Starting phenix.real_space_refine on Thu Dec 26 11:49:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkn_38421/12_2024/8xkn_38421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkn_38421/12_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/cci-nas-00/data/ceres_data/8xkn_38421/12_2024/8xkn_38421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkn_38421/12_2024/8xkn_38421.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkn_38421/12_2024/8xkn_38421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkn_38421/12_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. Time to flip 48 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 24.89, per 1000 atoms: 0.54 Number of scatterers: 45888 At special positions: 0 Unit cell: (143.65, 141.95, 195.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 9216 8.00 N 7416 7.00 C 29160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.44 Conformation dependent library (CDL) restraints added in 5.7 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: 4.49 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: 14.05 Time building geometry restraints manager: 12.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14916 1.34 - 1.45: 5865 1.45 - 1.57: 25683 1.57 - 1.69: 0 1.69 - 1.80: 192 Bond restraints: 46656 Sorted by residual: bond pdb=" N VAL Y 128 " pdb=" CA VAL Y 128 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.04e+00 bond pdb=" N VAL K 128 " pdb=" CA VAL K 128 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 8.80e+00 bond pdb=" N VAL S 128 " pdb=" CA VAL S 128 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.24e-02 6.50e+03 8.80e+00 bond pdb=" N VAL P 128 " pdb=" CA VAL P 128 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.41e+00 bond pdb=" N ILE H 59 " pdb=" CA ILE H 59 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 7.95e+00 ... (remaining 46651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 62223 2.03 - 4.05: 714 4.05 - 6.08: 71 6.08 - 8.11: 9 8.11 - 10.13: 19 Bond angle restraints: 63036 Sorted by residual: angle pdb=" N VAL B 111 " pdb=" CA VAL B 111 " pdb=" C VAL B 111 " ideal model delta sigma weight residual 113.53 107.89 5.64 9.80e-01 1.04e+00 3.31e+01 angle pdb=" CA ILE V 126 " pdb=" C ILE V 126 " pdb=" O ILE V 126 " ideal model delta sigma weight residual 121.92 117.68 4.24 1.17e+00 7.31e-01 1.31e+01 angle pdb=" C THR L 101 " pdb=" N ASN L 102 " pdb=" CA ASN L 102 " ideal model delta sigma weight residual 122.46 127.55 -5.09 1.41e+00 5.03e-01 1.30e+01 angle pdb=" C THR Q 101 " pdb=" N ASN Q 102 " pdb=" CA ASN Q 102 " ideal model delta sigma weight residual 122.82 127.94 -5.12 1.42e+00 4.96e-01 1.30e+01 angle pdb=" CA THR K 130 " pdb=" CB THR K 130 " pdb=" OG1 THR K 130 " ideal model delta sigma weight residual 109.60 104.37 5.23 1.50e+00 4.44e-01 1.21e+01 ... (remaining 63031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 24848 17.97 - 35.95: 2643 35.95 - 53.92: 758 53.92 - 71.90: 148 71.90 - 89.87: 55 Dihedral angle restraints: 28452 sinusoidal: 11364 harmonic: 17088 Sorted by residual: dihedral pdb=" CA ALA C 9 " pdb=" C ALA C 9 " pdb=" N ASP C 10 " pdb=" CA ASP C 10 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ALA J 25 " pdb=" C ALA J 25 " pdb=" N GLU J 26 " pdb=" CA GLU J 26 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ALA D 25 " pdb=" C ALA D 25 " pdb=" N GLU D 26 " pdb=" CA GLU D 26 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 28449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5386 0.050 - 0.099: 1390 0.099 - 0.149: 405 0.149 - 0.198: 17 0.198 - 0.248: 2 Chirality restraints: 7200 Sorted by residual: chirality pdb=" CA ILE V 126 " pdb=" N ILE V 126 " pdb=" C ILE V 126 " pdb=" CB ILE V 126 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE P 126 " pdb=" N ILE P 126 " pdb=" C ILE P 126 " pdb=" CB ILE P 126 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL V 128 " pdb=" N VAL V 128 " pdb=" C VAL V 128 " pdb=" CB VAL V 128 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 7197 not shown) Planarity restraints: 8100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 195 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO G 196 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 196 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 196 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 195 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO M 196 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO M 196 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 196 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE K 195 " -0.040 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO K 196 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 196 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 196 " -0.033 5.00e-02 4.00e+02 ... (remaining 8097 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1532 2.70 - 3.25: 40970 3.25 - 3.80: 65802 3.80 - 4.35: 89885 4.35 - 4.90: 158131 Nonbonded interactions: 356320 Sorted by model distance: nonbonded pdb=" OE2 GLU F 93 " pdb=" OH TYR F 151 " model vdw 2.145 3.040 nonbonded pdb=" OE2 GLU G 93 " pdb=" OH TYR G 151 " model vdw 2.164 3.040 nonbonded pdb=" OE2 GLU L 93 " pdb=" OH TYR L 151 " model vdw 2.167 3.040 nonbonded pdb=" OE2 GLU R 93 " pdb=" OH TYR R 151 " model vdw 2.173 3.040 nonbonded pdb=" OE2 GLU S 93 " pdb=" OH TYR S 151 " model vdw 2.175 3.040 ... (remaining 356315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'G' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'H' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = (chain 'L' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'M' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'N' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = (chain 'R' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'S' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'T' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = (chain 'X' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) selection = (chain 'Y' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 242)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.060 Extract box with map and model: 1.840 Check model and map are aligned: 0.360 Set scattering table: 0.420 Process input model: 89.660 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.240 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.810 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 5.169 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: 0.6088 time to fit residues: 306.3631 Evaluate side-chains 275 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 264 time to evaluate : 5.738 ------------------------------------------------------------------------------- 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: 9.9990 chunk 436 optimal weight: 0.6980 chunk 242 optimal weight: 8.9990 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: 2.9990 chunk 274 optimal weight: 20.0000 chunk 336 optimal weight: 10.0000 chunk 523 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN E 94 HIS G 77 GLN H 60 ASN H 77 GLN K 94 HIS M 77 GLN M 181 ASN N 77 GLN Q 94 HIS S 77 GLN S 181 ASN T 77 GLN V 152 GLN W 94 HIS W 242 ASN Y 77 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0715 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= 0.201 Angle : 0.460 8.641 63036 Z= 0.251 Chirality : 0.045 0.150 7200 Planarity : 0.003 0.043 8100 Dihedral : 4.176 47.533 6256 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.89 % Allowed : 20.54 % Favored : 76.57 % 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: -1.45 (0.10), residues: 5760 helix: 0.85 (0.37), residues: 216 sheet: -0.66 (0.10), residues: 2568 loop : -1.33 (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 F 94 PHE 0.011 0.001 PHE C 13 TYR 0.008 0.001 TYR B 12 ARG 0.003 0.000 ARG P 42 *********************** 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 445 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 301 time to evaluate : 5.486 Fit side-chains revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7349 (ptp90) REVERT: J 236 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8047 (tm-30) REVERT: K 236 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7968 (tm-30) REVERT: L 2 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7745 (mttm) REVERT: L 109 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8421 (mmmt) REVERT: N 82 GLN cc_start: 0.7790 (mp10) cc_final: 0.7332 (mp10) REVERT: P 82 GLN cc_start: 0.7986 (mp10) cc_final: 0.7511 (mp10) REVERT: P 240 ASP cc_start: 0.7798 (m-30) cc_final: 0.7550 (m-30) REVERT: Q 186 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6801 (mm-30) REVERT: Q 240 ASP cc_start: 0.7885 (m-30) cc_final: 0.7652 (m-30) REVERT: R 221 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: S 131 ASP cc_start: 0.7272 (t0) cc_final: 0.7015 (t0) REVERT: S 236 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: U 236 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7745 (tm-30) REVERT: V 56 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7243 (mp0) REVERT: V 131 ASP cc_start: 0.6920 (t0) cc_final: 0.6657 (t0) REVERT: W 212 ASN cc_start: 0.8536 (t0) cc_final: 0.8301 (t0) outliers start: 144 outliers final: 90 residues processed: 419 average time/residue: 0.5522 time to fit residues: 399.0555 Evaluate side-chains 376 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 282 time to evaluate : 5.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain P residue 227 ASP Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 229 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 435 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 524 optimal weight: 10.0000 chunk 566 optimal weight: 20.0000 chunk 466 optimal weight: 0.9980 chunk 519 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 420 optimal weight: 30.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 181 ASN O 181 ASN P 181 ASN S 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 46656 Z= 0.424 Angle : 0.559 10.108 63036 Z= 0.302 Chirality : 0.048 0.158 7200 Planarity : 0.004 0.057 8100 Dihedral : 4.564 47.332 6243 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.56 % Allowed : 21.08 % Favored : 74.36 % 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: -1.91 (0.10), residues: 5760 helix: 0.10 (0.34), residues: 216 sheet: -1.18 (0.10), residues: 2568 loop : -1.37 (0.10), residues: 2976 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 G 192 ARG 0.004 0.000 ARG M 239 *********************** 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 518 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 291 time to evaluate : 5.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7923 (t80) REVERT: C 88 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6937 (mtmm) REVERT: C 212 ASN cc_start: 0.8677 (t0) cc_final: 0.8371 (t0) REVERT: D 79 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: G 219 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8627 (mtpp) REVERT: G 229 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8538 (t70) REVERT: G 236 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: I 88 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7169 (mtmm) REVERT: L 2 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7791 (mttm) REVERT: L 109 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8455 (mmmt) REVERT: M 219 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8763 (mtpp) REVERT: N 82 GLN cc_start: 0.7833 (mp10) cc_final: 0.7247 (mp10) REVERT: O 166 LYS cc_start: 0.7965 (tttt) cc_final: 0.7654 (tptp) REVERT: O 176 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8414 (tmt170) REVERT: P 82 GLN cc_start: 0.8039 (mp10) cc_final: 0.7588 (mp10) REVERT: P 109 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8181 (mtpt) REVERT: P 240 ASP cc_start: 0.7868 (m-30) cc_final: 0.7621 (m-30) REVERT: Q 1 MET cc_start: 0.7486 (tpt) cc_final: 0.6790 (tpt) REVERT: R 221 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: S 131 ASP cc_start: 0.7328 (t0) cc_final: 0.7044 (t0) REVERT: S 219 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8178 (mtpp) REVERT: S 236 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: U 204 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8257 (p90) REVERT: W 56 GLU cc_start: 0.8015 (mp0) cc_final: 0.7767 (mp0) REVERT: W 212 ASN cc_start: 0.8622 (t0) cc_final: 0.8373 (t0) REVERT: Y 219 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8740 (mttm) outliers start: 227 outliers final: 160 residues processed: 500 average time/residue: 0.5588 time to fit residues: 477.9886 Evaluate side-chains 456 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 281 time to evaluate : 5.584 ------------------------------------------------------------------------------- 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 75 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 181 ASN Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 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 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 128 VAL Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain P residue 227 ASP Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 219 LYS Chi-restraints excluded: chain Y residue 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: 10.0000 chunk 271 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 351 optimal weight: 9.9990 chunk 525 optimal weight: 3.9990 chunk 556 optimal weight: 0.0970 chunk 274 optimal weight: 20.0000 chunk 498 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 181 ASN P 181 ASN S 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 46656 Z= 0.271 Angle : 0.476 8.608 63036 Z= 0.261 Chirality : 0.046 0.151 7200 Planarity : 0.003 0.055 8100 Dihedral : 4.242 47.877 6243 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.80 % Allowed : 21.39 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.94 (0.10), residues: 5760 helix: 0.34 (0.35), residues: 216 sheet: -1.25 (0.10), residues: 2568 loop : -1.35 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 72 HIS 0.002 0.001 HIS L 94 PHE 0.014 0.002 PHE K 13 TYR 0.009 0.001 TYR T 51 ARG 0.003 0.000 ARG J 42 *********************** 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 527 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 288 time to evaluate : 5.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8421 (t0) REVERT: C 212 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8325 (t0) REVERT: D 205 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: F 92 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7315 (ptp90) REVERT: F 191 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9196 (mm) REVERT: G 219 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8625 (mtpp) REVERT: G 236 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: I 64 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9036 (tttt) REVERT: J 236 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8033 (tm-30) REVERT: L 2 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7822 (mttm) REVERT: L 109 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8443 (mmmt) REVERT: M 219 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8749 (mtpp) REVERT: N 82 GLN cc_start: 0.7833 (mp10) cc_final: 0.7244 (mp10) REVERT: O 176 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8465 (tmt170) REVERT: P 82 GLN cc_start: 0.8024 (mp10) cc_final: 0.7578 (mp10) REVERT: P 240 ASP cc_start: 0.7872 (m-30) cc_final: 0.7604 (m-30) REVERT: R 191 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8891 (mm) REVERT: R 221 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: S 131 ASP cc_start: 0.7222 (t0) cc_final: 0.6980 (t0) REVERT: S 236 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: T 38 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7431 (mp0) REVERT: U 204 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8324 (p90) REVERT: V 24 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8902 (p) REVERT: W 56 GLU cc_start: 0.8013 (mp0) cc_final: 0.7753 (mp0) REVERT: W 212 ASN cc_start: 0.8594 (t0) cc_final: 0.8354 (t0) REVERT: Y 185 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6913 (mm-30) outliers start: 239 outliers final: 181 residues processed: 506 average time/residue: 0.5501 time to fit residues: 477.1708 Evaluate side-chains 475 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 278 time to evaluate : 5.831 ------------------------------------------------------------------------------- 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 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 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN 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 186 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 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 113 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 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 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 217 GLU Chi-restraints excluded: chain M residue 219 LYS 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 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 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 181 ASN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 181 ASN Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain P residue 226 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 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 181 ASN 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 51 TYR Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 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 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 113 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 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: 10.0000 chunk 316 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 475 optimal weight: 8.9990 chunk 384 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 499 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 181 ASN O 181 ASN P 181 ASN S 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 46656 Z= 0.364 Angle : 0.520 9.290 63036 Z= 0.283 Chirality : 0.047 0.156 7200 Planarity : 0.004 0.059 8100 Dihedral : 4.415 47.349 6243 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.06 % Allowed : 20.82 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.10), residues: 5760 helix: 0.02 (0.34), residues: 216 sheet: -1.45 (0.10), residues: 2568 loop : -1.38 (0.10), residues: 2976 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 Q 192 ARG 0.005 0.000 ARG J 42 *********************** 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 588 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 302 poor density : 286 time to evaluate : 5.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.7949 (t80) REVERT: B 212 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8429 (t0) REVERT: C 48 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8185 (mtmm) REVERT: C 88 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6914 (mtmm) REVERT: C 212 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8346 (t0) REVERT: D 79 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: D 205 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: F 191 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9206 (mm) REVERT: G 219 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8664 (mtpp) REVERT: G 229 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8552 (t70) REVERT: G 236 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: I 1 MET cc_start: 0.8098 (ttt) cc_final: 0.7878 (ttt) REVERT: I 64 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9070 (tttt) REVERT: J 236 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8051 (tm-30) REVERT: L 2 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7828 (mttm) REVERT: L 109 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8473 (mmmt) REVERT: M 26 GLU cc_start: 0.8198 (pm20) cc_final: 0.7989 (pm20) REVERT: M 219 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8817 (mtpp) REVERT: N 82 GLN cc_start: 0.7861 (mp10) cc_final: 0.7246 (mp10) REVERT: O 52 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7534 (mp) REVERT: O 176 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8467 (tmt170) REVERT: P 82 GLN cc_start: 0.8045 (mp10) cc_final: 0.7594 (mp10) REVERT: P 109 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8140 (mtpt) REVERT: P 240 ASP cc_start: 0.7926 (m-30) cc_final: 0.7652 (m-30) REVERT: R 191 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8930 (mm) REVERT: R 221 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: S 131 ASP cc_start: 0.7254 (t0) cc_final: 0.7020 (t0) REVERT: S 219 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8202 (mtpp) REVERT: S 236 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: U 204 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8243 (p90) REVERT: W 56 GLU cc_start: 0.8018 (mp0) cc_final: 0.7762 (mp0) REVERT: W 212 ASN cc_start: 0.8629 (t0) cc_final: 0.8382 (t0) REVERT: X 38 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7320 (mp0) REVERT: Y 163 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8582 (mmtt) REVERT: Y 185 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6950 (mm-30) REVERT: Y 219 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8807 (mttm) outliers start: 302 outliers final: 233 residues processed: 565 average time/residue: 0.5537 time to fit residues: 535.5985 Evaluate side-chains 534 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 278 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 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 113 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR 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 227 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 217 GLU Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 181 ASN Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain P residue 226 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 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 181 ASN Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 113 ASP Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 113 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 219 LYS Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 239 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 1.9990 chunk 501 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 557 optimal weight: 8.9990 chunk 462 optimal weight: 0.3980 chunk 258 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 292 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 46656 Z= 0.170 Angle : 0.425 8.513 63036 Z= 0.235 Chirality : 0.044 0.150 7200 Planarity : 0.003 0.052 8100 Dihedral : 3.908 48.080 6243 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.72 % Allowed : 22.19 % Favored : 73.09 % 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: -1.89 (0.10), residues: 5760 helix: 0.67 (0.37), residues: 216 sheet: -1.28 (0.10), residues: 2568 loop : -1.28 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP L 72 HIS 0.001 0.000 HIS O 94 PHE 0.011 0.001 PHE K 13 TYR 0.012 0.001 TYR Q 192 ARG 0.002 0.000 ARG J 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 545 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 310 time to evaluate : 5.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7937 (t80) REVERT: B 212 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8431 (t0) REVERT: C 88 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6829 (mtmm) REVERT: C 212 ASN cc_start: 0.8618 (t0) cc_final: 0.8337 (t0) REVERT: C 236 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8055 (tm-30) REVERT: D 205 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: G 236 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: I 1 MET cc_start: 0.8044 (ttt) cc_final: 0.7805 (ttt) REVERT: I 64 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9028 (tttt) REVERT: J 75 MET cc_start: 0.8419 (mtp) cc_final: 0.8193 (mtp) REVERT: J 236 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8005 (tm-30) REVERT: L 2 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7818 (mttm) REVERT: L 109 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8433 (mmmt) REVERT: M 26 GLU cc_start: 0.8150 (pm20) cc_final: 0.7943 (pm20) REVERT: M 219 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8768 (mtpp) REVERT: N 51 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.7272 (t80) REVERT: N 82 GLN cc_start: 0.7865 (mp10) cc_final: 0.7270 (mp10) REVERT: P 82 GLN cc_start: 0.7987 (mp10) cc_final: 0.7539 (mp10) REVERT: P 240 ASP cc_start: 0.7882 (m-30) cc_final: 0.7609 (m-30) REVERT: R 221 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: S 219 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8169 (mtpp) REVERT: U 236 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7754 (tm-30) REVERT: V 144 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7503 (tptt) REVERT: W 56 GLU cc_start: 0.7918 (mp0) cc_final: 0.7556 (mp0) REVERT: W 212 ASN cc_start: 0.8546 (t0) cc_final: 0.8336 (t0) REVERT: X 38 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7314 (mp0) REVERT: Y 24 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8845 (p) REVERT: Y 163 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8483 (mmtt) REVERT: Y 185 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6954 (mm-30) outliers start: 235 outliers final: 191 residues processed: 516 average time/residue: 0.5634 time to fit residues: 496.0983 Evaluate side-chains 501 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 296 time to evaluate : 5.750 ------------------------------------------------------------------------------- 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 212 ASN Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain 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 205 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 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 217 GLU 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 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 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 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 228 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 50 LEU 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 113 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 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 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 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 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 104 VAL Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 239 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 406 optimal weight: 0.9990 chunk 315 optimal weight: 6.9990 chunk 469 optimal weight: 30.0000 chunk 311 optimal weight: 5.9990 chunk 555 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 46656 Z= 0.354 Angle : 0.511 8.844 63036 Z= 0.278 Chirality : 0.047 0.154 7200 Planarity : 0.004 0.057 8100 Dihedral : 4.265 47.387 6242 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.86 % Allowed : 21.27 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.10), residues: 5760 helix: 0.21 (0.34), residues: 216 sheet: -1.45 (0.10), residues: 2568 loop : -1.33 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 72 HIS 0.002 0.001 HIS L 94 PHE 0.016 0.002 PHE K 13 TYR 0.011 0.001 TYR Q 192 ARG 0.004 0.000 ARG J 42 *********************** 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 575 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 283 time to evaluate : 5.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.7943 (t80) REVERT: B 212 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8436 (t0) REVERT: C 48 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8172 (mtmm) REVERT: C 88 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6928 (mtmm) REVERT: C 212 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8362 (t0) REVERT: C 236 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 79 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: D 205 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: G 236 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: I 1 MET cc_start: 0.8063 (ttt) cc_final: 0.7808 (ttt) REVERT: I 64 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9061 (tttt) REVERT: J 236 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8051 (tm-30) REVERT: L 2 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7815 (mttm) REVERT: L 109 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8466 (mmmt) REVERT: M 26 GLU cc_start: 0.8175 (pm20) cc_final: 0.7904 (pm20) REVERT: M 219 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8925 (mtpp) REVERT: N 51 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.7240 (t80) REVERT: N 82 GLN cc_start: 0.7907 (mp10) cc_final: 0.7279 (mp10) REVERT: O 52 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7550 (mp) REVERT: O 176 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8525 (tmt170) REVERT: P 109 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8144 (mtpt) REVERT: P 240 ASP cc_start: 0.7851 (m-30) cc_final: 0.7568 (m-30) REVERT: Q 1 MET cc_start: 0.7568 (tpt) cc_final: 0.6919 (tpt) REVERT: Q 229 ASP cc_start: 0.7745 (t70) cc_final: 0.7513 (t70) REVERT: R 191 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8940 (mm) REVERT: R 221 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: S 73 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8709 (mp) REVERT: S 219 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8222 (mtpp) REVERT: S 236 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: T 38 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7435 (mp0) REVERT: U 204 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8330 (p90) REVERT: V 24 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8882 (p) REVERT: V 144 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7540 (tptt) REVERT: V 236 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7281 (tm-30) REVERT: W 56 GLU cc_start: 0.8021 (mp0) cc_final: 0.7780 (mp0) REVERT: W 212 ASN cc_start: 0.8616 (t0) cc_final: 0.8377 (t0) REVERT: X 38 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7317 (mp0) REVERT: Y 163 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8564 (mmtt) REVERT: Y 219 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8833 (mttm) outliers start: 292 outliers final: 243 residues processed: 553 average time/residue: 0.5496 time to fit residues: 520.1357 Evaluate side-chains 545 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 278 time to evaluate : 5.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 THR 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 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 217 GLU 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 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 227 ASP Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 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 104 VAL Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 113 ASP Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 113 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 173 VAL Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 331 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 352 optimal weight: 1.9990 chunk 378 optimal weight: 7.9990 chunk 274 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 436 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 46656 Z= 0.267 Angle : 0.470 8.819 63036 Z= 0.258 Chirality : 0.045 0.151 7200 Planarity : 0.003 0.054 8100 Dihedral : 4.098 47.696 6242 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.84 % Allowed : 21.29 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.10), residues: 5760 helix: 0.35 (0.35), residues: 216 sheet: -1.44 (0.10), residues: 2568 loop : -1.32 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 72 HIS 0.002 0.001 HIS R 94 PHE 0.013 0.001 PHE K 13 TYR 0.011 0.001 TYR P 192 ARG 0.003 0.000 ARG J 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 584 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 293 time to evaluate : 5.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7952 (t80) REVERT: B 212 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8435 (t0) REVERT: C 69 ASP cc_start: 0.8096 (t0) cc_final: 0.7805 (t0) REVERT: C 88 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6906 (mtmm) REVERT: C 212 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8349 (t0) REVERT: C 236 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8054 (tm-30) REVERT: G 229 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8541 (t70) REVERT: G 236 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: I 1 MET cc_start: 0.8059 (ttt) cc_final: 0.7814 (ttt) REVERT: I 64 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9046 (tttt) REVERT: J 236 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8046 (tm-30) REVERT: L 2 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7796 (mttm) REVERT: L 109 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8459 (mmmt) REVERT: M 26 GLU cc_start: 0.8132 (pm20) cc_final: 0.7864 (pm20) REVERT: M 219 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8830 (mtpp) REVERT: N 51 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7198 (t80) REVERT: N 82 GLN cc_start: 0.7903 (mp10) cc_final: 0.7312 (mp10) REVERT: P 82 GLN cc_start: 0.8029 (mp10) cc_final: 0.7579 (mp10) REVERT: P 109 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8127 (mtpt) REVERT: P 240 ASP cc_start: 0.7831 (m-30) cc_final: 0.7553 (m-30) REVERT: Q 1 MET cc_start: 0.7548 (tpt) cc_final: 0.6881 (tpt) REVERT: Q 229 ASP cc_start: 0.7705 (t70) cc_final: 0.7472 (t70) REVERT: R 191 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8946 (mm) REVERT: R 221 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: S 73 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8749 (mp) REVERT: S 219 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: S 236 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: T 38 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7451 (mp0) REVERT: V 144 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7541 (tptt) REVERT: V 236 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7282 (tm-30) REVERT: W 56 GLU cc_start: 0.7948 (mp0) cc_final: 0.7700 (mp0) REVERT: W 212 ASN cc_start: 0.8599 (t0) cc_final: 0.8359 (t0) REVERT: X 38 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7302 (mp0) REVERT: Y 163 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8536 (mmtt) outliers start: 291 outliers final: 252 residues processed: 560 average time/residue: 0.5487 time to fit residues: 527.9469 Evaluate side-chains 553 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 284 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 THR 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 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 227 ASP Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 136 ILE 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 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 204 PHE Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 229 ASP Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 104 VAL 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 22 VAL 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 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 173 VAL Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 228 THR Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 239 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 10.0000 chunk 531 optimal weight: 6.9990 chunk 485 optimal weight: 9.9990 chunk 517 optimal weight: 0.0870 chunk 311 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 406 optimal weight: 5.9990 chunk 158 optimal weight: 0.0370 chunk 467 optimal weight: 10.0000 chunk 489 optimal weight: 7.9990 chunk 515 optimal weight: 6.9990 overall best weight: 4.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 46656 Z= 0.299 Angle : 0.488 8.400 63036 Z= 0.266 Chirality : 0.046 0.152 7200 Planarity : 0.003 0.056 8100 Dihedral : 4.172 47.565 6242 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.96 % Allowed : 21.22 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 5760 helix: 0.21 (0.35), residues: 216 sheet: -1.48 (0.10), residues: 2568 loop : -1.33 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 72 HIS 0.002 0.001 HIS R 94 PHE 0.015 0.002 PHE K 13 TYR 0.012 0.001 TYR P 192 ARG 0.003 0.000 ARG J 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 585 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 288 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.7948 (t80) REVERT: B 212 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8443 (t0) REVERT: C 48 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8162 (mtmm) REVERT: C 88 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6908 (mtmm) REVERT: C 212 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8367 (t0) REVERT: C 236 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8049 (tm-30) REVERT: G 229 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8531 (t70) REVERT: G 236 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: I 1 MET cc_start: 0.8059 (ttt) cc_final: 0.7803 (ttt) REVERT: I 64 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9051 (tttt) REVERT: J 236 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8038 (tm-30) REVERT: K 229 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8414 (t70) REVERT: L 2 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7811 (mttm) REVERT: L 109 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8461 (mmmt) REVERT: M 26 GLU cc_start: 0.8112 (pm20) cc_final: 0.7840 (pm20) REVERT: M 219 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8871 (mtpp) REVERT: N 51 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7195 (t80) REVERT: N 82 GLN cc_start: 0.7906 (mp10) cc_final: 0.7305 (mp10) REVERT: N 229 ASP cc_start: 0.7893 (t70) cc_final: 0.7467 (t70) REVERT: O 48 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7614 (mtmm) REVERT: P 82 GLN cc_start: 0.8043 (mp10) cc_final: 0.7593 (mp10) REVERT: P 109 LYS cc_start: 0.8384 (mmmt) cc_final: 0.8149 (mtpt) REVERT: P 240 ASP cc_start: 0.7844 (m-30) cc_final: 0.7560 (m-30) REVERT: Q 1 MET cc_start: 0.7548 (tpt) cc_final: 0.6859 (tpt) REVERT: R 191 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8944 (mm) REVERT: R 221 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: S 73 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8760 (mp) REVERT: S 219 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: S 236 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: T 38 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7449 (mp0) REVERT: U 204 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8331 (p90) REVERT: V 144 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7519 (tptt) REVERT: V 236 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7256 (tm-30) REVERT: W 56 GLU cc_start: 0.7975 (mp0) cc_final: 0.7737 (mp0) REVERT: W 212 ASN cc_start: 0.8604 (t0) cc_final: 0.8363 (t0) REVERT: X 38 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7304 (mp0) REVERT: Y 163 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8556 (mmtt) REVERT: Y 219 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8817 (mttm) outliers start: 297 outliers final: 258 residues processed: 563 average time/residue: 0.5524 time to fit residues: 532.9669 Evaluate side-chains 562 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 282 time to evaluate : 5.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 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 22 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 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 173 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 229 ASP Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 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 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 227 ASP Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 136 ILE 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 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 229 ASP Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 204 PHE Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 173 VAL Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 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 339 optimal weight: 8.9990 chunk 547 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 573 optimal weight: 3.9990 chunk 528 optimal weight: 0.4980 chunk 456 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 280 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 46656 Z= 0.249 Angle : 0.464 8.135 63036 Z= 0.254 Chirality : 0.045 0.152 7200 Planarity : 0.003 0.054 8100 Dihedral : 4.036 47.745 6242 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.68 % Allowed : 21.59 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.11), residues: 5760 helix: 0.38 (0.35), residues: 216 sheet: -1.43 (0.10), residues: 2568 loop : -1.31 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 72 HIS 0.001 0.000 HIS R 94 PHE 0.013 0.001 PHE K 13 TYR 0.012 0.001 TYR P 192 ARG 0.003 0.000 ARG J 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 575 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 283 poor density : 292 time to evaluate : 6.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7941 (t80) REVERT: B 212 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8421 (t0) REVERT: C 48 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8142 (mtmm) REVERT: C 88 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6882 (mtmm) REVERT: C 212 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8347 (t0) REVERT: C 236 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8053 (tm-30) REVERT: G 229 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8528 (t70) REVERT: G 236 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: I 1 MET cc_start: 0.8040 (ttt) cc_final: 0.7787 (ttt) REVERT: I 64 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9041 (tttt) REVERT: J 82 GLN cc_start: 0.8002 (mp10) cc_final: 0.7745 (mp10) REVERT: J 236 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8045 (tm-30) REVERT: L 109 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8447 (mmmt) REVERT: M 26 GLU cc_start: 0.8101 (pm20) cc_final: 0.7847 (pm20) REVERT: M 163 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8508 (mmtt) REVERT: M 219 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8805 (mtpp) REVERT: N 51 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7248 (t80) REVERT: N 82 GLN cc_start: 0.7904 (mp10) cc_final: 0.7310 (mp10) REVERT: O 48 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7613 (mtmm) REVERT: P 82 GLN cc_start: 0.8022 (mp10) cc_final: 0.7567 (mp10) REVERT: R 191 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8956 (mm) REVERT: R 221 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: S 73 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8760 (mp) REVERT: S 219 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8181 (mtpp) REVERT: S 236 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: T 38 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7438 (mp0) REVERT: V 144 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7530 (tptt) REVERT: V 236 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7270 (tm-30) REVERT: W 56 GLU cc_start: 0.7943 (mp0) cc_final: 0.7692 (mp0) REVERT: W 212 ASN cc_start: 0.8612 (t0) cc_final: 0.8389 (t0) REVERT: X 38 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7264 (mp0) REVERT: Y 1 MET cc_start: 0.7493 (ttt) cc_final: 0.7277 (ttt) REVERT: Y 163 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8534 (mmtt) REVERT: Y 219 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8791 (mttm) outliers start: 283 outliers final: 257 residues processed: 547 average time/residue: 0.5503 time to fit residues: 514.5320 Evaluate side-chains 566 residues out of total 4992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 289 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 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 22 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 204 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 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 173 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 204 PHE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 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 104 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain M residue 163 LYS Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 219 LYS Chi-restraints excluded: chain M residue 227 ASP Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 82 GLN Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 136 ILE 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 104 VAL Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 212 ASN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 174 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 219 LYS Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 174 GLU Chi-restraints excluded: chain T residue 177 THR Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 229 ASP Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 104 VAL 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 104 VAL Chi-restraints excluded: chain V residue 113 ASP Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 THR Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 229 ASP Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 177 THR Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 173 VAL Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 212 ASN Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 138 THR Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 173 VAL Chi-restraints excluded: chain Y residue 174 GLU Chi-restraints excluded: chain Y residue 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: 6.9990 chunk 486 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 421 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 457 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 469 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.130320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100330 restraints weight = 60318.798| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.56 r_work: 0.3176 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 46656 Z= 0.243 Angle : 0.460 8.125 63036 Z= 0.252 Chirality : 0.045 0.153 7200 Planarity : 0.003 0.048 8100 Dihedral : 3.995 47.973 6242 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.86 % Allowed : 21.47 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 5760 helix: 0.40 (0.35), residues: 216 sheet: -1.42 (0.10), residues: 2568 loop : -1.30 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 72 HIS 0.001 0.000 HIS R 94 PHE 0.013 0.001 PHE K 13 TYR 0.012 0.001 TYR P 192 ARG 0.003 0.000 ARG J 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10115.14 seconds wall clock time: 187 minutes 58.51 seconds (11278.51 seconds total)