Starting phenix.real_space_refine on Sun May 18 04:54:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v9d_43071/05_2025/8v9d_43071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v9d_43071/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v9d_43071/05_2025/8v9d_43071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v9d_43071/05_2025/8v9d_43071.map" model { file = "/net/cci-nas-00/data/ceres_data/8v9d_43071/05_2025/8v9d_43071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v9d_43071/05_2025/8v9d_43071.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.35, per 1000 atoms: 0.62 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: 4.19 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.13 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: 5.47 Time building geometry restraints manager: 4.89 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: 0.02 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: 7.660 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 38.310 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.013 0.001 TRP L 149 HIS 0.005 0.001 HIS K 212 PHE 0.016 0.001 PHE L 84 TYR 0.023 0.001 TYR D 118 ARG 0.002 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.27960 ( 832) hydrogen bonds : angle 9.38188 ( 2388) SS BOND : bond 0.00414 ( 12) SS BOND : angle 0.87095 ( 24) covalent geometry : bond 0.00280 (17006) covalent geometry : angle 0.47934 (23188) *********************** 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 : 1.647 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: 1.1935 time to fit residues: 305.5266 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 : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 87 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.179502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102222 restraints weight = 18508.040| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.68 r_work: 0.2948 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17018 Z= 0.215 Angle : 0.681 10.457 23212 Z= 0.351 Chirality : 0.047 0.172 2702 Planarity : 0.006 0.049 2920 Dihedral : 4.394 22.479 2343 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.36 % Allowed : 6.05 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2201 helix: 1.15 (0.19), residues: 664 sheet: 0.56 (0.22), residues: 618 loop : 0.53 (0.22), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 36 HIS 0.006 0.001 HIS B 201 PHE 0.020 0.002 PHE K 112 TYR 0.026 0.002 TYR D 118 ARG 0.005 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.07116 ( 832) hydrogen bonds : angle 5.99727 ( 2388) SS BOND : bond 0.00733 ( 12) SS BOND : angle 1.43834 ( 24) covalent geometry : bond 0.00524 (17006) covalent geometry : angle 0.67936 (23188) *********************** 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 163 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.747 Fit side-chains REVERT: K 74 ASP cc_start: 0.8420 (t0) cc_final: 0.7933 (t70) REVERT: K 135 PRO cc_start: 0.6555 (Cg_endo) cc_final: 0.6162 (Cg_exo) REVERT: N 138 ASN cc_start: 0.7428 (t0) cc_final: 0.7184 (t0) REVERT: N 147 VAL cc_start: 0.7396 (m) cc_final: 0.7167 (t) outliers start: 25 outliers final: 9 residues processed: 154 average time/residue: 1.0803 time to fit residues: 188.6136 Evaluate side-chains 126 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain I residue 75 THR 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 L residue 57 THR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain D residue 154 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 143 optimal weight: 0.6980 chunk 128 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 0.0670 chunk 195 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS K 176 HIS K 209 ASN L 38 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110176 restraints weight = 18458.235| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.81 r_work: 0.3015 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2047 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= 0.112 Angle : 0.547 8.763 23212 Z= 0.280 Chirality : 0.042 0.147 2702 Planarity : 0.005 0.044 2920 Dihedral : 4.110 21.542 2343 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.36 % Allowed : 8.44 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2201 helix: 2.03 (0.20), residues: 664 sheet: 0.62 (0.21), residues: 627 loop : 0.49 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 36 HIS 0.002 0.001 HIS B 201 PHE 0.012 0.001 PHE I 158 TYR 0.008 0.001 TYR I 188 ARG 0.003 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 832) hydrogen bonds : angle 5.34125 ( 2388) SS BOND : bond 0.00498 ( 12) SS BOND : angle 0.93454 ( 24) covalent geometry : bond 0.00243 (17006) covalent geometry : angle 0.54671 (23188) *********************** 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 149 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: K 74 ASP cc_start: 0.8321 (t0) cc_final: 0.7821 (t70) REVERT: L 144 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: C 154 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8615 (mp) REVERT: M 187 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7289 (mm) REVERT: N 66 SER cc_start: 0.7280 (m) cc_final: 0.6869 (p) REVERT: N 147 VAL cc_start: 0.7400 (m) cc_final: 0.7190 (t) REVERT: D 64 LYS cc_start: 0.8716 (tppt) cc_final: 0.8198 (mttp) outliers start: 25 outliers final: 7 residues processed: 141 average time/residue: 1.1177 time to fit residues: 179.0749 Evaluate side-chains 127 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 154 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 164 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 214 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 J 167 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 = 0.4134 r_free = 0.4134 target = 0.187414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116238 restraints weight = 18550.094| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.68 r_work: 0.3074 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17018 Z= 0.107 Angle : 0.522 8.463 23212 Z= 0.267 Chirality : 0.041 0.140 2702 Planarity : 0.005 0.042 2920 Dihedral : 3.969 21.128 2343 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.53 % Allowed : 9.48 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2201 helix: 2.37 (0.20), residues: 650 sheet: 0.53 (0.20), residues: 672 loop : 0.52 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 36 HIS 0.002 0.001 HIS B 201 PHE 0.021 0.001 PHE K 158 TYR 0.009 0.001 TYR I 188 ARG 0.003 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 832) hydrogen bonds : angle 4.99466 ( 2388) SS BOND : bond 0.00594 ( 12) SS BOND : angle 0.86230 ( 24) covalent geometry : bond 0.00238 (17006) covalent geometry : angle 0.52190 (23188) *********************** 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 151 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8222 (mt0) cc_final: 0.7993 (mt0) REVERT: B 84 MET cc_start: 0.9347 (mmp) cc_final: 0.8851 (mmp) REVERT: K 74 ASP cc_start: 0.8379 (t0) cc_final: 0.7964 (t70) REVERT: K 77 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6973 (mtpp) REVERT: K 91 ASP cc_start: 0.7270 (m-30) cc_final: 0.6960 (m-30) REVERT: L 144 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: C 154 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8663 (mp) REVERT: N 66 SER cc_start: 0.7399 (m) cc_final: 0.7026 (p) REVERT: D 64 LYS cc_start: 0.8664 (tppt) cc_final: 0.8139 (mttp) outliers start: 28 outliers final: 13 residues processed: 145 average time/residue: 1.1128 time to fit residues: 183.2511 Evaluate side-chains 124 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR 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 154 LEU Chi-restraints excluded: chain C residue 247 LEU 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 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 101 optimal weight: 0.0270 chunk 134 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN 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 = 0.4134 r_free = 0.4134 target = 0.187480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115222 restraints weight = 18726.630| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.57 r_work: 0.3086 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17018 Z= 0.105 Angle : 0.514 8.577 23212 Z= 0.262 Chirality : 0.041 0.138 2702 Planarity : 0.005 0.048 2920 Dihedral : 3.933 21.215 2343 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.63 % Allowed : 10.46 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.18), residues: 2201 helix: 2.44 (0.20), residues: 650 sheet: 0.56 (0.21), residues: 663 loop : 0.50 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 36 HIS 0.003 0.001 HIS B 201 PHE 0.012 0.001 PHE I 80 TYR 0.008 0.001 TYR C 118 ARG 0.004 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 832) hydrogen bonds : angle 4.83730 ( 2388) SS BOND : bond 0.00402 ( 12) SS BOND : angle 0.82612 ( 24) covalent geometry : bond 0.00235 (17006) covalent geometry : angle 0.51400 (23188) *********************** 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 146 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8207 (mt0) cc_final: 0.7989 (mt0) REVERT: K 74 ASP cc_start: 0.8342 (t0) cc_final: 0.7966 (t70) REVERT: K 77 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.6966 (mtpp) REVERT: K 91 ASP cc_start: 0.7323 (m-30) cc_final: 0.7021 (m-30) REVERT: K 129 LYS cc_start: 0.7952 (tppt) cc_final: 0.7335 (tmtt) REVERT: L 144 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: C 154 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8720 (mp) REVERT: M 187 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7149 (mm) REVERT: N 66 SER cc_start: 0.7360 (m) cc_final: 0.7003 (p) REVERT: D 64 LYS cc_start: 0.8674 (tppt) cc_final: 0.8162 (mttp) outliers start: 30 outliers final: 14 residues processed: 140 average time/residue: 1.1867 time to fit residues: 187.7008 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 : 1.649 ------------------------------------------------------------------------------- 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 K residue 77 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 55 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 183 GLN 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 = 0.4122 r_free = 0.4122 target = 0.186268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112202 restraints weight = 18682.376| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.82 r_work: 0.3075 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17018 Z= 0.120 Angle : 0.532 9.486 23212 Z= 0.270 Chirality : 0.042 0.140 2702 Planarity : 0.005 0.046 2920 Dihedral : 4.001 21.403 2343 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.69 % Allowed : 10.89 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2201 helix: 2.16 (0.20), residues: 668 sheet: 0.61 (0.20), residues: 657 loop : 0.40 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 36 HIS 0.005 0.001 HIS M 212 PHE 0.023 0.001 PHE K 158 TYR 0.010 0.001 TYR I 188 ARG 0.008 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 832) hydrogen bonds : angle 4.80773 ( 2388) SS BOND : bond 0.00483 ( 12) SS BOND : angle 0.88666 ( 24) covalent geometry : bond 0.00279 (17006) covalent geometry : angle 0.53148 (23188) *********************** 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 140 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8203 (mt0) cc_final: 0.7980 (mt0) REVERT: K 77 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7207 (mtpp) REVERT: K 91 ASP cc_start: 0.7437 (m-30) cc_final: 0.7133 (m-30) REVERT: L 144 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: C 154 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8753 (mp) REVERT: M 187 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7219 (mm) REVERT: N 66 SER cc_start: 0.7367 (m) cc_final: 0.7029 (p) REVERT: D 64 LYS cc_start: 0.8673 (tppt) cc_final: 0.8173 (mttp) outliers start: 31 outliers final: 16 residues processed: 133 average time/residue: 1.1793 time to fit residues: 176.8989 Evaluate side-chains 127 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 K residue 77 LYS Chi-restraints excluded: chain K residue 83 LYS 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 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 59 ILE Chi-restraints excluded: chain N residue 164 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 61 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 120 optimal weight: 40.0000 chunk 101 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 16 GLN D 229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.183796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109661 restraints weight = 18548.326| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.81 r_work: 0.3025 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17018 Z= 0.158 Angle : 0.577 9.645 23212 Z= 0.294 Chirality : 0.043 0.145 2702 Planarity : 0.005 0.046 2920 Dihedral : 4.214 22.038 2343 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.74 % Allowed : 11.22 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2201 helix: 1.88 (0.20), residues: 672 sheet: 0.57 (0.20), residues: 657 loop : 0.38 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 36 HIS 0.004 0.001 HIS B 201 PHE 0.015 0.002 PHE M 112 TYR 0.014 0.002 TYR I 188 ARG 0.008 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.05672 ( 832) hydrogen bonds : angle 4.91299 ( 2388) SS BOND : bond 0.00509 ( 12) SS BOND : angle 1.07545 ( 24) covalent geometry : bond 0.00384 (17006) covalent geometry : angle 0.57599 (23188) *********************** 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 149 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.847 Fit side-chains REVERT: I 3 GLN cc_start: 0.8252 (mt0) cc_final: 0.8023 (mt0) REVERT: K 77 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7344 (mtpp) REVERT: K 88 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7266 (p) REVERT: K 91 ASP cc_start: 0.7531 (m-30) cc_final: 0.7192 (m-30) REVERT: K 129 LYS cc_start: 0.7980 (tppt) cc_final: 0.7381 (tmtt) REVERT: K 135 PRO cc_start: 0.6706 (Cg_endo) cc_final: 0.6369 (Cg_exo) REVERT: K 157 TYR cc_start: 0.8391 (p90) cc_final: 0.8077 (p90) REVERT: L 144 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: C 154 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8809 (mp) REVERT: M 187 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7253 (mm) REVERT: N 66 SER cc_start: 0.7384 (m) cc_final: 0.7032 (p) REVERT: N 138 ASN cc_start: 0.7067 (t0) cc_final: 0.6817 (t0) REVERT: D 64 LYS cc_start: 0.8674 (tppt) cc_final: 0.7842 (tmtt) outliers start: 32 outliers final: 17 residues processed: 144 average time/residue: 1.1465 time to fit residues: 187.1418 Evaluate side-chains 133 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 K residue 77 LYS Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 88 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 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 59 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 61 optimal weight: 0.0870 chunk 110 optimal weight: 0.0970 chunk 181 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN 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 = 0.4129 r_free = 0.4129 target = 0.186963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113548 restraints weight = 18545.132| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.68 r_work: 0.3075 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17018 Z= 0.104 Angle : 0.524 10.464 23212 Z= 0.263 Chirality : 0.041 0.145 2702 Planarity : 0.005 0.045 2920 Dihedral : 3.989 21.294 2343 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.42 % Allowed : 11.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2201 helix: 2.38 (0.20), residues: 654 sheet: 0.55 (0.20), residues: 672 loop : 0.47 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.002 0.001 HIS M 212 PHE 0.027 0.001 PHE K 158 TYR 0.010 0.001 TYR I 188 ARG 0.008 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 832) hydrogen bonds : angle 4.71926 ( 2388) SS BOND : bond 0.00414 ( 12) SS BOND : angle 0.86032 ( 24) covalent geometry : bond 0.00233 (17006) covalent geometry : angle 0.52324 (23188) *********************** 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 140 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.678 Fit side-chains REVERT: I 3 GLN cc_start: 0.8282 (mt0) cc_final: 0.8033 (mt0) REVERT: J 62 ARG cc_start: 0.6604 (ptp-170) cc_final: 0.6302 (ptt180) REVERT: K 77 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7245 (mtpp) REVERT: K 83 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8271 (ttmm) REVERT: K 88 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7242 (p) REVERT: K 91 ASP cc_start: 0.7595 (m-30) cc_final: 0.7247 (m-30) REVERT: K 129 LYS cc_start: 0.7971 (tppt) cc_final: 0.7478 (tmtt) REVERT: K 135 PRO cc_start: 0.6716 (Cg_endo) cc_final: 0.6381 (Cg_exo) REVERT: L 144 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: C 154 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8774 (mp) REVERT: M 187 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7211 (mm) REVERT: D 64 LYS cc_start: 0.8633 (tppt) cc_final: 0.7785 (tmtt) outliers start: 26 outliers final: 16 residues processed: 134 average time/residue: 1.2075 time to fit residues: 186.1650 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 : 1.932 ------------------------------------------------------------------------------- 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 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 83 LYS Chi-restraints excluded: chain K residue 88 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 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 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 206 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 162 optimal weight: 2.9990 chunk 142 optimal weight: 0.1980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.183390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109782 restraints weight = 18532.340| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.71 r_work: 0.3012 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17018 Z= 0.164 Angle : 0.582 9.847 23212 Z= 0.295 Chirality : 0.043 0.144 2702 Planarity : 0.005 0.047 2920 Dihedral : 4.205 22.306 2343 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.58 % Allowed : 11.87 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2201 helix: 1.88 (0.19), residues: 672 sheet: 0.58 (0.20), residues: 657 loop : 0.34 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 36 HIS 0.005 0.001 HIS A 90 PHE 0.014 0.002 PHE M 112 TYR 0.015 0.002 TYR I 188 ARG 0.009 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 832) hydrogen bonds : angle 4.87554 ( 2388) SS BOND : bond 0.00538 ( 12) SS BOND : angle 1.08064 ( 24) covalent geometry : bond 0.00401 (17006) covalent geometry : angle 0.58113 (23188) *********************** 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 143 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.647 Fit side-chains REVERT: I 3 GLN cc_start: 0.8271 (mt0) cc_final: 0.8037 (mt0) REVERT: K 77 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7306 (mtpp) REVERT: K 88 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7300 (p) REVERT: K 91 ASP cc_start: 0.7644 (m-30) cc_final: 0.7345 (m-30) REVERT: K 129 LYS cc_start: 0.8038 (tppt) cc_final: 0.7639 (tmtt) REVERT: K 135 PRO cc_start: 0.6795 (Cg_endo) cc_final: 0.6493 (Cg_exo) REVERT: L 144 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: C 154 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8815 (mp) REVERT: M 16 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6272 (mt0) REVERT: M 187 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7296 (mm) REVERT: N 138 ASN cc_start: 0.7008 (t0) cc_final: 0.6786 (t0) REVERT: D 64 LYS cc_start: 0.8665 (tppt) cc_final: 0.7833 (tmtt) outliers start: 29 outliers final: 19 residues processed: 137 average time/residue: 1.1269 time to fit residues: 174.1686 Evaluate side-chains 135 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 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 K residue 77 LYS Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 171 LEU 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 154 LEU 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 59 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 210 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.186031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110164 restraints weight = 18661.968| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.70 r_work: 0.3090 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17018 Z= 0.110 Angle : 0.537 9.898 23212 Z= 0.269 Chirality : 0.041 0.149 2702 Planarity : 0.005 0.044 2920 Dihedral : 4.058 22.086 2343 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.31 % Allowed : 12.25 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.18), residues: 2201 helix: 2.31 (0.20), residues: 654 sheet: 0.56 (0.20), residues: 672 loop : 0.42 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.002 0.001 HIS B 201 PHE 0.029 0.001 PHE K 158 TYR 0.017 0.001 TYR K 157 ARG 0.009 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 832) hydrogen bonds : angle 4.73057 ( 2388) SS BOND : bond 0.00427 ( 12) SS BOND : angle 0.86885 ( 24) covalent geometry : bond 0.00249 (17006) covalent geometry : angle 0.53678 (23188) ********************** 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 136 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.690 Fit side-chains REVERT: I 3 GLN cc_start: 0.8270 (mt0) cc_final: 0.8018 (mt0) REVERT: K 77 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7241 (mtpp) REVERT: K 88 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7292 (p) REVERT: K 91 ASP cc_start: 0.7555 (m-30) cc_final: 0.7223 (m-30) REVERT: K 129 LYS cc_start: 0.8092 (tppt) cc_final: 0.7735 (tmtt) REVERT: K 135 PRO cc_start: 0.6840 (Cg_endo) cc_final: 0.6539 (Cg_exo) REVERT: L 144 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: C 154 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8718 (mp) REVERT: M 187 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7230 (mm) REVERT: D 64 LYS cc_start: 0.8658 (tppt) cc_final: 0.7847 (tmtt) outliers start: 24 outliers final: 16 residues processed: 131 average time/residue: 1.2126 time to fit residues: 178.9700 Evaluate side-chains 129 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 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 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 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 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 185 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 101 optimal weight: 0.0040 chunk 161 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.187076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113996 restraints weight = 18507.820| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.68 r_work: 0.3085 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17018 Z= 0.102 Angle : 0.528 11.064 23212 Z= 0.264 Chirality : 0.041 0.143 2702 Planarity : 0.005 0.045 2920 Dihedral : 3.936 20.874 2343 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.20 % Allowed : 12.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2201 helix: 2.19 (0.20), residues: 672 sheet: 0.68 (0.20), residues: 660 loop : 0.32 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.002 0.001 HIS B 201 PHE 0.012 0.001 PHE M 80 TYR 0.013 0.001 TYR K 157 ARG 0.009 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 832) hydrogen bonds : angle 4.64968 ( 2388) SS BOND : bond 0.00412 ( 12) SS BOND : angle 0.83210 ( 24) covalent geometry : bond 0.00227 (17006) covalent geometry : angle 0.52744 (23188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12518.72 seconds wall clock time: 216 minutes 30.34 seconds (12990.34 seconds total)