Starting phenix.real_space_refine on Tue Dec 31 19:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v9d_43071/12_2024/8v9d_43071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v9d_43071/12_2024/8v9d_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_43071/12_2024/8v9d_43071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v9d_43071/12_2024/8v9d_43071.map" model { file = "/net/cci-nas-00/data/ceres_data/8v9d_43071/12_2024/8v9d_43071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v9d_43071/12_2024/8v9d_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-5532/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: 11.56, per 1000 atoms: 0.69 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: 4.34 Conformation dependent library (CDL) restraints added in 2.6 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: 2.11 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: 5.30 Time building geometry restraints manager: 4.90 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: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 3.100 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: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.580 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: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.770 ------------------------------------------------------------------------------- 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 17006 Z= 0.184 Angle : 0.479 5.979 23188 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 *********************** 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 : 1.972 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: 1.3245 time to fit residues: 338.9378 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 : 1.901 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 17006 Z= 0.342 Angle : 0.679 10.457 23188 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 *********************** 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 : 1.810 Fit side-chains REVERT: K 74 ASP cc_start: 0.8290 (t0) cc_final: 0.8003 (t70) REVERT: K 135 PRO cc_start: 0.6796 (Cg_endo) cc_final: 0.6388 (Cg_exo) outliers start: 25 outliers final: 9 residues processed: 154 average time/residue: 1.2000 time to fit residues: 208.9463 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 : 1.979 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 229 ASN J 167 GLN K 176 HIS K 209 ASN L 38 GLN M 209 ASN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17006 Z= 0.189 Angle : 0.557 9.768 23188 Z= 0.285 Chirality : 0.043 0.144 2702 Planarity : 0.005 0.045 2920 Dihedral : 4.170 21.551 2343 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.42 % Allowed : 8.33 % Favored : 90.25 % 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: 1.33 (0.18), residues: 2201 helix: 1.95 (0.20), residues: 664 sheet: 0.53 (0.21), residues: 654 loop : 0.48 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS B 201 PHE 0.012 0.001 PHE I 158 TYR 0.011 0.001 TYR C 118 ARG 0.003 0.000 ARG D 108 *********************** 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 151 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: K 74 ASP cc_start: 0.8189 (t0) cc_final: 0.7969 (t70) REVERT: M 187 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8188 (mm) REVERT: D 64 LYS cc_start: 0.8825 (tppt) cc_final: 0.8617 (mttp) outliers start: 26 outliers final: 8 residues processed: 144 average time/residue: 1.2772 time to fit residues: 207.3305 Evaluate side-chains 127 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 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 195 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 209 ASN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17006 Z= 0.330 Angle : 0.624 10.501 23188 Z= 0.320 Chirality : 0.045 0.148 2702 Planarity : 0.006 0.052 2920 Dihedral : 4.399 22.517 2343 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.58 % Allowed : 10.40 % Favored : 88.02 % 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: 1.08 (0.18), residues: 2201 helix: 1.65 (0.19), residues: 664 sheet: 0.52 (0.21), residues: 651 loop : 0.29 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 36 HIS 0.005 0.001 HIS B 201 PHE 0.019 0.002 PHE K 158 TYR 0.018 0.002 TYR C 118 ARG 0.002 0.000 ARG M 40 *********************** 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 154 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.899 Fit side-chains revert: symmetry clash REVERT: K 77 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7264 (mtpp) REVERT: K 91 ASP cc_start: 0.7736 (m-30) cc_final: 0.7453 (m-30) REVERT: K 135 PRO cc_start: 0.7049 (Cg_endo) cc_final: 0.6678 (Cg_exo) REVERT: C 154 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8767 (mp) REVERT: M 187 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8198 (mm) outliers start: 29 outliers final: 14 residues processed: 147 average time/residue: 1.2895 time to fit residues: 212.8212 Evaluate side-chains 131 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR 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 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 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 107 ILE 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 174 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 0.0570 chunk 144 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 107 optimal weight: 50.0000 chunk 188 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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** D 229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17006 Z= 0.175 Angle : 0.531 9.797 23188 Z= 0.272 Chirality : 0.042 0.143 2702 Planarity : 0.005 0.047 2920 Dihedral : 4.145 22.019 2343 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.69 % Allowed : 11.11 % Favored : 87.20 % 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: 1.30 (0.18), residues: 2201 helix: 2.08 (0.20), residues: 664 sheet: 0.55 (0.20), residues: 660 loop : 0.29 (0.22), residues: 877 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 0.014 0.001 TYR I 188 ARG 0.003 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: K 91 ASP cc_start: 0.7731 (m-30) cc_final: 0.7470 (m-30) REVERT: K 129 LYS cc_start: 0.7837 (tppt) cc_final: 0.7596 (tmtt) REVERT: K 135 PRO cc_start: 0.7041 (Cg_endo) cc_final: 0.6695 (Cg_exo) REVERT: M 187 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8195 (mm) REVERT: D 64 LYS cc_start: 0.8794 (mttp) cc_final: 0.8458 (tppt) outliers start: 31 outliers final: 17 residues processed: 140 average time/residue: 1.2276 time to fit residues: 194.1779 Evaluate side-chains 125 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain K residue 83 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 C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 162 VAL 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 70 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 41 optimal weight: 0.0060 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 209 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 110 optimal weight: 0.0470 overall best weight: 0.7296 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17006 Z= 0.166 Angle : 0.525 9.345 23188 Z= 0.267 Chirality : 0.041 0.143 2702 Planarity : 0.005 0.045 2920 Dihedral : 4.055 21.425 2343 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.69 % Allowed : 11.49 % Favored : 86.82 % 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: 1.46 (0.18), residues: 2201 helix: 2.36 (0.20), residues: 650 sheet: 0.52 (0.20), residues: 666 loop : 0.40 (0.22), residues: 885 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 0.024 0.001 PHE K 158 TYR 0.013 0.001 TYR I 188 ARG 0.008 0.000 ARG D 108 *********************** 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 150 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.899 Fit side-chains REVERT: K 91 ASP cc_start: 0.7734 (m-30) cc_final: 0.7495 (m-30) REVERT: K 135 PRO cc_start: 0.6961 (Cg_endo) cc_final: 0.6715 (Cg_exo) REVERT: M 187 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (mm) REVERT: D 64 LYS cc_start: 0.8783 (mttp) cc_final: 0.8445 (tppt) outliers start: 31 outliers final: 20 residues processed: 145 average time/residue: 1.2704 time to fit residues: 210.1630 Evaluate side-chains 130 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 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 B residue 124 LEU Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 83 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 C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 162 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 153 optimal weight: 0.0980 chunk 118 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 209 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17006 Z= 0.180 Angle : 0.528 9.296 23188 Z= 0.269 Chirality : 0.042 0.145 2702 Planarity : 0.005 0.045 2920 Dihedral : 4.042 21.553 2343 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 11.98 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.25 (0.20), residues: 654 sheet: 0.52 (0.20), residues: 672 loop : 0.41 (0.22), residues: 875 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 0.013 0.001 PHE I 80 TYR 0.014 0.001 TYR I 188 ARG 0.008 0.000 ARG D 108 *********************** 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: 31 poor density : 118 time to evaluate : 1.814 Fit side-chains REVERT: J 62 ARG cc_start: 0.7207 (ptp-170) cc_final: 0.6968 (ptt180) REVERT: K 91 ASP cc_start: 0.7792 (m-30) cc_final: 0.7566 (m-30) REVERT: K 135 PRO cc_start: 0.7035 (Cg_endo) cc_final: 0.6802 (Cg_exo) REVERT: M 187 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8245 (mm) REVERT: D 64 LYS cc_start: 0.8779 (mttp) cc_final: 0.8441 (tppt) outliers start: 31 outliers final: 18 residues processed: 143 average time/residue: 1.2045 time to fit residues: 195.1862 Evaluate side-chains 130 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 83 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 C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 162 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 17006 Z= 0.464 Angle : 0.685 10.381 23188 Z= 0.350 Chirality : 0.048 0.176 2702 Planarity : 0.006 0.053 2920 Dihedral : 4.599 23.270 2343 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.91 % Allowed : 12.20 % Favored : 85.89 % 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: 0.90 (0.18), residues: 2201 helix: 1.46 (0.19), residues: 664 sheet: 0.49 (0.21), residues: 651 loop : 0.15 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP M 36 HIS 0.008 0.001 HIS A 90 PHE 0.027 0.002 PHE K 158 TYR 0.023 0.002 TYR I 188 ARG 0.007 0.001 ARG D 108 *********************** 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 160 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.866 Fit side-chains REVERT: I 45 LYS cc_start: 0.8100 (mtpm) cc_final: 0.7892 (mtpt) REVERT: I 213 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7961 (tptp) REVERT: K 82 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8724 (tp) REVERT: K 135 PRO cc_start: 0.7537 (Cg_endo) cc_final: 0.7332 (Cg_exo) REVERT: D 64 LYS cc_start: 0.8833 (mttp) cc_final: 0.8374 (tmtt) outliers start: 35 outliers final: 19 residues processed: 152 average time/residue: 1.3432 time to fit residues: 228.7526 Evaluate side-chains 139 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 B residue 124 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 162 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 197 VAL Chi-restraints excluded: chain D residue 154 LEU 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 190 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 84 optimal weight: 0.0670 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 127 optimal weight: 40.0000 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17006 Z= 0.169 Angle : 0.547 10.368 23188 Z= 0.275 Chirality : 0.041 0.171 2702 Planarity : 0.005 0.048 2920 Dihedral : 4.209 22.427 2343 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.20 % Allowed : 13.02 % Favored : 85.78 % 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: 1.33 (0.18), residues: 2201 helix: 2.21 (0.20), residues: 650 sheet: 0.49 (0.21), residues: 666 loop : 0.32 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.003 0.001 HIS A 90 PHE 0.013 0.001 PHE M 80 TYR 0.015 0.001 TYR I 188 ARG 0.008 0.000 ARG D 108 *********************** 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 137 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.860 Fit side-chains REVERT: I 3 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: L 167 GLN cc_start: 0.7737 (tt0) cc_final: 0.7536 (mt0) REVERT: M 16 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.5636 (mt0) REVERT: D 64 LYS cc_start: 0.8804 (mttp) cc_final: 0.8467 (tppt) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 1.3346 time to fit residues: 199.0380 Evaluate side-chains 136 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 75 THR 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 171 LEU 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 C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 16 GLN Chi-restraints excluded: chain M residue 162 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.0040 chunk 125 optimal weight: 7.9990 chunk 97 optimal weight: 0.0020 chunk 143 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 198 optimal weight: 0.2980 chunk 172 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17006 Z= 0.160 Angle : 0.548 10.257 23188 Z= 0.273 Chirality : 0.041 0.158 2702 Planarity : 0.005 0.090 2920 Dihedral : 4.116 21.920 2343 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.03 % Allowed : 13.45 % Favored : 85.51 % 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: 1.33 (0.18), residues: 2201 helix: 2.08 (0.20), residues: 672 sheet: 0.61 (0.21), residues: 660 loop : 0.27 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.003 0.001 HIS B 201 PHE 0.029 0.001 PHE K 158 TYR 0.014 0.001 TYR K 157 ARG 0.009 0.000 ARG D 108 ********************** 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 143 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.786 Fit side-chains REVERT: I 3 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7669 (mt0) REVERT: I 218 LYS cc_start: 0.7009 (mmmt) cc_final: 0.6790 (mtpp) REVERT: M 16 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.5850 (mt0) REVERT: D 64 LYS cc_start: 0.8797 (mttp) cc_final: 0.8464 (tppt) outliers start: 19 outliers final: 16 residues processed: 137 average time/residue: 1.3635 time to fit residues: 209.1954 Evaluate side-chains 137 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain M residue 16 GLN Chi-restraints excluded: chain M residue 162 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 158 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 216 ASN B 95 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN M 16 GLN ** 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 = 0.4107 r_free = 0.4107 target = 0.184822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113641 restraints weight = 18540.567| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.64 r_work: 0.3052 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17006 Z= 0.183 Angle : 0.552 10.089 23188 Z= 0.276 Chirality : 0.041 0.151 2702 Planarity : 0.005 0.079 2920 Dihedral : 4.114 22.031 2343 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.14 % Allowed : 13.40 % Favored : 85.46 % 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: 1.32 (0.18), residues: 2201 helix: 2.04 (0.20), residues: 672 sheet: 0.63 (0.21), residues: 654 loop : 0.26 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS B 201 PHE 0.013 0.001 PHE I 80 TYR 0.014 0.001 TYR K 157 ARG 0.009 0.000 ARG D 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.17 seconds wall clock time: 93 minutes 40.52 seconds (5620.52 seconds total)