Starting phenix.real_space_refine on Sat Jul 4 07:35:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmu_54068/07_2026/9rmu_54068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmu_54068/07_2026/9rmu_54068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rmu_54068/07_2026/9rmu_54068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmu_54068/07_2026/9rmu_54068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rmu_54068/07_2026/9rmu_54068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmu_54068/07_2026/9rmu_54068.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 sd= 0.484 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: 6 Type Number sf(0) Gaussians Zn 10 6.06 5 P 62 5.49 5 S 76 5.16 5 C 11756 2.51 5 N 3340 2.21 5 O 3632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18876 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2068 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 258, 2059 Classifications: {'peptide': 258} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 245} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 258, 2059 Classifications: {'peptide': 258} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 245} Chain breaks: 2 bond proxies already assigned to first conformer: 2095 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2104 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 252} Chain breaks: 1 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2127 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 252} Chain breaks: 1 Chain: "D" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2073 Classifications: {'peptide': 259} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 246} Chain breaks: 1 Chain: "J" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 352 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 16} Link IDs: {'rna3p': 15} Chain: "b" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2068 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 258, 2059 Classifications: {'peptide': 258} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 245} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 258, 2059 Classifications: {'peptide': 258} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 245} Chain breaks: 2 bond proxies already assigned to first conformer: 2095 Chain: "F" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2104 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 252} Chain breaks: 1 Chain: "G" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2127 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 252} Chain breaks: 1 Chain: "H" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2073 Classifications: {'peptide': 259} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 246} Chain breaks: 1 Chain: "I" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 352 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 16} Link IDs: {'rna3p': 15} Chain: "f" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 317 Classifications: {'RNA': 16} Modifications used: {'5*END': 1, 'rna3p_pyr': 16} Link IDs: {'rna3p': 15} Chain: "i" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 317 Classifications: {'RNA': 16} Modifications used: {'5*END': 1, 'rna3p_pyr': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 345 SG CYS A 40 26.659 43.283 60.779 1.00 95.71 S ATOM 367 SG CYS A 43 28.990 44.825 58.055 1.00 93.66 S ATOM 2404 SG CYS B 40 51.206 10.328 36.706 1.00122.82 S ATOM 2426 SG CYS B 43 53.326 13.314 38.123 1.00120.07 S ATOM 4508 SG CYS C 40 34.678 98.336 46.890 1.00115.46 S ATOM 4530 SG CYS C 43 35.873 96.536 50.192 1.00119.23 S ATOM 6635 SG CYS D 40 58.610 65.934 21.899 1.00122.38 S ATOM 6657 SG CYS D 43 55.182 65.452 23.704 1.00127.57 S ATOM 9060 SG CYS b 40 63.112 104.513 31.298 1.00122.99 S ATOM 9082 SG CYS b 43 64.845 107.333 33.298 1.00138.13 S ATOM 9461 SG CYS E 40 131.042 93.526 60.780 1.00 98.93 S ATOM 9483 SG CYS E 43 128.713 91.984 58.053 1.00 98.88 S ATOM 11520 SG CYS F 40 106.498 126.470 36.695 1.00120.87 S ATOM 11542 SG CYS F 43 104.344 123.502 38.109 1.00117.85 S ATOM 13624 SG CYS G 40 123.129 38.442 46.899 1.00113.89 S ATOM 13646 SG CYS G 43 121.906 40.253 50.187 1.00117.78 S ATOM 15751 SG CYS H 40 99.091 70.875 21.841 1.00127.96 S ATOM 15773 SG CYS H 43 102.500 71.270 23.741 1.00128.61 S ATOM 18176 SG CYS f 40 94.955 32.247 31.269 1.00114.11 S ATOM 18198 SG CYS f 43 93.153 29.503 33.220 1.00113.86 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLN A 9 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 9 " occ=0.50 residue: pdb=" N AGLN E 9 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN E 9 " occ=0.50 Time building chain proxies: 4.09, per 1000 atoms: 0.22 Number of scatterers: 18876 At special positions: 0 Unit cell: (156.75, 137.75, 95.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 10 29.99 S 76 16.00 P 62 15.00 O 3632 8.00 N 3340 7.00 C 11756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 786.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 43 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" ND1 HIS D 16 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 12 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 40 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 43 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 16 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 12 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 40 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 16 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " pdb=" ZN b 301 " pdb="ZN ZN b 301 " - pdb=" ND1 HIS b 16 " pdb="ZN ZN b 301 " - pdb=" NE2 HIS b 12 " pdb="ZN ZN b 301 " - pdb=" SG CYS b 40 " pdb="ZN ZN b 301 " - pdb=" SG CYS b 43 " pdb=" ZN f 301 " pdb="ZN ZN f 301 " - pdb=" ND1 HIS f 16 " pdb="ZN ZN f 301 " - pdb=" NE2 HIS f 12 " pdb="ZN ZN f 301 " - pdb=" SG CYS f 43 " pdb="ZN ZN f 301 " - pdb=" SG CYS f 40 " Number of angles added : 18 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 18 sheets defined 48.8% alpha, 16.7% beta 32 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 4.514A pdb=" N GLU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.959A pdb=" N ALA A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.769A pdb=" N SER A 150 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.511A pdb=" N ALA A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 220 removed outlier: 3.696A pdb=" N LEU A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 removed outlier: 4.238A pdb=" N GLU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.697A pdb=" N VAL B 122 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 172 through 185 Processing helix chain 'B' and resid 195 through 217 removed outlier: 3.798A pdb=" N ILE B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 4.714A pdb=" N GLU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 40 removed outlier: 3.620A pdb=" N CYS C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 123 through 133 Processing helix chain 'C' and resid 144 through 166 removed outlier: 3.868A pdb=" N GLN C 148 " --> pdb=" O ASN C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 171 through 186 Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.035A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.290A pdb=" N GLU D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 27 Processing helix chain 'D' and resid 29 through 40 removed outlier: 3.551A pdb=" N CYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 123 through 134 removed outlier: 3.515A pdb=" N GLN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 removed outlier: 3.785A pdb=" N GLN D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP D 167 " --> pdb=" O GLN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 186 Processing helix chain 'D' and resid 195 through 215 Processing helix chain 'b' and resid 3 through 15 removed outlier: 4.525A pdb=" N GLU b 7 " --> pdb=" O GLU b 3 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 27 Processing helix chain 'b' and resid 29 through 39 Processing helix chain 'E' and resid 3 through 16 removed outlier: 4.514A pdb=" N GLU E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 26 removed outlier: 3.960A pdb=" N ALA E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'E' and resid 93 through 108 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.773A pdb=" N SER E 150 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 165 " --> pdb=" O THR E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'E' and resid 171 through 186 removed outlier: 3.512A pdb=" N ALA E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 220 removed outlier: 3.701A pdb=" N LEU E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE E 220 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 15 removed outlier: 4.281A pdb=" N GLU F 7 " --> pdb=" O GLU F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 26 Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.676A pdb=" N VAL F 122 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 149 through 166 Processing helix chain 'F' and resid 172 through 185 Processing helix chain 'F' and resid 195 through 217 removed outlier: 3.770A pdb=" N ILE F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 removed outlier: 4.702A pdb=" N GLU G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 29 through 40 removed outlier: 3.615A pdb=" N CYS G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 106 Processing helix chain 'G' and resid 118 through 122 removed outlier: 3.642A pdb=" N VAL G 122 " --> pdb=" O PRO G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 133 Processing helix chain 'G' and resid 144 through 166 removed outlier: 3.884A pdb=" N GLN G 148 " --> pdb=" O ASN G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 169 No H-bonds generated for 'chain 'G' and resid 167 through 169' Processing helix chain 'G' and resid 171 through 186 Processing helix chain 'G' and resid 195 through 208 Processing helix chain 'G' and resid 208 through 221 removed outlier: 4.092A pdb=" N THR G 212 " --> pdb=" O LEU G 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 15 removed outlier: 4.321A pdb=" N GLU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 27 Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 93 through 106 Processing helix chain 'H' and resid 118 through 123 Processing helix chain 'H' and resid 123 through 134 removed outlier: 3.520A pdb=" N GLN H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 167 removed outlier: 3.662A pdb=" N GLN H 163 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN H 164 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE H 165 " --> pdb=" O THR H 161 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 186 Processing helix chain 'H' and resid 195 through 215 Processing helix chain 'f' and resid 3 through 15 removed outlier: 4.569A pdb=" N GLU f 7 " --> pdb=" O GLU f 3 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 27 Processing helix chain 'f' and resid 29 through 39 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 4.303A pdb=" N VAL A 72 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP A 61 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 113 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 262 removed outlier: 6.249A pdb=" N ARG A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU A 241 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 225 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 68 removed outlier: 4.211A pdb=" N VAL B 72 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 262 removed outlier: 6.175A pdb=" N ARG B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU B 241 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY B 237 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N TYR B 227 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 89 removed outlier: 4.203A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C 113 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 258 through 262 removed outlier: 5.866A pdb=" N ARG C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU C 241 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL C 225 " --> pdb=" O PRO C 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 84 through 89 removed outlier: 4.243A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU D 113 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 258 through 262 removed outlier: 6.242A pdb=" N ARG D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 241 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLY D 237 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR D 227 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 84 through 89 removed outlier: 4.304A pdb=" N VAL E 72 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP E 61 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU E 113 " --> pdb=" O THR E 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 258 through 262 removed outlier: 6.285A pdb=" N ARG E 252 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU E 241 " --> pdb=" O ARG E 252 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 225 " --> pdb=" O PRO E 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 64 through 68 removed outlier: 4.213A pdb=" N VAL F 72 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 112 through 115 removed outlier: 3.615A pdb=" N THR F 138 " --> pdb=" O LEU F 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 258 through 262 removed outlier: 6.211A pdb=" N ARG F 252 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU F 241 " --> pdb=" O ARG F 252 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY F 237 " --> pdb=" O TYR F 227 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR F 227 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 84 through 89 removed outlier: 4.237A pdb=" N VAL G 72 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU G 113 " --> pdb=" O THR G 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 258 through 262 removed outlier: 5.872A pdb=" N ARG G 252 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU G 241 " --> pdb=" O ARG G 252 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL G 225 " --> pdb=" O PRO G 238 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.254A pdb=" N VAL H 72 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 258 through 262 removed outlier: 6.250A pdb=" N ARG H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU H 241 " --> pdb=" O ARG H 252 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLY H 237 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR H 227 " --> pdb=" O GLY H 237 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.73 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: 5909 1.34 - 1.45: 2961 1.45 - 1.57: 10321 1.57 - 1.69: 123 1.69 - 1.81: 108 Bond restraints: 19422 Sorted by residual: bond pdb=" CB GLN H 216 " pdb=" CG GLN H 216 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.08e+00 bond pdb=" CB GLN D 216 " pdb=" CG GLN D 216 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CB ASP E 193 " pdb=" CG ASP E 193 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.73e+00 bond pdb=" CB ASP A 193 " pdb=" CG ASP A 193 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.71e+00 bond pdb=" C ILE C 5 " pdb=" N PRO C 6 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.69e+00 ... (remaining 19417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 26360 1.64 - 3.29: 210 3.29 - 4.93: 49 4.93 - 6.58: 11 6.58 - 8.22: 2 Bond angle restraints: 26632 Sorted by residual: angle pdb=" CB GLN H 216 " pdb=" CG GLN H 216 " pdb=" CD GLN H 216 " ideal model delta sigma weight residual 112.60 118.66 -6.06 1.70e+00 3.46e-01 1.27e+01 angle pdb=" CA GLN H 216 " pdb=" CB GLN H 216 " pdb=" CG GLN H 216 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C1' U j 4 " pdb=" N1 U j 4 " pdb=" C2 U j 4 " ideal model delta sigma weight residual 117.70 121.32 -3.62 1.20e+00 6.94e-01 9.09e+00 angle pdb=" C1' U i 4 " pdb=" N1 U i 4 " pdb=" C2 U i 4 " ideal model delta sigma weight residual 117.70 121.27 -3.57 1.20e+00 6.94e-01 8.87e+00 angle pdb=" CA GLU G 246 " pdb=" CB GLU G 246 " pdb=" CG GLU G 246 " ideal model delta sigma weight residual 114.10 119.82 -5.72 2.00e+00 2.50e-01 8.17e+00 ... (remaining 26627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10189 17.76 - 35.53: 1078 35.53 - 53.29: 244 53.29 - 71.05: 86 71.05 - 88.82: 27 Dihedral angle restraints: 11624 sinusoidal: 5266 harmonic: 6358 Sorted by residual: dihedral pdb=" CB GLU G 10 " pdb=" CG GLU G 10 " pdb=" CD GLU G 10 " pdb=" OE1 GLU G 10 " ideal model delta sinusoidal sigma weight residual 0.00 87.35 -87.35 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU C 10 " pdb=" CG GLU C 10 " pdb=" CD GLU C 10 " pdb=" OE1 GLU C 10 " ideal model delta sinusoidal sigma weight residual 0.00 87.04 -87.04 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU H 38 " pdb=" CG GLU H 38 " pdb=" CD GLU H 38 " pdb=" OE1 GLU H 38 " ideal model delta sinusoidal sigma weight residual 0.00 85.92 -85.92 1 3.00e+01 1.11e-03 9.91e+00 ... (remaining 11621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1863 0.025 - 0.051: 728 0.051 - 0.076: 218 0.076 - 0.101: 108 0.101 - 0.126: 97 Chirality restraints: 3014 Sorted by residual: chirality pdb=" CA ILE D 269 " pdb=" N ILE D 269 " pdb=" C ILE D 269 " pdb=" CB ILE D 269 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL H 141 " pdb=" N VAL H 141 " pdb=" C VAL H 141 " pdb=" CB VAL H 141 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL H 250 " pdb=" N VAL H 250 " pdb=" C VAL H 250 " pdb=" CB VAL H 250 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 3011 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 193 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ASP A 193 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A 193 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 194 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 193 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C ASP E 193 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP E 193 " 0.013 2.00e-02 2.50e+03 pdb=" N MET E 194 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU f 28 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO f 29 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO f 29 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO f 29 " -0.022 5.00e-02 4.00e+02 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 8379 2.97 - 3.45: 17833 3.45 - 3.93: 30128 3.93 - 4.42: 32732 4.42 - 4.90: 54276 Nonbonded interactions: 143348 Sorted by model distance: nonbonded pdb=" N GLU G 246 " pdb=" OE1 GLU G 246 " model vdw 2.484 3.120 nonbonded pdb=" O ASP A 193 " pdb=" OD1 ASP A 193 " model vdw 2.490 3.040 nonbonded pdb=" O ASP E 193 " pdb=" OD1 ASP E 193 " model vdw 2.492 3.040 nonbonded pdb=" N GLU C 246 " pdb=" OE1 GLU C 246 " model vdw 2.537 3.120 nonbonded pdb=" N GLN G 170 " pdb=" OE1 GLN G 170 " model vdw 2.547 3.120 ... (remaining 143343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 141 \ or resid 148 through 301)) selection = (chain 'B' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 269 \ or resid 301)) selection = (chain 'C' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 141 \ or resid 148 through 269 or resid 301)) selection = (chain 'D' and (resid 1 through 8 or resid 10 through 141 or resid 148 through 2 \ 69 or resid 301)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 141 \ or resid 148 through 301)) selection = (chain 'F' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 269 \ or resid 301)) selection = (chain 'G' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 141 \ or resid 148 through 269 or resid 301)) selection = (chain 'H' and (resid 1 through 8 or resid 10 through 141 or resid 148 through 2 \ 69 or resid 301)) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'i' selection = chain 'j' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.660 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.009 0.359 19462 Z= 0.216 Angle : 0.481 10.692 26650 Z= 0.253 Chirality : 0.037 0.126 3014 Planarity : 0.003 0.039 3188 Dihedral : 15.866 88.816 7496 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.12 % Allowed : 18.15 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 2156 helix: 2.65 (0.17), residues: 994 sheet: 0.58 (0.25), residues: 446 loop : -0.93 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 91 TYR 0.008 0.001 TYR E 205 PHE 0.011 0.001 PHE B 220 TRP 0.011 0.001 TRP D 19 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (19422) covalent geometry : angle 0.43957 / 0.25 (26632) hydrogen bonds : bond 0.12789 / 8.97 ( 985) hydrogen bonds : angle 4.92023 / 3.48 ( 2815) metal coordination : bond 0.19591 / 11.78 ( 40) metal coordination : angle 7.50233 / 4.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 385 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 SER cc_start: 0.8601 (t) cc_final: 0.8133 (p) REVERT: A 170 GLN cc_start: 0.7721 (tt0) cc_final: 0.7418 (tt0) REVERT: A 171 TYR cc_start: 0.8728 (m-80) cc_final: 0.8142 (m-80) REVERT: B 3 GLU cc_start: 0.8364 (tp30) cc_final: 0.7542 (mm-30) REVERT: B 15 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6019 (p90) REVERT: B 46 GLN cc_start: 0.8612 (pt0) cc_final: 0.8395 (pt0) REVERT: B 83 TYR cc_start: 0.8846 (t80) cc_final: 0.8636 (t80) REVERT: B 84 ILE cc_start: 0.9166 (mt) cc_final: 0.8815 (tt) REVERT: B 255 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7815 (mp0) REVERT: B 257 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8030 (mp0) REVERT: C 110 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8782 (tt) REVERT: C 203 MET cc_start: 0.8598 (mtp) cc_final: 0.8335 (mtm) REVERT: C 257 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8267 (mp0) REVERT: D 27 LYS cc_start: 0.8844 (mttt) cc_final: 0.8430 (mmtt) REVERT: b 10 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7320 (tm-30) REVERT: b 11 GLU cc_start: 0.7768 (tt0) cc_final: 0.7349 (tt0) REVERT: b 20 LYS cc_start: 0.8686 (tttt) cc_final: 0.7534 (pttm) REVERT: b 43 CYS cc_start: 0.5861 (m) cc_final: 0.5661 (m) REVERT: E 28 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8487 (pt) REVERT: E 170 GLN cc_start: 0.8058 (tt0) cc_final: 0.7678 (tt0) REVERT: F 15 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.6279 (p90) REVERT: F 46 GLN cc_start: 0.8685 (pt0) cc_final: 0.8223 (pp30) REVERT: F 84 ILE cc_start: 0.9203 (mt) cc_final: 0.8882 (tt) REVERT: F 246 GLU cc_start: 0.7880 (mp0) cc_final: 0.7570 (mp0) REVERT: G 10 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7369 (mt-10) REVERT: G 203 MET cc_start: 0.8691 (mtp) cc_final: 0.8432 (mtm) REVERT: G 257 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8138 (mp0) REVERT: G 264 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8223 (ptt-90) REVERT: H 19 TRP cc_start: 0.7843 (p-90) cc_final: 0.7595 (p-90) REVERT: H 23 LYS cc_start: 0.8516 (mttt) cc_final: 0.8254 (mttp) REVERT: H 34 LYS cc_start: 0.8351 (mtpp) cc_final: 0.7937 (mmtt) REVERT: H 63 MET cc_start: 0.8847 (ttm) cc_final: 0.8542 (ttm) REVERT: H 227 TYR cc_start: 0.8434 (p90) cc_final: 0.8132 (p90) REVERT: H 228 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7351 (tpp80) REVERT: H 257 GLU cc_start: 0.8002 (tp30) cc_final: 0.7677 (tt0) REVERT: f 20 LYS cc_start: 0.8093 (mttt) cc_final: 0.7302 (pttt) outliers start: 21 outliers final: 7 residues processed: 403 average time/residue: 0.1498 time to fit residues: 86.5701 Evaluate side-chains 336 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 325 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 253 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 117 ASN A 202 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN D 17 ASN D 114 HIS D 240 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 163 GLN H 17 ASN H 114 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.053420 restraints weight = 77584.131| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.33 r_work: 0.2486 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2487 r_free = 0.2487 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2487 r_free = 0.2487 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19462 Z= 0.145 Angle : 0.513 8.076 26650 Z= 0.274 Chirality : 0.040 0.218 3014 Planarity : 0.005 0.059 3188 Dihedral : 8.799 58.949 3226 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.05 % Allowed : 16.92 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 2156 helix: 2.53 (0.17), residues: 1020 sheet: 0.69 (0.24), residues: 454 loop : -1.03 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 95 TYR 0.015 0.001 TYR E 171 PHE 0.008 0.001 PHE F 220 TRP 0.012 0.001 TRP A 19 HIS 0.007 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (19422) covalent geometry : angle 0.50995 / 0.27 (26632) hydrogen bonds : bond 0.04616 / 3.13 ( 985) hydrogen bonds : angle 4.12255 / 2.88 ( 2815) metal coordination : bond 0.02143 / 1.27 ( 40) metal coordination : angle 2.30673 / 1.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 335 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.7965 (tt0) cc_final: 0.7762 (tt0) REVERT: A 171 TYR cc_start: 0.8894 (m-80) cc_final: 0.8617 (m-80) REVERT: B 15 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.6565 (p90) REVERT: B 46 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8195 (pp30) REVERT: B 84 ILE cc_start: 0.9077 (mt) cc_final: 0.8758 (tt) REVERT: C 203 MET cc_start: 0.8966 (mtp) cc_final: 0.8712 (mtm) REVERT: D 27 LYS cc_start: 0.9119 (mttt) cc_final: 0.8844 (mmtt) REVERT: D 63 MET cc_start: 0.9030 (ttm) cc_final: 0.8636 (ttm) REVERT: D 224 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8048 (mmtm) REVERT: b 4 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7422 (mm110) REVERT: b 10 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7773 (tm-30) REVERT: b 20 LYS cc_start: 0.8866 (tttt) cc_final: 0.7734 (pttt) REVERT: E 265 LYS cc_start: 0.7180 (ptpt) cc_final: 0.6927 (pttt) REVERT: F 15 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.6477 (p90) REVERT: F 46 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8397 (pp30) REVERT: F 84 ILE cc_start: 0.9090 (mt) cc_final: 0.8826 (tt) REVERT: F 116 ASP cc_start: 0.8065 (p0) cc_final: 0.7684 (p0) REVERT: F 136 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7478 (tm-30) REVERT: G 203 MET cc_start: 0.8959 (mtp) cc_final: 0.8713 (mtm) REVERT: G 264 ARG cc_start: 0.8915 (mtm-85) cc_final: 0.8529 (ptt-90) REVERT: H 34 LYS cc_start: 0.8966 (mtpp) cc_final: 0.8565 (mmtt) REVERT: H 224 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7983 (mmmt) REVERT: H 227 TYR cc_start: 0.8965 (p90) cc_final: 0.8723 (p90) REVERT: H 228 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7502 (mtp85) REVERT: f 20 LYS cc_start: 0.8456 (mttt) cc_final: 0.7514 (pttt) outliers start: 57 outliers final: 31 residues processed: 368 average time/residue: 0.1431 time to fit residues: 76.0711 Evaluate side-chains 357 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 321 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 GLN Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 117 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 114 HIS A 117 ASN B 163 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 114 HIS F 163 GLN H 17 ASN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.052270 restraints weight = 100389.783| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 3.80 r_work: 0.2450 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19462 Z= 0.119 Angle : 0.487 7.093 26650 Z= 0.259 Chirality : 0.039 0.156 3014 Planarity : 0.004 0.053 3188 Dihedral : 8.772 58.985 3218 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.36 % Allowed : 17.18 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 2156 helix: 2.53 (0.17), residues: 1020 sheet: 0.82 (0.24), residues: 466 loop : -1.21 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 91 TYR 0.017 0.001 TYR E 171 PHE 0.011 0.001 PHE F 220 TRP 0.013 0.001 TRP A 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19422) covalent geometry : angle 0.47849 / 0.26 (26632) hydrogen bonds : bond 0.04084 / 2.76 ( 985) hydrogen bonds : angle 3.96316 / 2.78 ( 2815) metal coordination : bond 0.01649 / 0.98 ( 40) metal coordination : angle 3.46204 / 2.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 338 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.8931 (m-80) cc_final: 0.8639 (m-80) REVERT: B 15 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.6375 (p90) REVERT: B 84 ILE cc_start: 0.9067 (mt) cc_final: 0.8745 (tt) REVERT: B 255 GLU cc_start: 0.8167 (mp0) cc_final: 0.7736 (pm20) REVERT: D 25 ARG cc_start: 0.8469 (tpp80) cc_final: 0.8196 (tpp80) REVERT: D 27 LYS cc_start: 0.9105 (mttt) cc_final: 0.8877 (mmtt) REVERT: D 63 MET cc_start: 0.9050 (ttm) cc_final: 0.8558 (ttm) REVERT: b 4 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7352 (mm110) REVERT: b 10 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7927 (tm-30) REVERT: b 11 GLU cc_start: 0.8040 (tt0) cc_final: 0.7771 (tp30) REVERT: b 20 LYS cc_start: 0.8890 (tttt) cc_final: 0.7815 (pttt) REVERT: F 46 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8346 (pp30) REVERT: F 84 ILE cc_start: 0.9076 (mt) cc_final: 0.8827 (tt) REVERT: F 116 ASP cc_start: 0.8064 (p0) cc_final: 0.7673 (p0) REVERT: F 255 GLU cc_start: 0.8287 (mp0) cc_final: 0.8059 (pm20) REVERT: F 263 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8156 (tpt-90) REVERT: G 203 MET cc_start: 0.9029 (mtp) cc_final: 0.8806 (mtm) REVERT: G 255 GLU cc_start: 0.8538 (tp30) cc_final: 0.8033 (tp30) REVERT: G 257 GLU cc_start: 0.8338 (mp0) cc_final: 0.8043 (mp0) REVERT: G 264 ARG cc_start: 0.8919 (mtm-85) cc_final: 0.8544 (ptt-90) REVERT: H 34 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8728 (mmtt) REVERT: H 224 LYS cc_start: 0.8301 (mmmt) cc_final: 0.8002 (mmmt) REVERT: H 227 TYR cc_start: 0.9024 (p90) cc_final: 0.8789 (p90) REVERT: f 10 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7912 (tm-30) REVERT: f 20 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7522 (pttp) outliers start: 44 outliers final: 29 residues processed: 361 average time/residue: 0.1466 time to fit residues: 76.2720 Evaluate side-chains 356 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 323 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 GLN Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 117 ASN B 163 GLN D 114 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN F 163 GLN G 170 GLN H 17 ASN H 114 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.072207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.052000 restraints weight = 100666.055| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 3.89 r_work: 0.2438 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19462 Z= 0.114 Angle : 0.479 7.175 26650 Z= 0.255 Chirality : 0.039 0.208 3014 Planarity : 0.005 0.059 3188 Dihedral : 8.806 59.000 3218 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.78 % Allowed : 17.45 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 2156 helix: 2.57 (0.17), residues: 1010 sheet: 0.96 (0.25), residues: 434 loop : -1.23 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 91 TYR 0.014 0.001 TYR D 171 PHE 0.011 0.001 PHE F 220 TRP 0.012 0.001 TRP E 19 HIS 0.005 0.001 HIS H 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (19422) covalent geometry : angle 0.47276 / 0.25 (26632) hydrogen bonds : bond 0.03884 / 2.62 ( 985) hydrogen bonds : angle 3.88984 / 2.74 ( 2815) metal coordination : bond 0.01267 / 0.77 ( 40) metal coordination : angle 3.03441 / 1.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 330 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9071 (mt) cc_final: 0.8734 (tt) REVERT: B 92 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 25 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8255 (tpp80) REVERT: D 27 LYS cc_start: 0.9128 (mttt) cc_final: 0.8864 (mmtt) REVERT: D 63 MET cc_start: 0.8994 (ttm) cc_final: 0.8587 (ttm) REVERT: b 4 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7404 (mm110) REVERT: b 20 LYS cc_start: 0.8923 (tttt) cc_final: 0.7806 (pttt) REVERT: F 84 ILE cc_start: 0.9081 (mt) cc_final: 0.8811 (tt) REVERT: F 116 ASP cc_start: 0.8081 (p0) cc_final: 0.7694 (p0) REVERT: F 170 GLN cc_start: 0.7836 (tt0) cc_final: 0.7506 (tt0) REVERT: F 255 GLU cc_start: 0.8315 (mp0) cc_final: 0.7991 (pm20) REVERT: G 203 MET cc_start: 0.8997 (mtp) cc_final: 0.8736 (mtm) REVERT: G 255 GLU cc_start: 0.8514 (tp30) cc_final: 0.8073 (tp30) REVERT: G 257 GLU cc_start: 0.8411 (mp0) cc_final: 0.8074 (mp0) REVERT: G 264 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8507 (ptt-90) REVERT: H 224 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7968 (mmmt) REVERT: H 228 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7791 (ttm110) REVERT: H 244 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7745 (tptt) REVERT: f 10 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8079 (tm-30) REVERT: f 11 GLU cc_start: 0.8168 (tt0) cc_final: 0.7742 (tt0) REVERT: f 20 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7510 (pttp) outliers start: 52 outliers final: 38 residues processed: 358 average time/residue: 0.1540 time to fit residues: 78.9843 Evaluate side-chains 359 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 319 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 GLN Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 105 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 111 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 117 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS G 170 GLN H 114 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.070525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.050744 restraints weight = 94782.868| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 3.68 r_work: 0.2410 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2410 r_free = 0.2410 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2410 r_free = 0.2410 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19462 Z= 0.142 Angle : 0.516 8.152 26650 Z= 0.274 Chirality : 0.040 0.196 3014 Planarity : 0.005 0.063 3188 Dihedral : 8.872 59.014 3218 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.73 % Allowed : 17.93 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 2156 helix: 2.47 (0.17), residues: 1010 sheet: 0.96 (0.24), residues: 430 loop : -1.26 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 91 TYR 0.029 0.002 TYR A 171 PHE 0.017 0.001 PHE D 26 TRP 0.012 0.001 TRP E 19 HIS 0.004 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (19422) covalent geometry : angle 0.51045 / 0.27 (26632) hydrogen bonds : bond 0.04290 / 2.89 ( 985) hydrogen bonds : angle 3.91625 / 2.76 ( 2815) metal coordination : bond 0.01231 / 0.76 ( 40) metal coordination : angle 3.02552 / 2.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 323 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9068 (mt) cc_final: 0.8736 (tt) REVERT: B 92 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 255 GLU cc_start: 0.8307 (mp0) cc_final: 0.8039 (pm20) REVERT: D 25 ARG cc_start: 0.8493 (tpp80) cc_final: 0.8202 (tpp80) REVERT: D 27 LYS cc_start: 0.9145 (mttt) cc_final: 0.8927 (mmtt) REVERT: D 63 MET cc_start: 0.8975 (ttm) cc_final: 0.8599 (ttm) REVERT: b 4 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7360 (mm110) REVERT: b 7 GLU cc_start: 0.8443 (tp30) cc_final: 0.7957 (tp30) REVERT: b 10 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7908 (tm-30) REVERT: b 11 GLU cc_start: 0.8464 (tp30) cc_final: 0.8194 (tp30) REVERT: b 20 LYS cc_start: 0.8945 (tttt) cc_final: 0.7799 (pttt) REVERT: F 84 ILE cc_start: 0.9083 (mt) cc_final: 0.8813 (tt) REVERT: F 116 ASP cc_start: 0.8104 (p0) cc_final: 0.7717 (p0) REVERT: F 170 GLN cc_start: 0.7835 (tt0) cc_final: 0.7485 (tt0) REVERT: F 255 GLU cc_start: 0.8301 (mp0) cc_final: 0.8082 (pm20) REVERT: G 203 MET cc_start: 0.9015 (mtp) cc_final: 0.8767 (mtm) REVERT: G 255 GLU cc_start: 0.8503 (tp30) cc_final: 0.8125 (tp30) REVERT: G 257 GLU cc_start: 0.8371 (mp0) cc_final: 0.8069 (mp0) REVERT: G 264 ARG cc_start: 0.9001 (mtm-85) cc_final: 0.8595 (ptt-90) REVERT: H 25 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7856 (tpp80) REVERT: H 34 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8218 (mmtt) REVERT: H 244 LYS cc_start: 0.8087 (tmtt) cc_final: 0.7797 (tptt) REVERT: f 10 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8005 (tm-30) REVERT: f 11 GLU cc_start: 0.8204 (tt0) cc_final: 0.7780 (tt0) REVERT: f 20 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7545 (pttp) outliers start: 51 outliers final: 40 residues processed: 349 average time/residue: 0.1502 time to fit residues: 75.7393 Evaluate side-chains 359 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 GLN Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 42 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 184 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 117 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 219 ASN F 163 GLN G 170 GLN H 114 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.051174 restraints weight = 97777.330| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 3.74 r_work: 0.2423 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19462 Z= 0.112 Angle : 0.497 6.873 26650 Z= 0.263 Chirality : 0.039 0.159 3014 Planarity : 0.005 0.061 3188 Dihedral : 8.870 59.473 3218 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.68 % Allowed : 19.11 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 2156 helix: 2.51 (0.17), residues: 1012 sheet: 1.01 (0.24), residues: 426 loop : -1.27 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 91 TYR 0.037 0.001 TYR A 171 PHE 0.014 0.001 PHE H 220 TRP 0.013 0.001 TRP E 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (19422) covalent geometry : angle 0.49133 / 0.26 (26632) hydrogen bonds : bond 0.03769 / 2.53 ( 985) hydrogen bonds : angle 3.82818 / 2.69 ( 2815) metal coordination : bond 0.01088 / 0.66 ( 40) metal coordination : angle 2.86320 / 1.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9064 (mt) cc_final: 0.8730 (tt) REVERT: B 92 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7555 (tm-30) REVERT: D 25 ARG cc_start: 0.8421 (tpp80) cc_final: 0.8126 (tpp80) REVERT: D 27 LYS cc_start: 0.9128 (mttt) cc_final: 0.8924 (mmtt) REVERT: D 63 MET cc_start: 0.8965 (ttm) cc_final: 0.8576 (ttm) REVERT: D 227 TYR cc_start: 0.9133 (p90) cc_final: 0.8714 (p90) REVERT: b 4 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7340 (mm110) REVERT: b 7 GLU cc_start: 0.8484 (tp30) cc_final: 0.7653 (tp30) REVERT: b 10 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7893 (tm-30) REVERT: b 20 LYS cc_start: 0.8933 (tttt) cc_final: 0.7821 (pttt) REVERT: F 84 ILE cc_start: 0.9079 (mt) cc_final: 0.8798 (tt) REVERT: F 116 ASP cc_start: 0.8069 (p0) cc_final: 0.7663 (p0) REVERT: F 170 GLN cc_start: 0.7872 (tt0) cc_final: 0.7515 (tt0) REVERT: G 203 MET cc_start: 0.9007 (mtp) cc_final: 0.8728 (mtm) REVERT: G 255 GLU cc_start: 0.8516 (tp30) cc_final: 0.8108 (tp30) REVERT: G 257 GLU cc_start: 0.8378 (mp0) cc_final: 0.8094 (mp0) REVERT: H 25 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7879 (tpp80) REVERT: H 30 THR cc_start: 0.8075 (p) cc_final: 0.7644 (t) REVERT: H 34 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8390 (mmtt) REVERT: H 244 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7719 (ttmm) REVERT: f 10 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8017 (tm-30) REVERT: f 11 GLU cc_start: 0.8230 (tt0) cc_final: 0.7822 (tt0) REVERT: f 20 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7535 (pttp) outliers start: 50 outliers final: 41 residues processed: 356 average time/residue: 0.1545 time to fit residues: 79.2208 Evaluate side-chains 360 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 317 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 GLN Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 42 LYS Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 46 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 148 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 117 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 170 GLN H 114 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.070177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.050349 restraints weight = 94877.203| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 3.77 r_work: 0.2404 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19462 Z= 0.136 Angle : 0.527 7.602 26650 Z= 0.279 Chirality : 0.040 0.172 3014 Planarity : 0.005 0.067 3188 Dihedral : 8.914 59.664 3218 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.84 % Allowed : 19.59 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.18), residues: 2156 helix: 2.44 (0.17), residues: 1016 sheet: 1.08 (0.24), residues: 426 loop : -1.42 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 91 TYR 0.022 0.001 TYR G 171 PHE 0.011 0.001 PHE E 220 TRP 0.019 0.001 TRP D 131 HIS 0.004 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (19422) covalent geometry : angle 0.52229 / 0.28 (26632) hydrogen bonds : bond 0.04195 / 2.83 ( 985) hydrogen bonds : angle 3.87440 / 2.73 ( 2815) metal coordination : bond 0.01154 / 0.68 ( 40) metal coordination : angle 2.67517 / 1.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 327 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9082 (mt) cc_final: 0.8725 (tt) REVERT: B 92 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 64 ASP cc_start: 0.8485 (m-30) cc_final: 0.8261 (m-30) REVERT: C 203 MET cc_start: 0.8963 (mtp) cc_final: 0.8714 (mtm) REVERT: D 27 LYS cc_start: 0.9178 (mttt) cc_final: 0.8955 (mmtt) REVERT: D 63 MET cc_start: 0.8960 (ttm) cc_final: 0.8583 (ttm) REVERT: D 227 TYR cc_start: 0.9168 (p90) cc_final: 0.8751 (p90) REVERT: b 4 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7356 (mm110) REVERT: b 7 GLU cc_start: 0.8475 (tp30) cc_final: 0.7693 (tp30) REVERT: b 10 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7953 (tm-30) REVERT: b 11 GLU cc_start: 0.8546 (tp30) cc_final: 0.8298 (tp30) REVERT: b 20 LYS cc_start: 0.8955 (tttt) cc_final: 0.7814 (pttm) REVERT: F 84 ILE cc_start: 0.9096 (mt) cc_final: 0.8800 (tt) REVERT: F 116 ASP cc_start: 0.8124 (p0) cc_final: 0.7717 (p0) REVERT: F 170 GLN cc_start: 0.7960 (tt0) cc_final: 0.7642 (tt0) REVERT: G 10 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7590 (mp0) REVERT: G 203 MET cc_start: 0.9002 (mtp) cc_final: 0.8727 (mtm) REVERT: G 255 GLU cc_start: 0.8505 (tp30) cc_final: 0.8060 (tp30) REVERT: G 257 GLU cc_start: 0.8417 (mp0) cc_final: 0.8097 (mp0) REVERT: H 30 THR cc_start: 0.8106 (p) cc_final: 0.7653 (t) REVERT: H 34 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8401 (mmtt) REVERT: H 224 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7755 (mmmt) REVERT: H 244 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7871 (tptt) REVERT: f 10 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8054 (tm-30) REVERT: f 20 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7493 (pttp) outliers start: 53 outliers final: 42 residues processed: 354 average time/residue: 0.1555 time to fit residues: 79.1403 Evaluate side-chains 362 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 318 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 GLN Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 42 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 103 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS F 163 GLN H 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.070285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.050807 restraints weight = 81934.045| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 3.44 r_work: 0.2420 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19462 Z= 0.122 Angle : 0.531 7.658 26650 Z= 0.279 Chirality : 0.039 0.144 3014 Planarity : 0.005 0.055 3188 Dihedral : 8.922 59.864 3218 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.78 % Allowed : 19.65 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.18), residues: 2156 helix: 2.47 (0.17), residues: 1018 sheet: 1.10 (0.24), residues: 426 loop : -1.43 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 91 TYR 0.040 0.002 TYR G 171 PHE 0.010 0.001 PHE F 220 TRP 0.012 0.001 TRP D 131 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (19422) covalent geometry : angle 0.52631 / 0.28 (26632) hydrogen bonds : bond 0.03942 / 2.65 ( 985) hydrogen bonds : angle 3.84049 / 2.70 ( 2815) metal coordination : bond 0.01064 / 0.64 ( 40) metal coordination : angle 2.66871 / 1.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 330 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9075 (mt) cc_final: 0.8716 (tt) REVERT: B 92 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 251 LEU cc_start: 0.8358 (mp) cc_final: 0.8086 (mt) REVERT: C 203 MET cc_start: 0.8960 (mtp) cc_final: 0.8723 (mtm) REVERT: D 63 MET cc_start: 0.8953 (ttm) cc_final: 0.8580 (ttm) REVERT: D 227 TYR cc_start: 0.9171 (p90) cc_final: 0.8765 (p90) REVERT: b 4 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7377 (mm110) REVERT: b 7 GLU cc_start: 0.8453 (tp30) cc_final: 0.7705 (tp30) REVERT: b 10 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7968 (tm-30) REVERT: b 11 GLU cc_start: 0.8523 (tp30) cc_final: 0.8267 (tp30) REVERT: b 20 LYS cc_start: 0.8931 (tttt) cc_final: 0.7804 (pttm) REVERT: F 84 ILE cc_start: 0.9096 (mt) cc_final: 0.8812 (tt) REVERT: F 116 ASP cc_start: 0.8103 (p0) cc_final: 0.7693 (p0) REVERT: F 170 GLN cc_start: 0.7935 (tt0) cc_final: 0.7617 (tt0) REVERT: G 10 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7532 (mp0) REVERT: G 203 MET cc_start: 0.8997 (mtp) cc_final: 0.8742 (mtm) REVERT: G 255 GLU cc_start: 0.8441 (tp30) cc_final: 0.8023 (tp30) REVERT: G 257 GLU cc_start: 0.8472 (mp0) cc_final: 0.8152 (mp0) REVERT: H 34 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8411 (mmtt) REVERT: H 224 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7780 (mmmt) REVERT: H 244 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7879 (tttm) REVERT: f 10 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8025 (tm-30) REVERT: f 11 GLU cc_start: 0.8249 (tt0) cc_final: 0.7925 (tt0) REVERT: f 20 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7471 (pttm) outliers start: 52 outliers final: 44 residues processed: 359 average time/residue: 0.1479 time to fit residues: 76.6341 Evaluate side-chains 367 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 321 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 9 GLN Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 42 LYS Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 46 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 59 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 83 optimal weight: 0.0770 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 84 optimal weight: 0.0000 overall best weight: 0.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS H 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.071057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.052088 restraints weight = 68407.978| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 3.07 r_work: 0.2461 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19462 Z= 0.110 Angle : 0.550 8.426 26650 Z= 0.285 Chirality : 0.039 0.136 3014 Planarity : 0.005 0.062 3188 Dihedral : 8.888 59.078 3218 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 2.30 % Allowed : 20.40 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 2156 helix: 2.59 (0.17), residues: 1014 sheet: 1.03 (0.24), residues: 444 loop : -1.35 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 91 TYR 0.047 0.001 TYR C 171 PHE 0.015 0.001 PHE E 1 TRP 0.011 0.001 TRP E 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (19422) covalent geometry : angle 0.54422 / 0.28 (26632) hydrogen bonds : bond 0.03497 / 2.34 ( 985) hydrogen bonds : angle 3.77579 / 2.67 ( 2815) metal coordination : bond 0.00991 / 0.62 ( 40) metal coordination : angle 3.19880 / 2.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 330 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9077 (mt) cc_final: 0.8723 (tt) REVERT: B 92 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 251 LEU cc_start: 0.8338 (mp) cc_final: 0.8091 (mt) REVERT: C 203 MET cc_start: 0.8949 (mtp) cc_final: 0.8725 (mtm) REVERT: D 227 TYR cc_start: 0.9138 (p90) cc_final: 0.8711 (p90) REVERT: b 4 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7355 (mm110) REVERT: b 7 GLU cc_start: 0.8430 (tp30) cc_final: 0.7662 (tp30) REVERT: b 10 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7885 (tm-30) REVERT: b 11 GLU cc_start: 0.8464 (tp30) cc_final: 0.8194 (tp30) REVERT: b 20 LYS cc_start: 0.8896 (tttt) cc_final: 0.7795 (pttt) REVERT: F 84 ILE cc_start: 0.9089 (mt) cc_final: 0.8795 (tt) REVERT: F 116 ASP cc_start: 0.8062 (p0) cc_final: 0.7662 (p0) REVERT: F 170 GLN cc_start: 0.7884 (tt0) cc_final: 0.7572 (tt0) REVERT: G 10 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7486 (mp0) REVERT: G 203 MET cc_start: 0.8985 (mtp) cc_final: 0.8735 (mtm) REVERT: G 255 GLU cc_start: 0.8362 (tp30) cc_final: 0.7913 (tp30) REVERT: G 257 GLU cc_start: 0.8398 (mp0) cc_final: 0.8097 (mp0) REVERT: H 34 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8365 (mmtt) REVERT: H 224 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7740 (mmmt) REVERT: H 244 LYS cc_start: 0.8101 (tmtt) cc_final: 0.7870 (tttm) REVERT: f 10 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7952 (tm-30) REVERT: f 11 GLU cc_start: 0.8181 (tt0) cc_final: 0.7738 (tt0) REVERT: f 20 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7473 (pttp) outliers start: 43 outliers final: 39 residues processed: 350 average time/residue: 0.1522 time to fit residues: 76.5277 Evaluate side-chains 368 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 46 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 136 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 0.0040 chunk 94 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN F 163 GLN H 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.069507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.049558 restraints weight = 106941.336| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 3.87 r_work: 0.2380 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19462 Z= 0.143 Angle : 0.582 7.715 26650 Z= 0.307 Chirality : 0.040 0.145 3014 Planarity : 0.005 0.068 3188 Dihedral : 8.967 58.923 3218 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.25 % Allowed : 20.02 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.18), residues: 2156 helix: 2.46 (0.17), residues: 1016 sheet: 1.09 (0.24), residues: 428 loop : -1.48 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 91 TYR 0.044 0.002 TYR G 171 PHE 0.011 0.001 PHE H 1 TRP 0.012 0.001 TRP D 131 HIS 0.005 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (19422) covalent geometry : angle 0.57831 / 0.31 (26632) hydrogen bonds : bond 0.04384 / 2.95 ( 985) hydrogen bonds : angle 3.87789 / 2.73 ( 2815) metal coordination : bond 0.01158 / 0.71 ( 40) metal coordination : angle 2.52438 / 1.73 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 331 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9076 (mt) cc_final: 0.8725 (tt) REVERT: B 92 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 251 LEU cc_start: 0.8504 (mp) cc_final: 0.8283 (mt) REVERT: C 203 MET cc_start: 0.8980 (mtp) cc_final: 0.8747 (mtm) REVERT: D 19 TRP cc_start: 0.8314 (p-90) cc_final: 0.7613 (p-90) REVERT: D 34 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8442 (mmtt) REVERT: D 227 TYR cc_start: 0.9181 (p90) cc_final: 0.8696 (p90) REVERT: b 4 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7393 (mm110) REVERT: b 7 GLU cc_start: 0.8497 (tp30) cc_final: 0.7781 (tp30) REVERT: b 10 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8028 (tm-30) REVERT: b 11 GLU cc_start: 0.8554 (tp30) cc_final: 0.8339 (tp30) REVERT: b 20 LYS cc_start: 0.8960 (tttt) cc_final: 0.7842 (pttm) REVERT: E 171 TYR cc_start: 0.8808 (m-10) cc_final: 0.8594 (m-10) REVERT: F 84 ILE cc_start: 0.9085 (mt) cc_final: 0.8817 (tt) REVERT: F 116 ASP cc_start: 0.8132 (p0) cc_final: 0.7708 (p0) REVERT: F 170 GLN cc_start: 0.8013 (tt0) cc_final: 0.7692 (tt0) REVERT: G 10 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7631 (mp0) REVERT: G 203 MET cc_start: 0.9020 (mtp) cc_final: 0.8770 (mtm) REVERT: G 255 GLU cc_start: 0.8459 (tp30) cc_final: 0.8087 (tp30) REVERT: H 224 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7825 (mmmt) REVERT: H 244 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7893 (ttmm) REVERT: f 10 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8158 (tm-30) REVERT: f 20 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.7583 (pttm) outliers start: 42 outliers final: 35 residues processed: 351 average time/residue: 0.1501 time to fit residues: 75.6552 Evaluate side-chains 362 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 325 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 179 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 113 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN E 170 GLN F 163 GLN H 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.070276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.050960 restraints weight = 79086.099| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 3.35 r_work: 0.2424 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19462 Z= 0.125 Angle : 0.592 9.644 26650 Z= 0.309 Chirality : 0.040 0.160 3014 Planarity : 0.005 0.087 3188 Dihedral : 8.967 58.928 3218 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 2.25 % Allowed : 20.56 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.18), residues: 2156 helix: 2.47 (0.17), residues: 1018 sheet: 1.11 (0.24), residues: 428 loop : -1.48 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 91 TYR 0.056 0.002 TYR C 171 PHE 0.016 0.001 PHE E 1 TRP 0.012 0.001 TRP A 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (19422) covalent geometry : angle 0.58763 / 0.31 (26632) hydrogen bonds : bond 0.03870 / 2.60 ( 985) hydrogen bonds : angle 3.82945 / 2.70 ( 2815) metal coordination : bond 0.01028 / 0.63 ( 40) metal coordination : angle 2.71110 / 1.86 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.16 seconds wall clock time: 71 minutes 16.39 seconds (4276.39 seconds total)