Starting phenix.real_space_refine on Sun Jul 28 10:14:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xkn_38421/07_2024/8xkn_38421.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xkn_38421/07_2024/8xkn_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xkn_38421/07_2024/8xkn_38421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xkn_38421/07_2024/8xkn_38421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xkn_38421/07_2024/8xkn_38421.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xkn_38421/07_2024/8xkn_38421.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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 Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 131": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "H TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 131": "OD1" <-> "OD2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I GLU 174": "OE1" <-> "OE2" Residue "I PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K ASP 131": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "L ASP 131": "OD1" <-> "OD2" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M GLU 236": "OE1" <-> "OE2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 26": "OE1" <-> "OE2" Residue "R ASP 131": "OD1" <-> "OD2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "R ASP 240": "OD1" <-> "OD2" Residue "S ASP 131": "OD1" <-> "OD2" Residue "T GLU 26": "OE1" <-> "OE2" Residue "T GLU 38": "OE1" <-> "OE2" Residue "T GLU 58": "OE1" <-> "OE2" Residue "T TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 174": "OE1" <-> "OE2" Residue "T PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 131": "OD1" <-> "OD2" Residue "U GLU 174": "OE1" <-> "OE2" Residue "U PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 131": "OD1" <-> "OD2" Residue "X GLU 56": "OE1" <-> "OE2" Residue "Y GLU 71": "OE1" <-> "OE2" Residue "Y ASP 131": "OD1" <-> "OD2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: 23.55, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.39 Conformation dependent library (CDL) restraints added in 8.6 seconds 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: 4.55 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: 13.02 Time building geometry restraints manager: 18.91 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: 99.70 - 106.54: 764 106.54 - 113.38: 25837 113.38 - 120.22: 15903 120.22 - 127.06: 20290 127.06 - 133.89: 242 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 2.440 nonbonded pdb=" OE2 GLU G 93 " pdb=" OH TYR G 151 " model vdw 2.164 2.440 nonbonded pdb=" OE2 GLU L 93 " pdb=" OH TYR L 151 " model vdw 2.167 2.440 nonbonded pdb=" OE2 GLU R 93 " pdb=" OH TYR R 151 " model vdw 2.173 2.440 nonbonded pdb=" OE2 GLU S 93 " pdb=" OH TYR S 151 " model vdw 2.175 2.440 ... (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 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.960 Check model and map are aligned: 0.370 Set scattering table: 0.410 Process input model: 108.800 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.860 ------------------------------------------------------------------------------- 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= 0.317 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (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 TRP 0.004 0.001 TRP X 72 HIS 0.005 0.001 HIS K 94 PHE 0.017 0.002 PHE C 13 TYR 0.016 0.001 TYR Q 192 ARG 0.005 0.000 ARG U 170 *********************** 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 fitting. rotamer outliers: 16 poor density : 279 time to evaluate : 5.276 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: 0.5381 time to fit residues: 270.4579 Evaluate side-chains 275 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 264 time to evaluate : 5.464 ------------------------------------------------------------------------------- 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 486 optimal weight: 10.0000 chunk 436 optimal weight: 0.5980 chunk 242 optimal weight: 0.0040 chunk 149 optimal weight: 1.9990 chunk 294 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 451 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 274 optimal weight: 20.0000 chunk 336 optimal weight: 9.9990 chunk 523 optimal weight: 3.9990 overall best weight: 2.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN C 77 GLN D 34 GLN E 94 HIS G 77 GLN H 60 ASN H 77 GLN I 77 GLN J 34 GLN J 77 GLN K 34 GLN K 94 HIS M 77 GLN M 181 ASN N 77 GLN O 77 GLN P 34 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 HIS R 77 GLN S 34 GLN S 77 GLN S 181 ASN T 77 GLN U 77 GLN V 34 GLN V 77 GLN V 152 GLN W 34 GLN W 94 HIS W 242 ASN Y 77 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 46656 Z= 0.170 Angle : 0.430 8.397 63036 Z= 0.233 Chirality : 0.044 0.150 7200 Planarity : 0.003 0.043 8100 Dihedral : 4.008 47.463 6256 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.15 % Allowed : 20.90 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.11), residues: 5760 helix: 0.99 (0.38), residues: 216 sheet: -0.55 (0.10), residues: 2568 loop : -1.28 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 72 HIS 0.002 0.001 HIS K 94 PHE 0.010 0.001 PHE C 13 TYR 0.008 0.001 TYR B 12 ARG 0.003 0.000 ARG U 170 *********************** 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 453 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 296 time to evaluate : 6.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: F 92 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7439 (ptp90) REVERT: I 79 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: L 2 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7664 (mttm) REVERT: L 109 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8404 (mmmt) REVERT: M 219 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8483 (mtpp) REVERT: P 82 GLN cc_start: 0.7956 (mp10) cc_final: 0.7488 (mp10) REVERT: P 240 ASP cc_start: 0.7767 (m-30) cc_final: 0.7525 (m-30) REVERT: Q 186 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6842 (mm-30) REVERT: Q 240 ASP cc_start: 0.7898 (m-30) cc_final: 0.7645 (m-30) REVERT: R 221 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: S 131 ASP cc_start: 0.7388 (t0) cc_final: 0.7167 (t0) REVERT: S 236 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: T 38 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7448 (mp0) REVERT: V 24 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8845 (p) REVERT: V 131 ASP cc_start: 0.7123 (t0) cc_final: 0.6913 (t0) REVERT: W 212 ASN cc_start: 0.8539 (t0) cc_final: 0.8312 (t0) outliers start: 157 outliers final: 100 residues processed: 427 average time/residue: 0.5183 time to fit residues: 381.2681 Evaluate side-chains 396 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 288 time to evaluate : 5.370 ------------------------------------------------------------------------------- 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 227 ASP 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 227 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 145 ASP 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 177 THR 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 227 ASP 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 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 177 THR 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 104 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 219 LYS 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 O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 22 VAL 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 Q residue 100 ASP Chi-restraints excluded: chain Q residue 227 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 100 ASP 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 10 ASP 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 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 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 100 ASP Chi-restraints excluded: chain W residue 145 ASP 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 100 ASP Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 174 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 1.9990 chunk 162 optimal weight: 0.0270 chunk 435 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 524 optimal weight: 10.0000 chunk 566 optimal weight: 20.0000 chunk 466 optimal weight: 30.0000 chunk 519 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 420 optimal weight: 30.0000 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 181 ASN I 77 GLN J 34 GLN O 181 ASN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 ASN ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN S 34 GLN U 77 GLN V 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 46656 Z= 0.422 Angle : 0.553 10.064 63036 Z= 0.298 Chirality : 0.048 0.159 7200 Planarity : 0.004 0.057 8100 Dihedral : 4.565 46.861 6245 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.42 % Allowed : 20.94 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.11), residues: 5760 helix: 0.21 (0.34), residues: 216 sheet: -0.78 (0.10), residues: 2784 loop : -1.36 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 72 HIS 0.003 0.001 HIS L 94 PHE 0.018 0.002 PHE K 13 TYR 0.011 0.002 TYR W 51 ARG 0.004 0.000 ARG I 15 *********************** 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 551 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 281 time to evaluate : 5.350 Fit side-chains revert: symmetry clash REVERT: C 88 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6915 (mtmm) REVERT: C 176 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8892 (tmt170) REVERT: C 204 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8266 (p90) REVERT: C 212 ASN cc_start: 0.8707 (t0) cc_final: 0.8405 (t0) REVERT: D 79 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: D 205 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: F 92 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7306 (ptp90) REVERT: G 219 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8585 (mtpp) REVERT: G 236 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: I 88 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7187 (mtmm) REVERT: J 79 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: L 109 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8452 (mmmt) REVERT: M 219 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8728 (mtpp) REVERT: O 176 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8459 (tmt170) REVERT: P 82 GLN cc_start: 0.8046 (mp10) cc_final: 0.7600 (mp10) REVERT: P 109 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8189 (mtpt) REVERT: P 240 ASP cc_start: 0.7840 (m-30) cc_final: 0.7590 (m-30) REVERT: R 221 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: S 131 ASP cc_start: 0.7367 (t0) cc_final: 0.7107 (t0) REVERT: S 219 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8202 (mtpp) REVERT: S 236 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: U 204 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8221 (p90) REVERT: W 212 ASN cc_start: 0.8606 (t0) cc_final: 0.8352 (t0) REVERT: Y 185 GLU cc_start: 0.7576 (mt-10) cc_final: 0.6772 (mm-30) REVERT: Y 219 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8664 (mttm) outliers start: 270 outliers final: 188 residues processed: 532 average time/residue: 0.5250 time to fit residues: 478.1405 Evaluate side-chains 475 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 270 time to evaluate : 5.126 ------------------------------------------------------------------------------- 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 148 THR 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 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 227 ASP 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 100 ASP 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 205 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 100 ASP Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 145 ASP 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 100 ASP Chi-restraints excluded: chain F residue 104 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 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 181 ASN Chi-restraints excluded: chain G residue 219 LYS 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 113 ASP Chi-restraints excluded: chain H residue 148 THR 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 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 79 GLU 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 J residue 229 ASP 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 79 GLU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 183 ASP 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 100 ASP Chi-restraints excluded: chain L residue 104 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 73 LEU 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 M residue 148 THR Chi-restraints excluded: chain M residue 174 GLU 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 24 THR Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 113 ASP 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 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 227 ASP 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 94 HIS Chi-restraints excluded: chain P residue 100 ASP 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 P residue 226 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 227 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 100 ASP 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 100 ASP Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 148 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 227 ASP Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 10 ASP 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 113 ASP Chi-restraints excluded: chain T residue 148 THR 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 T residue 228 THR Chi-restraints excluded: chain U residue 24 THR 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 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 79 GLU Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 145 ASP 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 73 LEU Chi-restraints excluded: chain X residue 177 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 100 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 219 LYS 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 517 optimal weight: 9.9990 chunk 393 optimal weight: 6.9990 chunk 271 optimal weight: 0.7980 chunk 58 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 351 optimal weight: 4.9990 chunk 525 optimal weight: 5.9990 chunk 556 optimal weight: 0.0060 chunk 274 optimal weight: 20.0000 chunk 498 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN E 34 GLN P 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1045 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= 0.198 Angle : 0.431 8.335 63036 Z= 0.236 Chirality : 0.045 0.152 7200 Planarity : 0.003 0.053 8100 Dihedral : 4.019 47.686 6245 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.50 % Allowed : 22.25 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.11), residues: 5760 helix: 0.65 (0.37), residues: 216 sheet: -0.71 (0.10), residues: 2784 loop : -1.31 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 72 HIS 0.002 0.001 HIS R 94 PHE 0.012 0.001 PHE K 13 TYR 0.007 0.001 TYR T 51 ARG 0.002 0.000 ARG G 92 *********************** 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 516 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 292 time to evaluate : 5.573 Fit side-chains revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7824 (t80) REVERT: B 212 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8454 (t0) REVERT: C 212 ASN cc_start: 0.8670 (t0) cc_final: 0.8367 (t0) REVERT: F 92 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7417 (ptp90) REVERT: F 191 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9165 (mm) REVERT: G 219 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8595 (mtpp) REVERT: G 236 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: I 79 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: L 109 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8420 (mmmt) REVERT: M 92 ARG cc_start: 0.8606 (ptt90) cc_final: 0.8355 (ptt-90) REVERT: M 217 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: M 219 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8531 (mtpp) REVERT: O 176 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8481 (tmt170) REVERT: P 82 GLN cc_start: 0.7959 (mp10) cc_final: 0.7528 (mp10) REVERT: P 240 ASP cc_start: 0.7840 (m-30) cc_final: 0.7562 (m-30) REVERT: R 221 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: S 219 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8156 (mtpp) REVERT: S 236 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: T 38 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7405 (mp0) REVERT: V 26 GLU cc_start: 0.6133 (tp30) cc_final: 0.5899 (tp30) REVERT: W 212 ASN cc_start: 0.8558 (t0) cc_final: 0.8337 (t0) REVERT: Y 185 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6823 (mm-30) REVERT: Y 219 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8725 (mttm) outliers start: 224 outliers final: 171 residues processed: 490 average time/residue: 0.5703 time to fit residues: 484.7609 Evaluate side-chains 467 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 282 time to evaluate : 5.890 ------------------------------------------------------------------------------- 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 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 C residue 18 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 73 LEU 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 227 ASP 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 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 100 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 227 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 100 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 191 ILE 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 219 LYS Chi-restraints excluded: chain G residue 228 THR 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 113 ASP Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 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 104 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 227 ASP 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 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 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 79 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 228 THR 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 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 98 VAL 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 N residue 8 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 113 ASP Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU 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 227 ASP 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 100 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 24 THR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 227 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 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 100 ASP Chi-restraints excluded: chain S residue 104 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 T residue 8 THR Chi-restraints excluded: chain T residue 10 ASP Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 113 ASP Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain U residue 24 THR 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 104 VAL Chi-restraints excluded: chain V residue 113 ASP Chi-restraints excluded: chain V residue 226 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 79 GLU Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 100 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 177 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 138 THR Chi-restraints excluded: chain Y residue 148 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 463 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 414 optimal weight: 1.9990 chunk 229 optimal weight: 0.0670 chunk 475 optimal weight: 9.9990 chunk 384 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 499 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 46656 Z= 0.149 Angle : 0.397 7.327 63036 Z= 0.218 Chirality : 0.044 0.151 7200 Planarity : 0.003 0.047 8100 Dihedral : 3.655 47.026 6244 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.08 % Allowed : 21.99 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 5760 helix: 0.92 (0.37), residues: 216 sheet: -0.54 (0.10), residues: 2784 loop : -1.22 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 72 HIS 0.001 0.000 HIS R 94 PHE 0.010 0.001 PHE K 13 TYR 0.008 0.001 TYR B 12 ARG 0.002 0.000 ARG R 170 *********************** 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 558 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 305 time to evaluate : 5.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7767 (t80) REVERT: B 212 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8460 (t0) REVERT: C 88 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6799 (mtmm) REVERT: C 212 ASN cc_start: 0.8656 (t0) cc_final: 0.8351 (t0) REVERT: G 219 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8595 (mtpp) REVERT: G 236 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: I 79 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: L 109 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8419 (mmmt) REVERT: M 92 ARG cc_start: 0.8620 (ptt90) cc_final: 0.8374 (ptt-90) REVERT: O 166 LYS cc_start: 0.7846 (tttt) cc_final: 0.7600 (mmmt) REVERT: O 176 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8502 (tmm160) REVERT: P 82 GLN cc_start: 0.7961 (mp10) cc_final: 0.7535 (mp10) REVERT: P 109 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8172 (mtpt) REVERT: P 240 ASP cc_start: 0.7767 (m-30) cc_final: 0.7481 (m-30) REVERT: R 221 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: S 73 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8733 (mp) REVERT: S 219 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8169 (mtpp) REVERT: V 26 GLU cc_start: 0.6231 (tp30) cc_final: 0.6020 (tp30) REVERT: W 212 ASN cc_start: 0.8545 (t0) cc_final: 0.8336 (t0) REVERT: Y 163 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8515 (mmtt) REVERT: Y 185 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6828 (mm-30) REVERT: Y 219 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8703 (mttm) outliers start: 253 outliers final: 208 residues processed: 530 average time/residue: 0.5195 time to fit residues: 472.7940 Evaluate side-chains 513 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 293 time to evaluate : 5.578 ------------------------------------------------------------------------------- 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 148 THR 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 18 ASP 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 177 THR Chi-restraints excluded: chain C residue 227 ASP 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 100 ASP 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 177 THR 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 145 ASP Chi-restraints excluded: chain E residue 148 THR 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 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 100 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP 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 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 217 GLU Chi-restraints excluded: chain G residue 219 LYS 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 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 148 THR 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 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 177 THR Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 228 THR 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 138 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 227 ASP 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 113 ASP 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 73 LEU Chi-restraints excluded: chain M residue 98 VAL 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 148 THR Chi-restraints excluded: chain M residue 177 THR 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 104 VAL Chi-restraints excluded: chain N residue 113 ASP 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 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 O residue 227 ASP 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 100 ASP 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 100 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 145 ASP 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 100 ASP Chi-restraints excluded: chain R residue 104 VAL 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 100 ASP 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 138 THR Chi-restraints excluded: chain S residue 148 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 227 ASP Chi-restraints excluded: chain T residue 8 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 113 ASP Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 228 THR 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 24 THR 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 79 GLU Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 145 ASP 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 100 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 177 THR Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 100 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 219 LYS Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 2.9990 chunk 501 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 326 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 557 optimal weight: 0.0970 chunk 462 optimal weight: 0.8980 chunk 258 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 77 GLN P 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1246 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= 0.161 Angle : 0.400 7.374 63036 Z= 0.220 Chirality : 0.044 0.151 7200 Planarity : 0.003 0.044 8100 Dihedral : 3.603 46.487 6244 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.60 % Allowed : 21.65 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.11), residues: 5760 helix: 0.91 (0.37), residues: 216 sheet: -0.47 (0.10), residues: 2784 loop : -1.17 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 72 HIS 0.001 0.000 HIS L 94 PHE 0.011 0.001 PHE K 13 TYR 0.010 0.001 TYR P 192 ARG 0.002 0.000 ARG L 42 *********************** 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 584 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 305 time to evaluate : 6.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7758 (t80) REVERT: B 212 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8443 (t0) REVERT: C 88 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6771 (mtmm) REVERT: C 212 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8355 (t0) REVERT: F 92 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7463 (ptp90) REVERT: G 219 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8577 (mtpp) REVERT: G 236 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: I 79 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: I 88 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.7081 (ttmt) REVERT: L 109 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8453 (mmmt) REVERT: M 217 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: M 219 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8589 (mtpp) REVERT: O 166 LYS cc_start: 0.7806 (tttt) cc_final: 0.7519 (mmmt) REVERT: O 176 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8516 (tmm160) REVERT: P 82 GLN cc_start: 0.7919 (mp10) cc_final: 0.7490 (mp10) REVERT: P 109 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8192 (mtpt) REVERT: P 240 ASP cc_start: 0.7705 (m-30) cc_final: 0.7410 (m-30) REVERT: R 221 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: S 73 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8740 (mp) REVERT: S 219 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8146 (mtpp) REVERT: S 236 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: T 1 MET cc_start: 0.7836 (ttt) cc_final: 0.7405 (ttt) REVERT: W 212 ASN cc_start: 0.8539 (t0) cc_final: 0.8335 (t0) REVERT: Y 163 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8509 (mmtt) REVERT: Y 185 GLU cc_start: 0.7595 (mt-10) cc_final: 0.6808 (mm-30) REVERT: Y 219 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8717 (mttm) outliers start: 279 outliers final: 245 residues processed: 557 average time/residue: 0.5159 time to fit residues: 494.8102 Evaluate side-chains 560 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 297 time to evaluate : 5.594 ------------------------------------------------------------------------------- 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 148 THR 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 18 ASP 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 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 227 ASP 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 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 177 THR 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 100 ASP 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 145 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 227 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 100 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP 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 138 THR Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR 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 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 113 ASP Chi-restraints excluded: chain H residue 148 THR 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 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 113 ASP 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 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 177 THR Chi-restraints excluded: chain J residue 228 THR 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 79 GLU 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 148 THR Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 228 THR 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 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 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 98 VAL 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 148 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 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 104 VAL Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 173 VAL 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 88 LYS 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 100 ASP 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 100 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 227 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 100 ASP Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP 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 100 ASP 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 138 THR Chi-restraints excluded: chain S residue 148 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 227 ASP 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 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 113 ASP Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 173 VAL 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 45 ILE Chi-restraints excluded: chain U residue 73 LEU 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 24 THR 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 138 THR Chi-restraints excluded: chain V residue 226 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 79 GLU Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain W residue 148 THR 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 100 ASP 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 177 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 100 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 148 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 317 optimal weight: 9.9990 chunk 406 optimal weight: 8.9990 chunk 315 optimal weight: 2.9990 chunk 469 optimal weight: 30.0000 chunk 311 optimal weight: 10.0000 chunk 555 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 338 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 ASN ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 46656 Z= 0.366 Angle : 0.506 8.840 63036 Z= 0.274 Chirality : 0.046 0.157 7200 Planarity : 0.004 0.050 8100 Dihedral : 4.228 46.332 6244 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.53 % Allowed : 21.29 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.11), residues: 5760 helix: 0.36 (0.35), residues: 216 sheet: -0.80 (0.10), residues: 2784 loop : -1.21 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 72 HIS 0.002 0.001 HIS L 94 PHE 0.017 0.002 PHE K 13 TYR 0.011 0.001 TYR P 192 ARG 0.003 0.000 ARG G 239 *********************** 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 604 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 279 time to evaluate : 5.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7927 (t80) REVERT: B 212 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8458 (t0) REVERT: C 88 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6847 (mtmm) REVERT: C 212 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8389 (t0) REVERT: D 79 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: G 219 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8610 (mtpp) REVERT: G 229 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8558 (t70) REVERT: G 236 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: I 88 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7112 (ttmt) REVERT: L 109 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8446 (mmmt) REVERT: M 219 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8723 (mtpp) REVERT: O 166 LYS cc_start: 0.7844 (tttt) cc_final: 0.7582 (mmmt) REVERT: O 176 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8533 (tmt170) REVERT: Q 1 MET cc_start: 0.7498 (tpt) cc_final: 0.6805 (tpt) REVERT: R 221 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: S 73 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8767 (mp) REVERT: S 219 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: S 236 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: W 212 ASN cc_start: 0.8592 (t0) cc_final: 0.8359 (t0) REVERT: Y 185 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6787 (mm-30) REVERT: Y 219 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8770 (mttm) outliers start: 325 outliers final: 271 residues processed: 579 average time/residue: 0.5155 time to fit residues: 512.1227 Evaluate side-chains 557 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 270 time to evaluate : 5.979 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 148 THR 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 227 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 18 ASP 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 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 227 ASP 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 100 ASP 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 177 THR 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 100 ASP 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 145 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 227 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 100 ASP 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 148 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 113 ASP Chi-restraints excluded: chain H residue 148 THR 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 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 177 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 79 GLU 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 148 THR Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 228 THR 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 100 ASP 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 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 98 VAL 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 148 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 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 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 113 ASP 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 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 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 100 ASP 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 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 73 LEU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 227 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 100 ASP 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 100 ASP 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 136 ILE Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 148 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 227 ASP 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 10 ASP 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 79 GLU Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 113 ASP Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 173 VAL 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 45 ILE Chi-restraints excluded: chain U residue 73 LEU 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 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 173 VAL Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 226 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 79 GLU Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain W residue 148 THR 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 100 ASP 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 177 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 100 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 148 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 10.0000 chunk 221 optimal weight: 0.0000 chunk 331 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 352 optimal weight: 3.9990 chunk 378 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 436 optimal weight: 0.8980 overall best weight: 1.3790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 46656 Z= 0.130 Angle : 0.391 6.684 63036 Z= 0.216 Chirality : 0.044 0.150 7200 Planarity : 0.003 0.041 8100 Dihedral : 3.597 46.867 6244 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.14 % Allowed : 22.55 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.11), residues: 5760 helix: 0.92 (0.38), residues: 216 sheet: -0.57 (0.10), residues: 2784 loop : -1.15 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP I 72 HIS 0.001 0.000 HIS O 94 PHE 0.009 0.001 PHE K 220 TYR 0.011 0.001 TYR P 192 ARG 0.002 0.000 ARG T 42 *********************** 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 551 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 295 time to evaluate : 5.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7774 (t80) REVERT: B 212 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8451 (t0) REVERT: C 88 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6762 (mtmm) REVERT: C 212 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8364 (t0) REVERT: G 24 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.8955 (p) REVERT: G 219 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8622 (mtpp) REVERT: G 236 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: H 79 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: I 79 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: L 109 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8446 (mmmt) REVERT: M 217 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: M 219 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8567 (mtpp) REVERT: O 166 LYS cc_start: 0.7805 (tttt) cc_final: 0.7521 (mmmt) REVERT: P 82 GLN cc_start: 0.7934 (mp10) cc_final: 0.7513 (mp10) REVERT: P 109 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8135 (mtpt) REVERT: R 221 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: S 73 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8717 (mp) REVERT: S 236 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: V 144 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7540 (tptt) REVERT: W 212 ASN cc_start: 0.8536 (t0) cc_final: 0.8330 (t0) REVERT: Y 24 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8844 (p) REVERT: Y 163 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8514 (mmtt) REVERT: Y 185 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6851 (mm-30) REVERT: Y 239 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7021 (ptp-170) outliers start: 256 outliers final: 211 residues processed: 526 average time/residue: 0.5201 time to fit residues: 471.8536 Evaluate side-chains 517 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 288 time to evaluate : 5.400 ------------------------------------------------------------------------------- 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 100 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 148 THR 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 18 ASP Chi-restraints excluded: chain C residue 45 ILE 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 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 100 ASP 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 177 THR 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 100 ASP Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 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 100 ASP 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 177 THR 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 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR 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 236 GLU 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 79 GLU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 148 THR 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 79 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 227 ASP 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 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 177 THR Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 THR 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 100 ASP 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 228 THR 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 113 ASP Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 148 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 228 THR Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 113 ASP 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 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 104 VAL Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 177 THR 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 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 145 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 100 ASP 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 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 148 THR 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 10 ASP 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 79 GLU Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 113 ASP Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 173 VAL 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 113 ASP 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 24 THR 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 130 THR 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 226 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 22 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 79 GLU Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain W residue 148 THR 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 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 100 ASP 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 177 THR 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 100 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 148 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 505 optimal weight: 10.0000 chunk 531 optimal weight: 10.0000 chunk 485 optimal weight: 8.9990 chunk 517 optimal weight: 30.0000 chunk 311 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 406 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 467 optimal weight: 2.9990 chunk 489 optimal weight: 6.9990 chunk 515 optimal weight: 4.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1376 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= 0.336 Angle : 0.489 8.560 63036 Z= 0.265 Chirality : 0.046 0.158 7200 Planarity : 0.003 0.047 8100 Dihedral : 4.098 46.628 6244 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.84 % Allowed : 21.81 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.11), residues: 5760 helix: 0.37 (0.35), residues: 216 sheet: -0.79 (0.10), residues: 2784 loop : -1.19 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 72 HIS 0.002 0.001 HIS R 94 PHE 0.016 0.002 PHE K 13 TYR 0.012 0.001 TYR P 192 ARG 0.003 0.000 ARG T 42 *********************** 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 568 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 277 time to evaluate : 5.757 Fit side-chains revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7930 (t80) REVERT: B 212 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8444 (t0) REVERT: C 48 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8113 (mtmm) REVERT: C 88 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6847 (mtmm) REVERT: C 212 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8375 (t0) REVERT: D 79 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: G 219 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8623 (mtpp) REVERT: G 236 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: I 79 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: L 109 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8456 (mmmt) REVERT: M 219 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8732 (mtpp) REVERT: O 166 LYS cc_start: 0.7831 (tttt) cc_final: 0.7535 (mmmt) REVERT: P 109 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8147 (mtpt) REVERT: R 221 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: S 73 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8784 (mp) REVERT: S 219 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: S 236 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: V 144 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7517 (tptt) REVERT: V 239 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.5785 (ttm170) REVERT: W 212 ASN cc_start: 0.8557 (t0) cc_final: 0.8330 (t0) REVERT: Y 56 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7449 (mp0) REVERT: Y 163 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8608 (mmtt) REVERT: Y 219 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8776 (mttp) outliers start: 291 outliers final: 255 residues processed: 551 average time/residue: 0.5209 time to fit residues: 491.9849 Evaluate side-chains 546 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 273 time to evaluate : 5.064 ------------------------------------------------------------------------------- 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 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 148 THR 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 18 ASP Chi-restraints excluded: chain C residue 24 THR 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 100 ASP 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 212 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 100 ASP 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 177 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR 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 100 ASP 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 145 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 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 100 ASP 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 148 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 184 THR 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 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 113 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 148 THR 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 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 177 THR Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 228 THR 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 177 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 75 MET Chi-restraints excluded: chain K residue 79 GLU 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 148 THR Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 228 THR 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 100 ASP 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 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 98 VAL 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 148 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 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 104 VAL Chi-restraints excluded: chain N residue 113 ASP 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 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 104 VAL Chi-restraints excluded: chain O residue 138 THR 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 100 ASP 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 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 73 LEU Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain Q residue 227 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 82 GLN Chi-restraints excluded: chain R residue 100 ASP 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 100 ASP 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 148 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 227 ASP 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 10 ASP 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 79 GLU Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 113 ASP Chi-restraints excluded: chain T residue 148 THR 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 226 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR 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 228 THR 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 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 226 THR Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain V residue 239 ARG Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 79 GLU Chi-restraints excluded: chain W residue 100 ASP 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 145 ASP Chi-restraints excluded: chain W residue 148 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 100 ASP 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 177 THR 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 100 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 148 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 9.9990 chunk 547 optimal weight: 0.9990 chunk 333 optimal weight: 0.0970 chunk 259 optimal weight: 4.9990 chunk 380 optimal weight: 2.9990 chunk 573 optimal weight: 5.9990 chunk 528 optimal weight: 5.9990 chunk 456 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 352 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 46656 Z= 0.139 Angle : 0.404 8.805 63036 Z= 0.223 Chirality : 0.044 0.153 7200 Planarity : 0.003 0.035 8100 Dihedral : 3.642 46.849 6244 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.30 % Allowed : 22.39 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 5760 helix: 0.86 (0.38), residues: 216 sheet: -0.59 (0.10), residues: 2784 loop : -1.14 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP V 72 HIS 0.001 0.000 HIS R 94 PHE 0.010 0.001 PHE K 13 TYR 0.014 0.001 TYR P 192 ARG 0.002 0.000 ARG T 42 ********************** 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 556 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 292 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7767 (t80) REVERT: B 212 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8456 (t0) REVERT: C 88 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6785 (mtmm) REVERT: C 212 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8348 (t0) REVERT: G 219 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8615 (mtpp) REVERT: G 236 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: I 79 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: J 82 GLN cc_start: 0.8043 (mp10) cc_final: 0.7803 (mp10) REVERT: L 109 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8459 (mmmt) REVERT: M 26 GLU cc_start: 0.8129 (pm20) cc_final: 0.7823 (pm20) REVERT: M 217 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: M 219 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8613 (mtpp) REVERT: O 166 LYS cc_start: 0.7801 (tttt) cc_final: 0.7517 (mmmt) REVERT: P 109 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8128 (mtpt) REVERT: Q 240 ASP cc_start: 0.7894 (m-30) cc_final: 0.7608 (m-30) REVERT: R 221 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: S 73 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8742 (mp) REVERT: S 219 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8149 (mtpp) REVERT: S 236 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: V 144 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7553 (tptt) REVERT: W 38 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7318 (mp0) REVERT: W 212 ASN cc_start: 0.8544 (t0) cc_final: 0.8340 (t0) REVERT: X 38 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7350 (mp0) REVERT: Y 163 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8545 (mmtt) REVERT: Y 219 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8739 (mttp) outliers start: 264 outliers final: 236 residues processed: 529 average time/residue: 0.5208 time to fit residues: 473.7250 Evaluate side-chains 540 residues out of total 4992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 288 time to evaluate : 5.241 ------------------------------------------------------------------------------- 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 100 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 148 THR 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 18 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 ILE 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 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 100 ASP 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 177 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 100 ASP 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 145 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 227 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 100 ASP 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 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 148 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 184 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 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 113 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 148 THR 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 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 227 ASP 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 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 177 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 75 MET Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 228 THR 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 100 ASP 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 73 LEU Chi-restraints excluded: chain M residue 98 VAL 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 148 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 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 73 LEU Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 113 ASP 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 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 104 VAL Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 100 ASP 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 100 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 145 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 100 ASP 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 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 148 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 227 ASP 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 10 ASP 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 113 ASP Chi-restraints excluded: chain T residue 148 THR 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 113 ASP 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 24 THR 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 226 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 79 GLU Chi-restraints excluded: chain W residue 100 ASP 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 145 ASP Chi-restraints excluded: chain W residue 148 THR 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 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 100 ASP 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 177 THR 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 100 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 177 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 9.9990 chunk 486 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 421 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 457 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 469 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.129390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099793 restraints weight = 60538.342| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.52 r_work: 0.3173 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1430 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= 0.322 Angle : 0.485 8.458 63036 Z= 0.263 Chirality : 0.046 0.158 7200 Planarity : 0.003 0.044 8100 Dihedral : 4.062 46.920 6244 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.72 % Allowed : 22.03 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.11), residues: 5760 helix: 0.34 (0.35), residues: 216 sheet: -0.78 (0.10), residues: 2784 loop : -1.17 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 72 HIS 0.002 0.001 HIS R 94 PHE 0.016 0.002 PHE K 13 TYR 0.014 0.001 TYR P 192 ARG 0.003 0.000 ARG T 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10396.50 seconds wall clock time: 188 minutes 19.27 seconds (11299.27 seconds total)