in a simple way. whole: -1.42 (0.10), residues: 5760 helix: 0.97 (0.38), residues: 216 sheet: -0.59 (0.10), residues: 2568 loop : -1.37 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 170 TYR 0.016 0.001 TYR Q 192 PHE 0.017 0.002 PHE C 13 TRP 0.004 0.001 TRP X 72 HIS 0.005 0.001 HIS K 94 Details of bonding type rmsd covalent geometry : bond 0.00482 (46656) covalent geometry : angle 0.60493 (63036) hydrogen bonds : bond 0.11226 ( 290) hydrogen bonds : angle 6.13252 ( 840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 163 LYS cc_start: 0.8406 (mttm) cc_final: 0.8057 (mtmm) REVERT: P 240 ASP cc_start: 0.7763 (m-30) cc_final: 0.7540 (m-30) REVERT: R 191 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8843 (mm) REVERT: Y 133 THR cc_start: 0.6258 (p) cc_final: 0.5856 (t) outliers start: 16 outliers final: 10 residues processed: 293 average time/residue: 0.2168 time to fit residues: 108.3359 Evaluate side-chains 275 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 264 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 177 THR Chi-restraints excluded: chain Y residue 128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN E 94 HIS G 77 GLN H 60 ASN H 77 GLN K 94 HIS M 77 GLN M 181 ASN N 77 GLN Q 94 HIS S 77 GLN S 181 ASN T 77 GLN V 152 GLN W 94 HIS W 242 ASN Y 77 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103033 restraints weight = 60287.256| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.57 r_work: 0.3242 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 46656 Z= 0.122 Angle : 0.455 8.479 63036 Z= 0.248 Chirality : 0.045 0.150 7200 Planarity : 0.003 0.043 8100 Dihedral : 4.123 47.588 6256 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.85 % Allowed : 20.54 % Favored : 76.61 % 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 aren not related in a simple way. whole: -1.42 (0.10), residues: 5760 helix: 0.93 (0.38), residues: 216 sheet: -0.64 (0.10), residues: 2568 loop : -1.32 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 170 TYR 0.008 0.001 TYR B 51 PHE 0.011 0.001 PHE C 13 TRP 0.003 0.001 TRP O 72 HIS 0.002 0.001 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00290 (46656) covalent geometry : angle 0.45460 (63036) hydrogen bonds : bond 0.03268 ( 290) hydrogen bonds : angle 4.73423 ( 840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 304 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 236 GLU cc_start: 0.8604 (tm-30) cc_final: 0.7770 (tm-30) REVERT: I 79 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: J 236 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8336 (tm-30) REVERT: K 236 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8238 (tm-30) REVERT: L 2 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7755 (mttm) REVERT: L 109 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8450 (mmmt) REVERT: P 82 GLN cc_start: 0.8041 (mp10) cc_final: 0.7564 (mp10) REVERT: P 133 THR cc_start: 0.6812 (p) cc_final: 0.6546 (p) REVERT: P 240 ASP cc_start: 0.8103 (m-30) cc_final: 0.7842 (m-30) REVERT: Q 186 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6914 (mm-30) REVERT: Q 240 ASP cc_start: 0.8187 (m-30) cc_final: 0.7918 (m-30) REVERT: S 131 ASP cc_start: 0.7292 (t0) cc_final: 0.7070 (t0) REVERT: S 236 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: T 38 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7704 (mp0) REVERT: U 236 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8091 (tm-30) REVERT: V 56 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7316 (mp0) REVERT: V 131 ASP cc_start: 0.7009 (t0) cc_final: 0.6778 (t0) REVERT: W 212 ASN cc_start: 0.8491 (t0) cc_final: 0.8261 (t0) outliers start: 142 outliers final: 92 residues processed: 419 average time/residue: 0.2017 time to fit residues: 145.1978 Evaluate side-chains 382 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 287 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain P residue 227 ASP Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 229 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 468 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 568 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100853 restraints weight = 60280.558| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.57 r_work: 0.3186 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 46656 Z= 0.189 Angle : 0.491 9.011 63036 Z= 0.267 Chirality : 0.046 0.152 7200 Planarity : 0.003 0.051 8100 Dihedral : 4.232 47.648 6243 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.88 % Allowed : 20.98 % Favored : 75.14 % 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 aren not related in a simple way. whole: -1.64 (0.10), residues: 5760 helix: 0.50 (0.35), residues: 216 sheet: -0.92 (0.10), residues: 2568 loop : -1.30 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 92 TYR 0.010 0.001 TYR B 12 PHE 0.015 0.002 PHE K 13 TRP 0.006 0.001 TRP I 72 HIS 0.002 0.001 HIS L 94 Details of bonding type rmsd covalent geometry : bond 0.00455 (46656) covalent geometry : angle 0.49072 (63036) hydrogen bonds : bond 0.03972 ( 290) hydrogen bonds : angle 4.83109 ( 840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 296 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 ASN cc_start: 0.8632 (t0) cc_final: 0.8331 (t0) REVERT: E 236 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7821 (tm-30) REVERT: G 236 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: I 79 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: I 88 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7175 (mtmm) REVERT: J 236 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8344 (tm-30) REVERT: L 2 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7814 (mttm) REVERT: L 109 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8459 (mmmt) REVERT: M 219 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8700 (mtpp) REVERT: O 176 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8502 (tmt170) REVERT: P 82 GLN cc_start: 0.8065 (mp10) cc_final: 0.7615 (mp10) REVERT: P 109 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8218 (mtpt) REVERT: P 240 ASP cc_start: 0.8155 (m-30) cc_final: 0.7888 (m-30) REVERT: Q 186 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7071 (mm-30) REVERT: R 221 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: S 131 ASP cc_start: 0.7249 (t0) cc_final: 0.6990 (t0) REVERT: S 236 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: U 204 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8363 (p90) REVERT: W 212 ASN cc_start: 0.8475 (t0) cc_final: 0.8244 (t0) outliers start: 193 outliers final: 141 residues processed: 462 average time/residue: 0.2595 time to fit residues: 207.6739 Evaluate side-chains 436 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 286 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain P residue 227 ASP Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 229 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 154 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 432 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 446 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 379 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 181 ASN S 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.130540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100501 restraints weight = 60395.305| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.57 r_work: 0.3179 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 46656 Z= 0.179 Angle : 0.477 8.546 63036 Z= 0.261 Chirality : 0.046 0.151 7200 Planarity : 0.003 0.053 8100 Dihedral : 4.175 46.821 6243 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.74 % Allowed : 21.24 % Favored : 74.02 % 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 aren not related in a simple way. whole: -1.77 (0.10), residues: 5760 helix: 0.41 (0.35), residues: 216 sheet: -1.10 (0.10), residues: 2568 loop : -1.29 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 170 TYR 0.009 0.001 TYR T 51 PHE 0.015 0.002 PHE K 13 TRP 0.005 0.001 TRP I 72 HIS 0.002 0.001 HIS L 94 Details of bonding type rmsd covalent geometry : bond 0.00431 (46656) covalent geometry : angle 0.47740 (63036) hydrogen bonds : bond 0.03776 ( 290) hydrogen bonds : angle 4.77780 ( 840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 287 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.7983 (t80) REVERT: B 212 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8438 (t0) REVERT: C 88 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6844 (mtmm) REVERT: C 212 ASN cc_start: 0.8648 (t0) cc_final: 0.8356 (t0) REVERT: E 236 GLU cc_start: 0.8671 (tm-30) cc_final: 0.7862 (tm-30) REVERT: F 92 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7333 (ptp90) REVERT: G 39 GLU cc_start: 0.7643 (pt0) cc_final: 0.7414 (pt0) REVERT: G 219 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8640 (mtpp) REVERT: G 229 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8479 (t70) REVERT: G 236 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: I 88 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7195 (mtmm) REVERT: J 236 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8385 (tm-30) REVERT: L 2 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7821 (mttm) REVERT: L 109 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8464 (mmmt) REVERT: M 26 GLU cc_start: 0.8007 (pm20) cc_final: 0.7745 (pm20) REVERT: M 219 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8714 (mtpp) REVERT: O 176 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8516 (tmt170) REVERT: P 82 GLN cc_start: 0.8063 (mp10) cc_final: 0.7603 (mp10) REVERT: P 240 ASP cc_start: 0.8175 (m-30) cc_final: 0.7901 (m-30) REVERT: Q 1 MET cc_start: 0.7455 (tpt) cc_final: 0.6777 (tpt) REVERT: R 221 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: S 73 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8681 (mp) REVERT: S 131 ASP cc_start: 0.7194 (t0) cc_final: 0.6946 (t0) REVERT: S 219 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8232 (mtpp) REVERT: S 236 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: T 38 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7628 (mp0) REVERT: U 204 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8361 (p90) REVERT: W 212 ASN cc_start: 0.8512 (t0) cc_final: 0.8273 (t0) REVERT: Y 185 GLU cc_start: 0.7783 (mt-10) cc_final: 0.6974 (mm-30) REVERT: Y 219 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8826 (mttm) outliers start: 236 outliers final: 182 residues processed: 498 average time/residue: 0.2607 time to fit residues: 223.0905 Evaluate side-chains 472 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 273 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 217 GLU Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 113 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 219 LYS Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 18 optimal weight: 8.9990 chunk 432 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 484 optimal weight: 3.9990 chunk 398 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 280 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 181 ASN S 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099554 restraints weight = 60683.277| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.55 r_work: 0.3161 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 46656 Z= 0.214 Angle : 0.504 8.919 63036 Z= 0.275 Chirality : 0.047 0.154 7200 Planarity : 0.003 0.057 8100 Dihedral : 4.300 46.628 6242 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.56 % Allowed : 21.16 % Favored : 73.27 % 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 aren not related in a simple way. whole: -1.95 (0.10), residues: 5760 helix: 0.21 (0.34), residues: 216 sheet: -1.30 (0.10), residues: 2568 loop : -1.30 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 15 TYR 0.010 0.001 TYR T 51 PHE 0.016 0.002 PHE K 13 TRP 0.005 0.001 TRP L 72 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00518 (46656) covalent geometry : angle 0.50445 (63036) hydrogen bonds : bond 0.04126 ( 290) hydrogen bonds : angle 4.88336 ( 840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 285 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7984 (t80) REVERT: B 212 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8405 (t0) REVERT: C 88 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6917 (mtmm) REVERT: C 212 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8335 (t0) REVERT: D 79 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: G 39 GLU cc_start: 0.7666 (pt0) cc_final: 0.7442 (pt0) REVERT: G 219 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8677 (mtpp) REVERT: G 229 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8515 (t70) REVERT: G 236 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: I 1 MET cc_start: 0.8030 (ttt) cc_final: 0.7821 (ttt) REVERT: I 64 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8943 (tttt) REVERT: I 88 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7225 (mtmm) REVERT: J 236 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8385 (tm-30) REVERT: L 2 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7817 (mttm) REVERT: L 109 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8488 (mmmt) REVERT: M 219 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8756 (mtpp) REVERT: O 1 MET cc_start: 0.8184 (ttt) cc_final: 0.7896 (ttt) REVERT: O 176 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8534 (tmt170) REVERT: P 82 GLN cc_start: 0.8091 (mp10) cc_final: 0.7646 (mp10) REVERT: P 109 LYS cc_start: 0.8386 (mmmt) cc_final: 0.8129 (mtpt) REVERT: P 240 ASP cc_start: 0.8196 (m-30) cc_final: 0.7929 (m-30) REVERT: R 191 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8888 (mm) REVERT: R 221 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: S 73 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8706 (mp) REVERT: S 131 ASP cc_start: 0.7194 (t0) cc_final: 0.6989 (t0) REVERT: S 219 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8276 (mtpp) REVERT: S 236 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: T 38 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7625 (mp0) REVERT: U 204 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8392 (p90) REVERT: W 212 ASN cc_start: 0.8555 (t0) cc_final: 0.8304 (t0) REVERT: X 38 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7715 (mp0) REVERT: Y 163 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8552 (mmtt) REVERT: Y 185 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7059 (mm-30) REVERT: Y 219 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8851 (mttm) outliers start: 277 outliers final: 215 residues processed: 537 average time/residue: 0.2574 time to fit residues: 236.0574 Evaluate side-chains 511 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 275 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 217 GLU Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 181 ASN Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain P residue 226 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 219 LYS Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 239 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 553 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 337 optimal weight: 0.3980 chunk 412 optimal weight: 6.9990 chunk 534 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 417 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.130405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100383 restraints weight = 60639.619| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.57 r_work: 0.3175 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 46656 Z= 0.165 Angle : 0.464 8.242 63036 Z= 0.254 Chirality : 0.045 0.151 7200 Planarity : 0.003 0.054 8100 Dihedral : 4.106 47.203 6242 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.60 % Allowed : 21.12 % Favored : 73.27 % 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 aren not related in a simple way. whole: -1.93 (0.10), residues: 5760 helix: 0.41 (0.35), residues: 216 sheet: -1.31 (0.10), residues: 2568 loop : -1.29 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 42 TYR 0.009 0.001 TYR T 51 PHE 0.014 0.001 PHE K 13 TRP 0.004 0.001 TRP L 72 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00396 (46656) covalent geometry : angle 0.46376 (63036) hydrogen bonds : bond 0.03613 ( 290) hydrogen bonds : angle 4.77048 ( 840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 298 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.7988 (t80) REVERT: B 212 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8418 (t0) REVERT: C 48 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8081 (mtmm) REVERT: C 88 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6859 (mtmm) REVERT: C 212 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8306 (t0) REVERT: C 236 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8321 (tm-30) REVERT: G 39 GLU cc_start: 0.7629 (pt0) cc_final: 0.7402 (pt0) REVERT: G 219 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8667 (mtpp) REVERT: G 229 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8487 (t70) REVERT: G 236 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: I 1 MET cc_start: 0.8016 (ttt) cc_final: 0.7762 (ttt) REVERT: I 64 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8949 (tttt) REVERT: I 88 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7183 (mtmm) REVERT: J 1 MET cc_start: 0.8206 (ttt) cc_final: 0.7979 (ttt) REVERT: J 236 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8387 (tm-30) REVERT: L 2 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7801 (mttm) REVERT: L 109 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8495 (mmmt) REVERT: M 26 GLU cc_start: 0.8004 (pm20) cc_final: 0.7766 (pm20) REVERT: M 219 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8735 (mtpp) REVERT: N 51 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.7155 (t80) REVERT: O 176 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8554 (tmt170) REVERT: O 212 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7891 (t0) REVERT: P 240 ASP cc_start: 0.8190 (m-30) cc_final: 0.7910 (m-30) REVERT: R 221 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: S 73 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8667 (mp) REVERT: S 131 ASP cc_start: 0.7215 (t0) cc_final: 0.7013 (t0) REVERT: S 219 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8240 (mtpp) REVERT: S 236 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: U 204 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8378 (p90) REVERT: V 24 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8845 (p) REVERT: W 212 ASN cc_start: 0.8515 (t0) cc_final: 0.8270 (t0) REVERT: X 38 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7732 (mp0) REVERT: Y 56 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7417 (mp0) REVERT: Y 163 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8538 (mmtt) REVERT: Y 185 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7043 (mm-30) outliers start: 279 outliers final: 219 residues processed: 550 average time/residue: 0.2565 time to fit residues: 241.5429 Evaluate side-chains 526 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 285 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 212 ASN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 135 THR Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 113 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 318 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 420 optimal weight: 4.9990 chunk 399 optimal weight: 0.9990 chunk 328 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 181 ASN S 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100353 restraints weight = 60395.578| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.56 r_work: 0.3172 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 46656 Z= 0.163 Angle : 0.462 8.191 63036 Z= 0.254 Chirality : 0.045 0.152 7200 Planarity : 0.003 0.053 8100 Dihedral : 4.057 47.223 6242 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.96 % Allowed : 21.08 % Favored : 72.95 % 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 aren not related in a simple way. whole: -1.93 (0.10), residues: 5760 helix: 0.40 (0.35), residues: 216 sheet: -1.31 (0.10), residues: 2568 loop : -1.28 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 42 TYR 0.010 0.001 TYR P 192 PHE 0.014 0.001 PHE K 13 TRP 0.004 0.001 TRP F 72 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00390 (46656) covalent geometry : angle 0.46243 (63036) hydrogen bonds : bond 0.03590 ( 290) hydrogen bonds : angle 4.76699 ( 840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 300 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8203 (ttt) cc_final: 0.8000 (ttt) REVERT: B 51 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8018 (t80) REVERT: B 212 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8414 (t0) REVERT: C 48 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8068 (mtmm) REVERT: C 88 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6879 (mtmm) REVERT: C 212 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8316 (t0) REVERT: C 236 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8305 (tm-30) REVERT: G 39 GLU cc_start: 0.7628 (pt0) cc_final: 0.7406 (pt0) REVERT: G 219 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8670 (mtpp) REVERT: G 229 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8486 (t70) REVERT: G 236 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: I 1 MET cc_start: 0.8035 (ttt) cc_final: 0.7792 (ttt) REVERT: I 64 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8946 (tttt) REVERT: J 236 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8371 (tm-30) REVERT: L 2 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7796 (mttm) REVERT: L 109 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8501 (mmmt) REVERT: M 26 GLU cc_start: 0.7984 (pm20) cc_final: 0.7724 (pm20) REVERT: M 219 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8761 (mtpp) REVERT: N 51 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.7106 (t80) REVERT: O 176 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8574 (tmt170) REVERT: O 212 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.7906 (t0) REVERT: P 109 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8130 (mtpt) REVERT: Q 69 ASP cc_start: 0.8229 (t0) cc_final: 0.8016 (t0) REVERT: Q 229 ASP cc_start: 0.7671 (t70) cc_final: 0.7440 (t70) REVERT: R 191 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8901 (mm) REVERT: R 221 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: S 73 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8664 (mp) REVERT: S 219 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: S 236 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: T 185 GLU cc_start: 0.7710 (mt-10) cc_final: 0.6727 (mm-30) REVERT: U 204 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8362 (p90) REVERT: V 24 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8841 (p) REVERT: V 144 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7557 (tptt) REVERT: W 212 ASN cc_start: 0.8509 (t0) cc_final: 0.8268 (t0) REVERT: X 38 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7722 (mp0) REVERT: Y 56 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7459 (mp0) REVERT: Y 163 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8547 (mmtt) outliers start: 297 outliers final: 249 residues processed: 570 average time/residue: 0.2165 time to fit residues: 211.7984 Evaluate side-chains 561 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 289 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 217 GLU Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 227 ASP Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 212 ASN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 181 ASN Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 136 ILE Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 113 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 239 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 90 optimal weight: 6.9990 chunk 337 optimal weight: 0.0070 chunk 139 optimal weight: 5.9990 chunk 405 optimal weight: 8.9990 chunk 429 optimal weight: 7.9990 chunk 325 optimal weight: 20.0000 chunk 354 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 304 optimal weight: 0.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 77 GLN S 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.130310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100385 restraints weight = 60567.134| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.56 r_work: 0.3178 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 46656 Z= 0.163 Angle : 0.465 8.740 63036 Z= 0.255 Chirality : 0.045 0.151 7200 Planarity : 0.003 0.054 8100 Dihedral : 4.037 47.291 6242 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.96 % Allowed : 21.06 % Favored : 72.97 % 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 aren not related in a simple way. whole: -1.92 (0.10), residues: 5760 helix: 0.40 (0.35), residues: 216 sheet: -1.31 (0.10), residues: 2568 loop : -1.27 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 42 TYR 0.011 0.001 TYR P 192 PHE 0.013 0.001 PHE K 13 TRP 0.004 0.001 TRP F 72 HIS 0.001 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00390 (46656) covalent geometry : angle 0.46462 (63036) hydrogen bonds : bond 0.03583 ( 290) hydrogen bonds : angle 4.75992 ( 840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 292 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8010 (t80) REVERT: B 212 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8407 (t0) REVERT: C 48 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8074 (mtmm) REVERT: C 88 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6862 (mtmm) REVERT: C 212 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8309 (t0) REVERT: C 236 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8305 (tm-30) REVERT: G 39 GLU cc_start: 0.7631 (pt0) cc_final: 0.7405 (pt0) REVERT: G 219 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8657 (mtpp) REVERT: G 229 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8457 (t70) REVERT: G 236 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: I 1 MET cc_start: 0.8023 (ttt) cc_final: 0.7766 (ttt) REVERT: I 64 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8948 (tttt) REVERT: J 236 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8369 (tm-30) REVERT: L 2 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7781 (mttm) REVERT: L 109 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8509 (mmmt) REVERT: M 26 GLU cc_start: 0.7975 (pm20) cc_final: 0.7714 (pm20) REVERT: M 163 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8688 (mmtt) REVERT: M 219 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8710 (mtpp) REVERT: N 51 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.7145 (t80) REVERT: O 176 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8579 (tmt170) REVERT: O 212 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.7905 (t0) REVERT: P 82 GLN cc_start: 0.8115 (mp10) cc_final: 0.7666 (mp10) REVERT: P 109 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8122 (mtpt) REVERT: Q 69 ASP cc_start: 0.8231 (t0) cc_final: 0.8015 (t0) REVERT: Q 229 ASP cc_start: 0.7682 (t70) cc_final: 0.7439 (t70) REVERT: R 191 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8902 (mm) REVERT: R 221 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: S 73 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8670 (mp) REVERT: S 219 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8267 (mtpp) REVERT: S 236 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: T 38 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7703 (mp0) REVERT: T 185 GLU cc_start: 0.7721 (mt-10) cc_final: 0.6725 (mm-30) REVERT: U 204 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8355 (p90) REVERT: V 24 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8842 (p) REVERT: V 144 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7535 (tptt) REVERT: W 212 ASN cc_start: 0.8506 (t0) cc_final: 0.8262 (t0) REVERT: X 38 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7731 (mp0) REVERT: Y 56 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7459 (mp0) REVERT: Y 163 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8524 (mmtt) outliers start: 297 outliers final: 253 residues processed: 562 average time/residue: 0.2197 time to fit residues: 212.8767 Evaluate side-chains 563 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 286 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 163 LYS Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 217 GLU Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 227 ASP Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 212 ASN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 136 ILE Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 239 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 77 optimal weight: 4.9990 chunk 523 optimal weight: 0.7980 chunk 309 optimal weight: 4.9990 chunk 567 optimal weight: 7.9990 chunk 451 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 543 optimal weight: 6.9990 chunk 569 optimal weight: 6.9990 chunk 483 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 181 ASN P 181 ASN S 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099124 restraints weight = 60710.462| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.56 r_work: 0.3163 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 46656 Z= 0.212 Angle : 0.506 8.637 63036 Z= 0.275 Chirality : 0.046 0.154 7200 Planarity : 0.003 0.058 8100 Dihedral : 4.239 47.172 6242 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.98 % Allowed : 21.00 % Favored : 73.01 % 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 aren not related in a simple way. whole: -2.05 (0.10), residues: 5760 helix: 0.16 (0.34), residues: 216 sheet: -1.43 (0.10), residues: 2568 loop : -1.31 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 42 TYR 0.012 0.001 TYR P 192 PHE 0.016 0.002 PHE K 13 TRP 0.005 0.001 TRP F 72 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00512 (46656) covalent geometry : angle 0.50591 (63036) hydrogen bonds : bond 0.04080 ( 290) hydrogen bonds : angle 4.90300 ( 840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 298 poor density : 287 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.7971 (t80) REVERT: B 212 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8386 (t0) REVERT: C 48 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8029 (mtmm) REVERT: C 88 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6929 (mtmm) REVERT: C 212 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8310 (t0) REVERT: C 236 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8313 (tm-30) REVERT: D 79 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: G 39 GLU cc_start: 0.7644 (pt0) cc_final: 0.7403 (pt0) REVERT: G 219 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8665 (mtpp) REVERT: G 229 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8456 (t70) REVERT: G 236 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: I 1 MET cc_start: 0.8022 (ttt) cc_final: 0.7776 (ttt) REVERT: I 64 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8959 (tttt) REVERT: I 88 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7294 (ttmt) REVERT: J 236 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8395 (tm-30) REVERT: L 109 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8510 (mmmt) REVERT: M 26 GLU cc_start: 0.8005 (pm20) cc_final: 0.7779 (pm20) REVERT: M 219 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8791 (mtpp) REVERT: N 51 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.7018 (t80) REVERT: O 176 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8555 (tmt170) REVERT: P 82 GLN cc_start: 0.8084 (mp10) cc_final: 0.7629 (mp10) REVERT: P 109 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8131 (mtpt) REVERT: Q 229 ASP cc_start: 0.7591 (t70) cc_final: 0.7352 (t70) REVERT: R 191 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8900 (mm) REVERT: R 221 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: S 73 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8662 (mp) REVERT: S 219 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8272 (mtpp) REVERT: S 236 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: T 38 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7694 (mp0) REVERT: T 185 GLU cc_start: 0.7781 (mt-10) cc_final: 0.6763 (mm-30) REVERT: U 204 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8339 (p90) REVERT: V 144 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7507 (tptt) REVERT: W 212 ASN cc_start: 0.8506 (t0) cc_final: 0.8242 (t0) REVERT: X 38 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7723 (mp0) REVERT: Y 56 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7448 (mp0) REVERT: Y 163 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8543 (mmtt) outliers start: 298 outliers final: 263 residues processed: 559 average time/residue: 0.2114 time to fit residues: 203.7102 Evaluate side-chains 568 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 285 poor density : 283 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 217 GLU Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 227 ASP Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 181 ASN Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 136 ILE Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 113 ASP Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 173 VAL Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 239 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 448 optimal weight: 0.0980 chunk 169 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 538 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 396 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 262 optimal weight: 0.7980 chunk 338 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102443 restraints weight = 60392.018| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.56 r_work: 0.3208 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 46656 Z= 0.098 Angle : 0.419 7.791 63036 Z= 0.232 Chirality : 0.044 0.150 7200 Planarity : 0.003 0.049 8100 Dihedral : 3.769 47.724 6242 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.88 % Allowed : 23.11 % Favored : 73.01 % 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 aren not related in a simple way. whole: -1.78 (0.11), residues: 5760 helix: 0.83 (0.38), residues: 216 sheet: -1.20 (0.10), residues: 2568 loop : -1.22 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 42 TYR 0.013 0.001 TYR P 192 PHE 0.011 0.001 PHE K 220 TRP 0.002 0.000 TRP I 72 HIS 0.001 0.000 HIS O 94 Details of bonding type rmsd covalent geometry : bond 0.00226 (46656) covalent geometry : angle 0.41947 (63036) hydrogen bonds : bond 0.02762 ( 290) hydrogen bonds : angle 4.57646 ( 840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11520 Ramachandran restraints generated. 5760 Oldfield, 0 Emsley, 5760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 307 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7925 (t80) REVERT: B 212 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8341 (t0) REVERT: C 88 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6797 (mtmm) REVERT: C 212 ASN cc_start: 0.8573 (t0) cc_final: 0.8280 (t0) REVERT: C 236 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8340 (tm-30) REVERT: G 39 GLU cc_start: 0.7619 (pt0) cc_final: 0.7376 (pt0) REVERT: G 236 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: I 1 MET cc_start: 0.7942 (ttt) cc_final: 0.7691 (ttt) REVERT: I 64 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8940 (tttt) REVERT: I 79 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: I 236 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8020 (tm-30) REVERT: J 82 GLN cc_start: 0.7993 (mp10) cc_final: 0.7703 (mp10) REVERT: J 236 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8388 (tm-30) REVERT: K 236 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8158 (tm-30) REVERT: L 109 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8460 (mmmt) REVERT: M 26 GLU cc_start: 0.7950 (pm20) cc_final: 0.7646 (pm20) REVERT: N 51 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6949 (t80) REVERT: P 82 GLN cc_start: 0.7928 (mp10) cc_final: 0.7467 (mp10) REVERT: P 109 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8088 (mtpt) REVERT: Q 229 ASP cc_start: 0.7496 (t70) cc_final: 0.7244 (t70) REVERT: R 191 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8823 (mm) REVERT: R 221 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: S 73 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8526 (mp) REVERT: T 38 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7767 (mp0) REVERT: T 185 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6733 (mm-30) REVERT: V 144 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7523 (tptt) REVERT: V 236 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7557 (tm-30) REVERT: W 56 GLU cc_start: 0.7931 (mp0) cc_final: 0.7432 (mp0) REVERT: W 212 ASN cc_start: 0.8385 (t0) cc_final: 0.8152 (t0) REVERT: X 38 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7698 (mp0) REVERT: Y 163 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8423 (mmtt) outliers start: 193 outliers final: 161 residues processed: 473 average time/residue: 0.1602 time to fit residues: 130.8089 Evaluate side-chains 474 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 301 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 217 GLU Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 173 VAL Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 229 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 169 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 497 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 478 optimal weight: 2.9990 chunk 461 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 102 ASN S 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098233 restraints weight = 61088.546| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.57 r_work: 0.3148 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 46656 Z= 0.267 Angle : 0.551 9.412 63036 Z= 0.298 Chirality : 0.048 0.158 7200 Planarity : 0.004 0.057 8100 Dihedral : 4.345 46.971 6242 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.24 % Allowed : 22.77 % Favored : 72.99 % 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 aren not related in a simple way. whole: -2.08 (0.11), residues: 5760 helix: 0.07 (0.34), residues: 216 sheet: -1.46 (0.10), residues: 2568 loop : -1.31 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 42 TYR 0.013 0.002 TYR P 192 PHE 0.018 0.002 PHE K 13 TRP 0.006 0.001 TRP L 72 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00646 (46656) covalent geometry : angle 0.55065 (63036) hydrogen bonds : bond 0.04470 ( 290) hydrogen bonds : angle 5.01769 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11897.11 seconds wall clock time: 204 minutes 14.77 seconds (12254.77 seconds total)