Starting phenix.real_space_refine on Sun Aug 24 03:11:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v9d_43071/08_2025/8v9d_43071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v9d_43071/08_2025/8v9d_43071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v9d_43071/08_2025/8v9d_43071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v9d_43071/08_2025/8v9d_43071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v9d_43071/08_2025/8v9d_43071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v9d_43071/08_2025/8v9d_43071.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.070 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 82 5.16 5 C 10632 2.51 5 N 2758 2.21 5 O 3211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16683 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "I" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1690 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1639 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "B" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "K" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1690 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1639 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "C" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "M" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1690 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1639 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "D" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 4.64, per 1000 atoms: 0.28 Number of scatterers: 16683 At special positions: 0 Unit cell: (104.25, 159.294, 147.618, 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 82 16.00 O 3211 8.00 N 2758 7.00 C 10632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 152 " - pdb=" SG CYS I 208 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 97 " distance=2.04 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 208 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.04 Simple disulfide: pdb=" SG CYS M 152 " - pdb=" SG CYS M 208 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " distance=2.04 Simple disulfide: pdb=" SG CYS N 135 " - pdb=" SG CYS N 195 " distance=2.04 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: 1.43 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4012 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 30 sheets defined 34.4% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 32 through 55 Processing helix chain 'A' and resid 69 through 93 removed outlier: 5.422A pdb=" N HIS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 111 through 137 removed outlier: 3.821A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 178 removed outlier: 3.730A pdb=" N LEU A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 205 removed outlier: 3.506A pdb=" N ILE A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 231 through 251 Proline residue: A 237 - end of helix Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 199 through 201 No H-bonds generated for 'chain 'I' and resid 199 through 201' Processing helix chain 'J' and resid 29 through 32 removed outlier: 3.968A pdb=" N ARG J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 29 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 4.199A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 128 removed outlier: 3.722A pdb=" N SER J 128 " --> pdb=" O GLU J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 69 through 93 removed outlier: 5.516A pdb=" N HIS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 111 through 137 removed outlier: 3.652A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 178 removed outlier: 3.504A pdb=" N LEU B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 205 removed outlier: 3.541A pdb=" N GLY B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 231 through 251 Proline residue: B 237 - end of helix Processing helix chain 'K' and resid 63 through 66 removed outlier: 3.544A pdb=" N LYS K 66 " --> pdb=" O PRO K 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 63 through 66' Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 139 through 141 No H-bonds generated for 'chain 'K' and resid 139 through 141' Processing helix chain 'K' and resid 168 through 170 No H-bonds generated for 'chain 'K' and resid 168 through 170' Processing helix chain 'K' and resid 199 through 201 No H-bonds generated for 'chain 'K' and resid 199 through 201' Processing helix chain 'L' and resid 29 through 32 removed outlier: 3.803A pdb=" N ARG L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.150A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 128 removed outlier: 3.977A pdb=" N SER L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 190 Processing helix chain 'C' and resid 33 through 55 Processing helix chain 'C' and resid 69 through 93 removed outlier: 5.543A pdb=" N HIS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.806A pdb=" N PHE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 178 removed outlier: 3.671A pdb=" N LEU C 170 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 205 removed outlier: 3.528A pdb=" N ILE C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Proline residue: C 220 - end of helix Processing helix chain 'C' and resid 231 through 251 Proline residue: C 237 - end of helix Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'M' and resid 139 through 141 No H-bonds generated for 'chain 'M' and resid 139 through 141' Processing helix chain 'M' and resid 168 through 170 No H-bonds generated for 'chain 'M' and resid 168 through 170' Processing helix chain 'M' and resid 199 through 201 No H-bonds generated for 'chain 'M' and resid 199 through 201' Processing helix chain 'N' and resid 29 through 32 removed outlier: 3.837A pdb=" N ARG N 32 " --> pdb=" O VAL N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 32' Processing helix chain 'N' and resid 80 through 84 removed outlier: 4.182A pdb=" N PHE N 84 " --> pdb=" O PRO N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 128 removed outlier: 3.749A pdb=" N SER N 128 " --> pdb=" O GLU N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 190 Processing helix chain 'D' and resid 33 through 55 Processing helix chain 'D' and resid 69 through 93 removed outlier: 5.455A pdb=" N HIS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 111 through 137 removed outlier: 3.695A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 178 removed outlier: 3.637A pdb=" N LEU D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 205 Processing helix chain 'D' and resid 213 through 225 Proline residue: D 220 - end of helix Processing helix chain 'D' and resid 231 through 251 Proline residue: D 237 - end of helix Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.521A pdb=" N GLY I 37 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP I 36 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG I 52 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP I 38 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN I 60 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 134 through 136 removed outlier: 6.575A pdb=" N TYR I 188 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 143 through 144 removed outlier: 6.575A pdb=" N TYR I 188 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 163 through 166 Processing sheet with id=AA6, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.571A pdb=" N SER J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'J' and resid 54 through 55 removed outlier: 6.512A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR J 50 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR J 98 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 115 through 119 removed outlier: 3.603A pdb=" N ASN J 138 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL J 134 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 154 through 156 removed outlier: 4.759A pdb=" N TRP J 149 " --> pdb=" O GLN J 156 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS J 146 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN J 148 " --> pdb=" O GLU J 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU J 196 " --> pdb=" O GLN J 148 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR J 193 " --> pdb=" O PHE J 210 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS J 208 " --> pdb=" O CYS J 195 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 197 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL J 206 " --> pdb=" O VAL J 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.636A pdb=" N GLY K 37 " --> pdb=" O ALA K 98 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP K 36 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG K 52 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP K 38 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN K 60 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 134 through 136 removed outlier: 6.466A pdb=" N TYR K 188 " --> pdb=" O ASP K 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 143 through 144 removed outlier: 6.466A pdb=" N TYR K 188 " --> pdb=" O ASP K 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER K 189 " --> pdb=" O VAL K 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 163 through 166 Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.585A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.286A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.496A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.631A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.734A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN L 148 " --> pdb=" O GLU L 196 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL L 206 " --> pdb=" O VAL L 197 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.542A pdb=" N GLY M 37 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP M 36 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN M 60 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 134 through 136 removed outlier: 6.455A pdb=" N TYR M 188 " --> pdb=" O ASP M 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 143 through 144 removed outlier: 6.455A pdb=" N TYR M 188 " --> pdb=" O ASP M 156 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER M 189 " --> pdb=" O VAL M 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 163 through 166 Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.609A pdb=" N SER N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.451A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR N 98 " --> pdb=" O GLN N 91 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 115 through 119 removed outlier: 3.582A pdb=" N ASN N 138 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL N 134 " --> pdb=" O PHE N 119 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 154 through 156 removed outlier: 4.730A pdb=" N TRP N 149 " --> pdb=" O GLN N 156 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS N 146 " --> pdb=" O THR N 198 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN N 148 " --> pdb=" O GLU N 196 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU N 196 " --> pdb=" O GLN N 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR N 193 " --> pdb=" O PHE N 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE N 210 " --> pdb=" O TYR N 193 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS N 208 " --> pdb=" O CYS N 195 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL N 197 " --> pdb=" O VAL N 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL N 206 " --> pdb=" O VAL N 197 " (cutoff:3.500A) 859 hydrogen bonds defined for protein. 2388 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: 3.20 Time building geometry restraints manager: 1.92 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: 5220 1.34 - 1.46: 4034 1.46 - 1.58: 7642 1.58 - 1.70: 0 1.70 - 1.82: 110 Bond restraints: 17006 Sorted by residual: bond pdb=" CB PRO I 114 " pdb=" CG PRO I 114 " ideal model delta sigma weight residual 1.506 1.464 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CB PRO K 114 " pdb=" CG PRO K 114 " ideal model delta sigma weight residual 1.506 1.465 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" CB PRO M 114 " pdb=" CG PRO M 114 " ideal model delta sigma weight residual 1.506 1.467 0.039 3.90e-02 6.57e+02 1.01e+00 bond pdb=" CA ILE K 53 " pdb=" CB ILE K 53 " ideal model delta sigma weight residual 1.550 1.541 0.010 1.03e-02 9.43e+03 9.34e-01 bond pdb=" CA ILE I 53 " pdb=" CB ILE I 53 " ideal model delta sigma weight residual 1.550 1.541 0.009 1.03e-02 9.43e+03 8.06e-01 ... (remaining 17001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 22566 1.20 - 2.39: 458 2.39 - 3.59: 144 3.59 - 4.78: 17 4.78 - 5.98: 3 Bond angle restraints: 23188 Sorted by residual: angle pdb=" OG1 THR M 122 " pdb=" CB THR M 122 " pdb=" CG2 THR M 122 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.94e+00 angle pdb=" OG1 THR K 122 " pdb=" CB THR K 122 " pdb=" CG2 THR K 122 " ideal model delta sigma weight residual 109.30 103.34 5.96 2.00e+00 2.50e-01 8.89e+00 angle pdb=" OG1 THR I 122 " pdb=" CB THR I 122 " pdb=" CG2 THR I 122 " ideal model delta sigma weight residual 109.30 103.38 5.92 2.00e+00 2.50e-01 8.75e+00 angle pdb=" CA VAL M 196 " pdb=" C VAL M 196 " pdb=" N PRO M 197 " ideal model delta sigma weight residual 116.57 119.17 -2.60 9.80e-01 1.04e+00 7.05e+00 angle pdb=" CA VAL K 196 " pdb=" C VAL K 196 " pdb=" N PRO K 197 " ideal model delta sigma weight residual 116.57 119.17 -2.60 9.80e-01 1.04e+00 7.04e+00 ... (remaining 23183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 9287 16.26 - 32.51: 515 32.51 - 48.77: 128 48.77 - 65.02: 19 65.02 - 81.28: 18 Dihedral angle restraints: 9967 sinusoidal: 3669 harmonic: 6298 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 32.58 60.42 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS N 135 " pdb=" SG CYS N 135 " pdb=" SG CYS N 195 " pdb=" CB CYS N 195 " ideal model delta sinusoidal sigma weight residual 93.00 35.97 57.03 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS K 152 " pdb=" SG CYS K 152 " pdb=" SG CYS K 208 " pdb=" CB CYS K 208 " ideal model delta sinusoidal sigma weight residual 93.00 37.02 55.98 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 9964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2436 0.066 - 0.131: 253 0.131 - 0.197: 10 0.197 - 0.262: 0 0.262 - 0.328: 3 Chirality restraints: 2702 Sorted by residual: chirality pdb=" CA ILE C 96 " pdb=" N ILE C 96 " pdb=" C ILE C 96 " pdb=" CB ILE C 96 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ILE D 96 " pdb=" N ILE D 96 " pdb=" C ILE D 96 " pdb=" CB ILE D 96 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ILE A 96 " pdb=" N ILE A 96 " pdb=" C ILE A 96 " pdb=" CB ILE A 96 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2699 not shown) Planarity restraints: 2920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 7 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO J 8 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO J 8 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 8 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 7 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO N 8 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO N 8 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 8 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO L 8 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.020 5.00e-02 4.00e+02 ... (remaining 2917 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 110 2.53 - 3.13: 12986 3.13 - 3.72: 24423 3.72 - 4.31: 36291 4.31 - 4.90: 62118 Nonbonded interactions: 135928 Sorted by model distance: nonbonded pdb=" OE1 GLU L 196 " pdb=" OG1 THR L 207 " model vdw 1.943 3.040 nonbonded pdb=" ND2 ASN A 226 " pdb=" O HOH A 401 " model vdw 1.970 3.120 nonbonded pdb=" OD2 ASP I 74 " pdb=" NZ LYS I 77 " model vdw 2.166 3.120 nonbonded pdb=" O TYR D 134 " pdb=" O HOH D 401 " model vdw 2.175 3.040 nonbonded pdb=" OG SER J 30 " pdb=" OG1 THR B 62 " model vdw 2.201 3.040 ... (remaining 135923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.870 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.003 0.042 17018 Z= 0.114 Angle : 0.480 5.979 23212 Z= 0.249 Chirality : 0.043 0.328 2702 Planarity : 0.004 0.040 2920 Dihedral : 11.625 81.278 5919 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.18), residues: 2201 helix: -0.42 (0.19), residues: 604 sheet: 0.74 (0.22), residues: 585 loop : 0.62 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.023 0.001 TYR D 118 PHE 0.016 0.001 PHE L 84 TRP 0.013 0.001 TRP L 149 HIS 0.005 0.001 HIS K 212 Details of bonding type rmsd covalent geometry : bond 0.00280 (17006) covalent geometry : angle 0.47934 (23188) SS BOND : bond 0.00414 ( 12) SS BOND : angle 0.87095 ( 24) hydrogen bonds : bond 0.27960 ( 832) hydrogen bonds : angle 9.38188 ( 2388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9093 (mmt) cc_final: 0.8321 (mmt) REVERT: K 74 ASP cc_start: 0.8229 (t0) cc_final: 0.8023 (t70) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.6473 time to fit residues: 164.8199 Evaluate side-chains 145 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 213 ASN I 176 HIS J 199 HIS B 226 ASN K 41 GLN L 38 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS C 213 ASN M 176 HIS ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 HIS D 97 ASN D 213 ASN D 226 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.183682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107511 restraints weight = 18549.198| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.60 r_work: 0.3028 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17018 Z= 0.134 Angle : 0.604 10.089 23212 Z= 0.312 Chirality : 0.044 0.160 2702 Planarity : 0.005 0.043 2920 Dihedral : 4.121 22.494 2343 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.98 % Allowed : 6.05 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2201 helix: 1.79 (0.19), residues: 646 sheet: 0.57 (0.21), residues: 630 loop : 0.65 (0.22), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 108 TYR 0.017 0.002 TYR D 118 PHE 0.018 0.002 PHE I 158 TRP 0.012 0.001 TRP K 36 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00292 (17006) covalent geometry : angle 0.60349 (23188) SS BOND : bond 0.00639 ( 12) SS BOND : angle 1.09089 ( 24) hydrogen bonds : bond 0.06047 ( 832) hydrogen bonds : angle 5.87668 ( 2388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.660 Fit side-chains REVERT: K 74 ASP cc_start: 0.8297 (t0) cc_final: 0.7814 (t70) REVERT: N 146 LYS cc_start: 0.7026 (tptm) cc_final: 0.6804 (tptt) REVERT: N 147 VAL cc_start: 0.7397 (m) cc_final: 0.7063 (t) outliers start: 18 outliers final: 4 residues processed: 157 average time/residue: 0.5580 time to fit residues: 99.3592 Evaluate side-chains 121 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain C residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 138 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 167 GLN K 209 ASN L 38 GLN M 209 ASN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105891 restraints weight = 18765.900| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.69 r_work: 0.2986 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17018 Z= 0.149 Angle : 0.581 8.992 23212 Z= 0.298 Chirality : 0.043 0.144 2702 Planarity : 0.005 0.075 2920 Dihedral : 4.189 21.750 2343 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.74 % Allowed : 7.63 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.18), residues: 2201 helix: 1.93 (0.20), residues: 664 sheet: 0.55 (0.21), residues: 651 loop : 0.53 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 108 TYR 0.018 0.002 TYR C 118 PHE 0.015 0.002 PHE M 112 TRP 0.012 0.002 TRP K 36 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00351 (17006) covalent geometry : angle 0.58016 (23188) SS BOND : bond 0.00495 ( 12) SS BOND : angle 1.01641 ( 24) hydrogen bonds : bond 0.05697 ( 832) hydrogen bonds : angle 5.36635 ( 2388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: K 74 ASP cc_start: 0.8364 (t0) cc_final: 0.7904 (t70) REVERT: L 144 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: C 154 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8729 (mp) REVERT: M 187 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7370 (mm) REVERT: N 66 SER cc_start: 0.7280 (m) cc_final: 0.6879 (p) REVERT: N 146 LYS cc_start: 0.6999 (tptm) cc_final: 0.6771 (tptt) REVERT: N 147 VAL cc_start: 0.7522 (m) cc_final: 0.7259 (t) outliers start: 32 outliers final: 15 residues processed: 155 average time/residue: 0.5823 time to fit residues: 101.8705 Evaluate side-chains 138 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain D residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 80 optimal weight: 0.4980 chunk 165 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN I 209 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.186643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113617 restraints weight = 18621.078| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.62 r_work: 0.3070 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17018 Z= 0.115 Angle : 0.532 9.297 23212 Z= 0.272 Chirality : 0.042 0.141 2702 Planarity : 0.005 0.054 2920 Dihedral : 4.043 21.576 2343 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.58 % Allowed : 9.26 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.18), residues: 2201 helix: 2.17 (0.20), residues: 664 sheet: 0.59 (0.20), residues: 666 loop : 0.44 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.009 0.001 TYR C 118 PHE 0.022 0.001 PHE K 158 TRP 0.010 0.001 TRP K 36 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00263 (17006) covalent geometry : angle 0.53171 (23188) SS BOND : bond 0.00428 ( 12) SS BOND : angle 0.87858 ( 24) hydrogen bonds : bond 0.04629 ( 832) hydrogen bonds : angle 5.03373 ( 2388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: K 74 ASP cc_start: 0.8379 (t0) cc_final: 0.7969 (t70) REVERT: K 91 ASP cc_start: 0.7260 (m-30) cc_final: 0.6945 (m-30) REVERT: L 144 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: C 154 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8771 (mp) REVERT: M 187 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7288 (mm) REVERT: N 66 SER cc_start: 0.7381 (m) cc_final: 0.7002 (p) REVERT: D 64 LYS cc_start: 0.8710 (tppt) cc_final: 0.8315 (tptp) outliers start: 29 outliers final: 14 residues processed: 138 average time/residue: 0.5691 time to fit residues: 88.4555 Evaluate side-chains 121 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain D residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 90 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 194 optimal weight: 0.0030 chunk 70 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.184638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110124 restraints weight = 18528.484| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.77 r_work: 0.3014 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17018 Z= 0.142 Angle : 0.555 8.687 23212 Z= 0.285 Chirality : 0.043 0.142 2702 Planarity : 0.005 0.051 2920 Dihedral : 4.152 21.929 2343 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.63 % Allowed : 10.51 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2201 helix: 2.01 (0.19), residues: 664 sheet: 0.60 (0.21), residues: 657 loop : 0.39 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 108 TYR 0.015 0.002 TYR C 118 PHE 0.014 0.001 PHE M 112 TRP 0.012 0.001 TRP K 36 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00335 (17006) covalent geometry : angle 0.55461 (23188) SS BOND : bond 0.00465 ( 12) SS BOND : angle 1.00635 ( 24) hydrogen bonds : bond 0.05440 ( 832) hydrogen bonds : angle 4.98839 ( 2388) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: K 74 ASP cc_start: 0.8387 (t0) cc_final: 0.8034 (t70) REVERT: K 77 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7162 (mtpp) REVERT: K 91 ASP cc_start: 0.7506 (m-30) cc_final: 0.7200 (m-30) REVERT: K 135 PRO cc_start: 0.6430 (Cg_endo) cc_final: 0.6091 (Cg_exo) REVERT: L 144 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: M 187 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7213 (mm) REVERT: N 66 SER cc_start: 0.7490 (m) cc_final: 0.7111 (p) REVERT: D 64 LYS cc_start: 0.8682 (tppt) cc_final: 0.8152 (mttp) outliers start: 30 outliers final: 15 residues processed: 140 average time/residue: 0.6032 time to fit residues: 94.6890 Evaluate side-chains 126 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain K residue 77 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain D residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 188 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 203 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 50.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN D 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.180940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104210 restraints weight = 18589.250| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.64 r_work: 0.3005 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17018 Z= 0.234 Angle : 0.648 9.808 23212 Z= 0.333 Chirality : 0.046 0.151 2702 Planarity : 0.006 0.052 2920 Dihedral : 4.525 22.882 2343 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.07 % Allowed : 11.00 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.18), residues: 2201 helix: 1.57 (0.19), residues: 664 sheet: 0.51 (0.21), residues: 651 loop : 0.24 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 108 TYR 0.020 0.002 TYR I 188 PHE 0.022 0.002 PHE M 112 TRP 0.014 0.002 TRP L 149 HIS 0.006 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00587 (17006) covalent geometry : angle 0.64732 (23188) SS BOND : bond 0.00654 ( 12) SS BOND : angle 1.33529 ( 24) hydrogen bonds : bond 0.06934 ( 832) hydrogen bonds : angle 5.18132 ( 2388) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.704 Fit side-chains REVERT: K 74 ASP cc_start: 0.8388 (t0) cc_final: 0.8034 (t70) REVERT: K 77 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7121 (mtpp) REVERT: K 91 ASP cc_start: 0.7714 (m-30) cc_final: 0.7505 (m-30) REVERT: K 129 LYS cc_start: 0.7894 (tppt) cc_final: 0.7319 (tmtt) REVERT: K 135 PRO cc_start: 0.6806 (Cg_endo) cc_final: 0.6481 (Cg_exo) REVERT: K 157 TYR cc_start: 0.8319 (p90) cc_final: 0.8073 (p90) REVERT: L 144 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: M 5 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: M 187 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7286 (mm) REVERT: N 66 SER cc_start: 0.7415 (m) cc_final: 0.7025 (p) REVERT: N 138 ASN cc_start: 0.7206 (t0) cc_final: 0.6997 (t0) REVERT: D 64 LYS cc_start: 0.8690 (tppt) cc_final: 0.7923 (tmtt) outliers start: 38 outliers final: 18 residues processed: 144 average time/residue: 0.5775 time to fit residues: 93.5802 Evaluate side-chains 130 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain K residue 77 LYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 5 GLN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 197 VAL Chi-restraints excluded: chain D residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 132 optimal weight: 0.0060 chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 206 optimal weight: 0.0970 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 176 HIS K 183 GLN M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.185873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114796 restraints weight = 18606.387| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.57 r_work: 0.3064 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17018 Z= 0.103 Angle : 0.521 9.215 23212 Z= 0.265 Chirality : 0.041 0.201 2702 Planarity : 0.005 0.045 2920 Dihedral : 4.104 21.828 2343 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.53 % Allowed : 11.76 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.18), residues: 2201 helix: 2.10 (0.20), residues: 668 sheet: 0.61 (0.20), residues: 660 loop : 0.33 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 108 TYR 0.013 0.001 TYR K 102 PHE 0.013 0.001 PHE I 80 TRP 0.011 0.001 TRP I 36 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00221 (17006) covalent geometry : angle 0.52035 (23188) SS BOND : bond 0.00407 ( 12) SS BOND : angle 0.83457 ( 24) hydrogen bonds : bond 0.04196 ( 832) hydrogen bonds : angle 4.80358 ( 2388) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.466 Fit side-chains REVERT: K 77 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7365 (mtpp) REVERT: K 88 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7395 (p) REVERT: K 91 ASP cc_start: 0.7640 (m-30) cc_final: 0.7321 (m-30) REVERT: K 129 LYS cc_start: 0.7863 (tppt) cc_final: 0.7400 (tmtt) REVERT: K 135 PRO cc_start: 0.6775 (Cg_endo) cc_final: 0.6485 (Cg_exo) REVERT: L 144 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: M 187 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7263 (mm) REVERT: N 66 SER cc_start: 0.7387 (m) cc_final: 0.7056 (p) REVERT: D 64 LYS cc_start: 0.8677 (tppt) cc_final: 0.7862 (tmtt) outliers start: 28 outliers final: 18 residues processed: 135 average time/residue: 0.5786 time to fit residues: 88.0749 Evaluate side-chains 129 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain K residue 77 LYS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 197 VAL Chi-restraints excluded: chain D residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 12 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 128 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 196 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111076 restraints weight = 18587.143| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.73 r_work: 0.3012 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17018 Z= 0.143 Angle : 0.560 9.825 23212 Z= 0.284 Chirality : 0.042 0.148 2702 Planarity : 0.005 0.047 2920 Dihedral : 4.175 22.077 2343 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.96 % Allowed : 11.55 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.18), residues: 2201 helix: 2.02 (0.20), residues: 664 sheet: 0.59 (0.21), residues: 660 loop : 0.28 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 108 TYR 0.014 0.002 TYR I 188 PHE 0.028 0.001 PHE K 158 TRP 0.010 0.001 TRP K 36 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00344 (17006) covalent geometry : angle 0.55953 (23188) SS BOND : bond 0.00493 ( 12) SS BOND : angle 1.05279 ( 24) hydrogen bonds : bond 0.05259 ( 832) hydrogen bonds : angle 4.86109 ( 2388) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.680 Fit side-chains REVERT: K 77 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7326 (mtpp) REVERT: K 88 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7400 (p) REVERT: K 91 ASP cc_start: 0.7702 (m-30) cc_final: 0.7419 (m-30) REVERT: K 135 PRO cc_start: 0.6817 (Cg_endo) cc_final: 0.6521 (Cg_exo) REVERT: L 144 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: M 16 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6153 (mt0) REVERT: M 187 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7239 (mm) REVERT: N 66 SER cc_start: 0.7425 (m) cc_final: 0.7093 (p) REVERT: D 64 LYS cc_start: 0.8703 (tppt) cc_final: 0.7884 (tmtt) outliers start: 36 outliers final: 19 residues processed: 134 average time/residue: 0.5379 time to fit residues: 81.6006 Evaluate side-chains 127 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain K residue 77 LYS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 16 GLN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN L 138 ASN M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.184018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112013 restraints weight = 18549.400| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.75 r_work: 0.3033 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17018 Z= 0.133 Angle : 0.556 10.025 23212 Z= 0.281 Chirality : 0.042 0.149 2702 Planarity : 0.005 0.046 2920 Dihedral : 4.151 21.949 2343 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.47 % Allowed : 12.20 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.18), residues: 2201 helix: 2.00 (0.20), residues: 668 sheet: 0.60 (0.21), residues: 660 loop : 0.31 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 108 TYR 0.013 0.001 TYR I 188 PHE 0.013 0.001 PHE I 80 TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00315 (17006) covalent geometry : angle 0.55498 (23188) SS BOND : bond 0.00485 ( 12) SS BOND : angle 1.01623 ( 24) hydrogen bonds : bond 0.05001 ( 832) hydrogen bonds : angle 4.82456 ( 2388) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.644 Fit side-chains REVERT: K 77 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7303 (mtpp) REVERT: K 88 THR cc_start: 0.7714 (OUTLIER) cc_final: 0.7329 (p) REVERT: K 91 ASP cc_start: 0.7676 (m-30) cc_final: 0.7390 (m-30) REVERT: K 129 LYS cc_start: 0.7984 (tppt) cc_final: 0.7399 (tmtt) REVERT: K 135 PRO cc_start: 0.6932 (Cg_endo) cc_final: 0.6668 (Cg_exo) REVERT: L 144 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: M 187 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7300 (mm) REVERT: N 66 SER cc_start: 0.7402 (m) cc_final: 0.7061 (p) REVERT: D 64 LYS cc_start: 0.8682 (tppt) cc_final: 0.7875 (tmtt) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.5848 time to fit residues: 83.7350 Evaluate side-chains 127 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain K residue 77 LYS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 124 optimal weight: 8.9990 chunk 32 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 163 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.184987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112782 restraints weight = 18665.910| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.59 r_work: 0.3048 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17018 Z= 0.119 Angle : 0.540 9.747 23212 Z= 0.272 Chirality : 0.041 0.146 2702 Planarity : 0.005 0.049 2920 Dihedral : 4.047 21.733 2343 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.53 % Allowed : 12.15 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2201 helix: 2.10 (0.20), residues: 668 sheet: 0.63 (0.20), residues: 660 loop : 0.28 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 108 TYR 0.015 0.001 TYR K 157 PHE 0.030 0.001 PHE K 158 TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00276 (17006) covalent geometry : angle 0.53917 (23188) SS BOND : bond 0.00442 ( 12) SS BOND : angle 0.93808 ( 24) hydrogen bonds : bond 0.04549 ( 832) hydrogen bonds : angle 4.73310 ( 2388) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.498 Fit side-chains REVERT: K 77 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7362 (mtpp) REVERT: K 88 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7346 (p) REVERT: K 91 ASP cc_start: 0.7692 (m-30) cc_final: 0.7394 (m-30) REVERT: K 129 LYS cc_start: 0.8107 (tppt) cc_final: 0.7545 (tmtt) REVERT: K 135 PRO cc_start: 0.6921 (Cg_endo) cc_final: 0.6658 (Cg_exo) REVERT: L 144 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: M 187 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7284 (mm) REVERT: D 64 LYS cc_start: 0.8670 (tppt) cc_final: 0.7861 (tmtt) outliers start: 28 outliers final: 22 residues processed: 136 average time/residue: 0.5513 time to fit residues: 84.4742 Evaluate side-chains 132 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain K residue 77 LYS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 15 optimal weight: 0.3980 chunk 111 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 140 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.186963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115468 restraints weight = 18571.733| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.64 r_work: 0.3101 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17018 Z= 0.098 Angle : 0.520 9.538 23212 Z= 0.261 Chirality : 0.041 0.152 2702 Planarity : 0.005 0.066 2920 Dihedral : 3.934 21.373 2343 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.31 % Allowed : 12.58 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.18), residues: 2201 helix: 2.39 (0.20), residues: 654 sheet: 0.60 (0.20), residues: 666 loop : 0.40 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 108 TYR 0.011 0.001 TYR K 102 PHE 0.012 0.001 PHE M 80 TRP 0.011 0.001 TRP K 36 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00218 (17006) covalent geometry : angle 0.51957 (23188) SS BOND : bond 0.00394 ( 12) SS BOND : angle 0.81291 ( 24) hydrogen bonds : bond 0.03884 ( 832) hydrogen bonds : angle 4.63187 ( 2388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6268.68 seconds wall clock time: 107 minutes 49.33 seconds (6469.33 seconds total)