Starting phenix.real_space_refine on Fri Aug 7 04:08:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmu_54068/08_2026/9rmu_54068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmu_54068/08_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_54068/08_2026/9rmu_54068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmu_54068/08_2026/9rmu_54068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rmu_54068/08_2026/9rmu_54068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmu_54068/08_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 4.79, per 1000 atoms: 0.25 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: 1.56 Conformation dependent library (CDL) restraints added in 606.8 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: 1.73 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: 2.54 Time building geometry restraints manager: 1.94 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: 26168 1.64 - 3.29: 402 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=" O5' U j 4 " pdb=" C5' U j 4 " pdb=" C4' U j 4 " ideal model delta sigma weight residual 109.40 112.23 -2.83 8.00e-01 1.56e+00 1.25e+01 angle pdb=" O5' U i 4 " pdb=" C5' U i 4 " pdb=" C4' U i 4 " ideal model delta sigma weight residual 109.40 112.19 -2.79 8.00e-01 1.56e+00 1.21e+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=" O5' A I 16 " pdb=" C5' A I 16 " pdb=" C4' A I 16 " ideal model delta sigma weight residual 109.40 111.95 -2.55 8.00e-01 1.56e+00 1.02e+01 ... (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 - 0.028: 1905 0.028 - 0.056: 710 0.056 - 0.084: 153 0.084 - 0.112: 148 0.112 - 0.140: 98 Chirality restraints: 3014 Sorted by residual: chirality pdb=" C2' A J 13 " pdb=" C3' A J 13 " pdb=" O2' A J 13 " pdb=" C1' A J 13 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" C2' A J 14 " pdb=" C3' A J 14 " pdb=" O2' A J 14 " pdb=" C1' A J 14 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" C2' A I 14 " pdb=" C3' A I 14 " pdb=" O2' A I 14 " pdb=" C1' A I 14 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.79e-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: 4.500 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.680 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- 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= 0.218 Angle : 0.521 10.692 26650 Z= 0.295 Chirality : 0.042 0.140 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 0.00204 / 0.10 (19422) covalent geometry : angle 0.48303 / 0.29 (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 : 0.573 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: 0.8637 (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: 0.8268 (mp0) REVERT: D 27 LYS cc_start: 0.8844 (mttt) cc_final: 0.8431 (mmtt) REVERT: b 10 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7321 (tm-30) REVERT: b 11 GLU cc_start: 0.7768 (tt0) cc_final: 0.7348 (tt0) REVERT: b 20 LYS cc_start: 0.8686 (tttt) cc_final: 0.7532 (pttm) REVERT: b 43 CYS cc_start: 0.5861 (m) cc_final: 0.5657 (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: 0.7677 (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: 0.8222 (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: H 19 TRP cc_start: 0.7843 (p-90) cc_final: 0.7594 (p-90) REVERT: H 23 LYS cc_start: 0.8516 (mttt) cc_final: 0.8253 (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: 0.8134 (p90) REVERT: H 228 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7353 (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: 0.1723 time to fit residues: 98.9690 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 : 0.500 ------------------------------------------------------------------------------- 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 = 0.3096 r_free = 0.3096 target = 0.072550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.053131 restraints weight = 78187.783| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 3.33 r_work: 0.2484 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 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 = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.2483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19462 Z= 0.148 Angle : 0.528 8.572 26650 Z= 0.282 Chirality : 0.041 0.237 3014 Planarity : 0.005 0.072 3188 Dihedral : 8.920 59.311 3226 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.05 % Allowed : 16.81 % Favored : 80.14 % 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: 1.56 (0.19), residues: 2156 helix: 2.49 (0.17), residues: 1020 sheet: 0.70 (0.24), residues: 458 loop : -1.06 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 95 TYR 0.016 0.002 TYR E 171 PHE 0.009 0.001 PHE F 220 TRP 0.012 0.001 TRP A 19 HIS 0.009 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (19422) covalent geometry : angle 0.52566 / 0.28 (26632) hydrogen bonds : bond 0.04445 / 3.02 ( 985) hydrogen bonds : angle 4.10708 / 2.87 ( 2815) metal coordination : bond 0.01604 / 0.96 ( 40) metal coordination : angle 1.98646 / 1.34 ( 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 395 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 338 time to evaluate : 0.547 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.6598 (p90) REVERT: B 46 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8164 (pp30) REVERT: B 84 ILE cc_start: 0.9063 (mt) cc_final: 0.8757 (tt) REVERT: C 203 MET cc_start: 0.8990 (mtp) cc_final: 0.8736 (mtm) REVERT: D 27 LYS cc_start: 0.9097 (mttt) cc_final: 0.8863 (mmtt) REVERT: D 63 MET cc_start: 0.9021 (ttm) cc_final: 0.8623 (ttm) REVERT: D 224 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8058 (mmtm) REVERT: b 4 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7426 (mm110) REVERT: b 10 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7786 (tm-30) REVERT: b 20 LYS cc_start: 0.8854 (tttt) cc_final: 0.7749 (pttt) REVERT: E 265 LYS cc_start: 0.7185 (ptpt) cc_final: 0.6959 (pttt) REVERT: F 15 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.6536 (p90) REVERT: F 23 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8924 (tptp) REVERT: F 46 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8378 (pp30) REVERT: F 84 ILE cc_start: 0.9087 (mt) cc_final: 0.8837 (tt) REVERT: F 116 ASP cc_start: 0.8040 (p0) cc_final: 0.7633 (p0) REVERT: F 136 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7444 (tm-30) REVERT: G 203 MET cc_start: 0.8997 (mtp) cc_final: 0.8744 (mtm) REVERT: H 224 LYS cc_start: 0.8262 (mmmt) cc_final: 0.8051 (mmmt) REVERT: H 227 TYR cc_start: 0.8990 (p90) cc_final: 0.8739 (p90) REVERT: H 228 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7495 (mtp85) REVERT: f 20 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7521 (pttp) outliers start: 57 outliers final: 31 residues processed: 371 average time/residue: 0.1513 time to fit residues: 81.2295 Evaluate side-chains 364 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 326 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 23 LYS 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 20 LYS 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: 2.9990 chunk 160 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 114 HIS A 117 ASN B 163 GLN D 17 ASN D 114 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 114 HIS E 219 ASN F 163 GLN H 17 ASN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.071116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.051165 restraints weight = 99833.097| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 3.86 r_work: 0.2414 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2413 r_free = 0.2413 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 = 0.2413 r_free = 0.2413 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19462 Z= 0.143 Angle : 0.509 7.104 26650 Z= 0.273 Chirality : 0.040 0.163 3014 Planarity : 0.005 0.054 3188 Dihedral : 8.914 59.077 3218 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.68 % Allowed : 17.02 % Favored : 80.30 % 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: 1.52 (0.19), residues: 2156 helix: 2.45 (0.17), residues: 1018 sheet: 0.94 (0.24), residues: 434 loop : -1.19 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 91 TYR 0.013 0.001 TYR G 272 PHE 0.011 0.001 PHE F 220 TRP 0.015 0.001 TRP H 19 HIS 0.004 0.001 HIS H 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (19422) covalent geometry : angle 0.50107 / 0.27 (26632) hydrogen bonds : bond 0.04531 / 3.07 ( 985) hydrogen bonds : angle 4.01218 / 2.81 ( 2815) metal coordination : bond 0.01801 / 1.07 ( 40) metal coordination : angle 3.53737 / 2.24 ( 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 387 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 0.725 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: B 84 ILE cc_start: 0.9090 (mt) cc_final: 0.8751 (tt) REVERT: B 255 GLU cc_start: 0.8273 (mp0) cc_final: 0.7827 (pm20) REVERT: C 203 MET cc_start: 0.8999 (mtp) cc_final: 0.8743 (mtm) REVERT: C 257 GLU cc_start: 0.8423 (mp0) cc_final: 0.8211 (mp0) REVERT: D 25 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8252 (tpp80) REVERT: D 27 LYS cc_start: 0.9154 (mttt) cc_final: 0.8911 (mmtt) REVERT: D 63 MET cc_start: 0.9061 (ttm) cc_final: 0.8556 (ttm) REVERT: b 4 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7390 (mm110) REVERT: b 10 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7966 (tm-30) REVERT: b 11 GLU cc_start: 0.8097 (tt0) cc_final: 0.7858 (tp30) REVERT: b 20 LYS cc_start: 0.8916 (tttt) cc_final: 0.7745 (pttt) REVERT: F 46 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8403 (pp30) REVERT: F 84 ILE cc_start: 0.9093 (mt) cc_final: 0.8820 (tt) REVERT: F 116 ASP cc_start: 0.8092 (p0) cc_final: 0.7716 (p0) REVERT: F 136 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7591 (tm-30) REVERT: F 255 GLU cc_start: 0.8362 (mp0) cc_final: 0.8158 (pm20) REVERT: G 203 MET cc_start: 0.9012 (mtp) cc_final: 0.8741 (mtm) REVERT: G 255 GLU cc_start: 0.8530 (tp30) cc_final: 0.8183 (tp30) REVERT: G 257 GLU cc_start: 0.8600 (mp0) cc_final: 0.8305 (mp0) REVERT: H 125 GLU cc_start: 0.8345 (mp0) cc_final: 0.8132 (mp0) REVERT: H 224 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7952 (mmmt) REVERT: H 226 TYR cc_start: 0.7914 (m-10) cc_final: 0.7669 (m-10) REVERT: H 227 TYR cc_start: 0.9086 (p90) cc_final: 0.8871 (p90) REVERT: f 7 GLU cc_start: 0.8638 (tp30) cc_final: 0.8382 (tp30) REVERT: f 10 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8051 (tm-30) REVERT: f 20 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7499 (pttp) outliers start: 50 outliers final: 33 residues processed: 364 average time/residue: 0.1670 time to fit residues: 87.4276 Evaluate side-chains 356 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 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 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 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 31 ILE 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 42 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: 0.2980 chunk 193 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 B 163 GLN D 240 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS F 163 GLN H 17 ASN H 114 HIS f 46 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.071111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.050971 restraints weight = 100901.299| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 3.86 r_work: 0.2412 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 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 = 0.2412 r_free = 0.2412 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: 0.2412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19462 Z= 0.125 Angle : 0.497 7.359 26650 Z= 0.264 Chirality : 0.040 0.216 3014 Planarity : 0.005 0.057 3188 Dihedral : 8.952 59.069 3218 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.57 % Allowed : 17.88 % Favored : 79.55 % 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 (0.19), residues: 2156 helix: 2.46 (0.17), residues: 1010 sheet: 0.91 (0.24), residues: 432 loop : -1.24 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 91 TYR 0.023 0.001 TYR A 171 PHE 0.015 0.001 PHE E 220 TRP 0.013 0.001 TRP A 19 HIS 0.004 0.001 HIS H 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (19422) covalent geometry : angle 0.49000 / 0.26 (26632) hydrogen bonds : bond 0.04123 / 2.78 ( 985) hydrogen bonds : angle 3.92581 / 2.76 ( 2815) metal coordination : bond 0.01233 / 0.74 ( 40) metal coordination : angle 3.19107 / 2.06 ( 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 373 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 325 time to evaluate : 0.716 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: 0.9057 (mt) cc_final: 0.8730 (tt) REVERT: B 92 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7529 (tm-30) REVERT: C 257 GLU cc_start: 0.8378 (mp0) cc_final: 0.8159 (mp0) REVERT: D 25 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8215 (tpp80) REVERT: D 27 LYS cc_start: 0.9143 (mttt) cc_final: 0.8919 (mmtt) REVERT: D 63 MET cc_start: 0.8993 (ttm) cc_final: 0.8605 (ttm) REVERT: b 4 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7351 (mm110) REVERT: b 7 GLU cc_start: 0.8486 (tp30) cc_final: 0.8164 (tp30) REVERT: b 20 LYS cc_start: 0.8929 (tttt) cc_final: 0.7817 (pttt) REVERT: F 84 ILE cc_start: 0.9072 (mt) cc_final: 0.8801 (tt) REVERT: F 116 ASP cc_start: 0.8056 (p0) cc_final: 0.7673 (p0) REVERT: F 170 GLN cc_start: 0.7804 (tt0) cc_final: 0.7461 (tt0) REVERT: G 91 ARG cc_start: 0.8514 (ptp-110) cc_final: 0.8296 (ptp-110) REVERT: G 203 MET cc_start: 0.9028 (mtp) cc_final: 0.8784 (mtm) REVERT: G 255 GLU cc_start: 0.8467 (tp30) cc_final: 0.8094 (tp30) REVERT: G 257 GLU cc_start: 0.8502 (mp0) cc_final: 0.8187 (mp0) REVERT: H 227 TYR cc_start: 0.9087 (p90) cc_final: 0.8855 (p90) REVERT: H 228 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7823 (ttm110) REVERT: f 10 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8013 (tm-30) REVERT: f 11 GLU cc_start: 0.8192 (tt0) cc_final: 0.7795 (tt0) REVERT: f 20 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7569 (pttp) outliers start: 48 outliers final: 36 residues processed: 349 average time/residue: 0.1553 time to fit residues: 77.9192 Evaluate side-chains 354 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 316 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 261 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 105 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 B 163 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN E 170 GLN F 163 GLN G 170 GLN H 17 ASN H 114 HIS f 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.051257 restraints weight = 94216.833| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 3.68 r_work: 0.2427 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2427 r_free = 0.2427 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 = 0.2427 r_free = 0.2427 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19462 Z= 0.116 Angle : 0.499 8.002 26650 Z= 0.264 Chirality : 0.039 0.218 3014 Planarity : 0.005 0.063 3188 Dihedral : 8.941 59.926 3218 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.78 % Allowed : 18.68 % Favored : 78.53 % 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: 2.48 (0.17), residues: 1010 sheet: 0.93 (0.24), residues: 432 loop : -1.26 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 91 TYR 0.033 0.002 TYR A 171 PHE 0.018 0.001 PHE D 26 TRP 0.012 0.001 TRP E 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (19422) covalent geometry : angle 0.49294 / 0.26 (26632) hydrogen bonds : bond 0.03921 / 2.64 ( 985) hydrogen bonds : angle 3.88244 / 2.74 ( 2815) metal coordination : bond 0.01133 / 0.70 ( 40) metal coordination : angle 3.11105 / 2.06 ( 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 376 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 0.725 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: 0.9050 (mt) cc_final: 0.8720 (tt) REVERT: B 92 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 255 GLU cc_start: 0.8260 (mp0) cc_final: 0.7948 (pm20) REVERT: D 25 ARG cc_start: 0.8488 (tpp80) cc_final: 0.8185 (tpp80) REVERT: D 27 LYS cc_start: 0.9107 (mttt) cc_final: 0.8905 (mmtt) REVERT: D 63 MET cc_start: 0.8970 (ttm) cc_final: 0.8588 (ttm) REVERT: D 227 TYR cc_start: 0.9109 (p90) cc_final: 0.8722 (p90) REVERT: b 4 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7358 (mm110) REVERT: b 7 GLU cc_start: 0.8509 (tp30) cc_final: 0.8188 (tp30) REVERT: b 20 LYS cc_start: 0.8896 (tttt) cc_final: 0.7815 (pttt) REVERT: F 84 ILE cc_start: 0.9071 (mt) cc_final: 0.8798 (tt) REVERT: F 116 ASP cc_start: 0.8034 (p0) cc_final: 0.7638 (p0) REVERT: F 170 GLN cc_start: 0.7819 (tt0) cc_final: 0.7468 (tt0) REVERT: G 91 ARG cc_start: 0.8503 (ptp-110) cc_final: 0.8298 (ptp-110) REVERT: G 203 MET cc_start: 0.9022 (mtp) cc_final: 0.8745 (mtm) REVERT: G 255 GLU cc_start: 0.8461 (tp30) cc_final: 0.8042 (tp30) REVERT: G 257 GLU cc_start: 0.8405 (mp0) cc_final: 0.8084 (mp0) REVERT: H 227 TYR cc_start: 0.9103 (p90) cc_final: 0.8861 (p90) REVERT: H 244 LYS cc_start: 0.8033 (tttm) cc_final: 0.7808 (ttmm) REVERT: f 10 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8050 (tm-30) REVERT: f 11 GLU cc_start: 0.8206 (tt0) cc_final: 0.7796 (tt0) REVERT: f 20 LYS cc_start: 0.8600 (mttt) cc_final: 0.7566 (pttp) outliers start: 52 outliers final: 36 residues processed: 353 average time/residue: 0.1696 time to fit residues: 86.3132 Evaluate side-chains 353 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 316 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 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 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 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 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 184 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 219 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 170 GLN F 163 GLN H 114 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.071000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.050983 restraints weight = 97200.270| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 3.75 r_work: 0.2419 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 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 = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2706 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= 0.120 Angle : 0.511 7.263 26650 Z= 0.270 Chirality : 0.039 0.162 3014 Planarity : 0.005 0.064 3188 Dihedral : 8.958 59.996 3218 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.36 % Allowed : 19.70 % Favored : 77.94 % 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: 1.50 (0.19), residues: 2156 helix: 2.50 (0.17), residues: 1010 sheet: 0.94 (0.24), residues: 432 loop : -1.26 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 91 TYR 0.026 0.001 TYR C 171 PHE 0.012 0.001 PHE D 26 TRP 0.012 0.001 TRP E 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (19422) covalent geometry : angle 0.50552 / 0.27 (26632) hydrogen bonds : bond 0.03891 / 2.62 ( 985) hydrogen bonds : angle 3.85537 / 2.71 ( 2815) metal coordination : bond 0.01094 / 0.68 ( 40) metal coordination : angle 2.96249 / 1.95 ( 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 371 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 327 time to evaluate : 0.683 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: 0.9050 (mt) cc_final: 0.8713 (tt) REVERT: B 92 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 25 ARG cc_start: 0.8457 (tpp80) cc_final: 0.8146 (tpp80) REVERT: D 27 LYS cc_start: 0.9118 (mttt) cc_final: 0.8912 (mmtt) REVERT: D 63 MET cc_start: 0.8971 (ttm) cc_final: 0.8600 (ttm) REVERT: D 227 TYR cc_start: 0.9130 (p90) cc_final: 0.8760 (p90) REVERT: b 4 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7397 (mm110) REVERT: b 7 GLU cc_start: 0.8499 (tp30) cc_final: 0.7703 (tp30) REVERT: b 10 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7766 (tm-30) REVERT: b 20 LYS cc_start: 0.8905 (tttt) cc_final: 0.7823 (pttt) REVERT: F 84 ILE cc_start: 0.9072 (mt) cc_final: 0.8794 (tt) REVERT: F 116 ASP cc_start: 0.8049 (p0) cc_final: 0.7648 (p0) REVERT: F 170 GLN cc_start: 0.7847 (tt0) cc_final: 0.7488 (tt0) REVERT: G 203 MET cc_start: 0.9032 (mtp) cc_final: 0.8765 (mtm) REVERT: G 255 GLU cc_start: 0.8474 (tp30) cc_final: 0.8043 (tp30) REVERT: G 257 GLU cc_start: 0.8397 (mp0) cc_final: 0.8068 (mp0) REVERT: H 25 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8000 (tpp80) REVERT: H 224 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7936 (mmmt) REVERT: H 227 TYR cc_start: 0.9112 (p90) cc_final: 0.8877 (p90) REVERT: f 10 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8025 (tm-30) REVERT: f 11 GLU cc_start: 0.8187 (tt0) cc_final: 0.7787 (tt0) REVERT: f 20 LYS cc_start: 0.8585 (mttt) cc_final: 0.7556 (pttp) outliers start: 44 outliers final: 39 residues processed: 351 average time/residue: 0.1791 time to fit residues: 90.0089 Evaluate side-chains 360 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 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 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 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 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 45 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 148 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 146 optimal weight: 0.7980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS H 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.071328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.051488 restraints weight = 94679.316| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 3.78 r_work: 0.2437 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 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 = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19462 Z= 0.105 Angle : 0.510 7.612 26650 Z= 0.268 Chirality : 0.039 0.142 3014 Planarity : 0.005 0.063 3188 Dihedral : 8.933 59.665 3218 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 19.81 % Favored : 77.78 % 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: 1.56 (0.19), residues: 2156 helix: 2.54 (0.17), residues: 1014 sheet: 1.04 (0.24), residues: 426 loop : -1.28 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 91 TYR 0.036 0.001 TYR G 171 PHE 0.010 0.001 PHE D 26 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 0.00236 / 0.11 (19422) covalent geometry : angle 0.50438 / 0.27 (26632) hydrogen bonds : bond 0.03537 / 2.37 ( 985) hydrogen bonds : angle 3.78567 / 2.67 ( 2815) metal coordination : bond 0.01017 / 0.63 ( 40) metal coordination : angle 2.91633 / 1.87 ( 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 373 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 328 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9077 (mt) cc_final: 0.8728 (tt) REVERT: B 92 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7758 (tm-30) REVERT: D 27 LYS cc_start: 0.9133 (mttt) cc_final: 0.8917 (mmtt) REVERT: D 63 MET cc_start: 0.8965 (ttm) cc_final: 0.8599 (ttm) REVERT: D 131 TRP cc_start: 0.9121 (t60) cc_final: 0.8920 (t60) REVERT: D 227 TYR cc_start: 0.9147 (p90) cc_final: 0.8743 (p90) REVERT: b 4 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7335 (mm110) REVERT: b 7 GLU cc_start: 0.8480 (tp30) cc_final: 0.7740 (tp30) REVERT: b 10 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7819 (tm-30) REVERT: b 11 GLU cc_start: 0.8120 (tt0) cc_final: 0.7856 (tt0) REVERT: b 20 LYS cc_start: 0.8921 (tttt) cc_final: 0.7796 (pttt) REVERT: b 38 GLU cc_start: 0.8542 (tp30) cc_final: 0.8187 (tp30) REVERT: F 84 ILE cc_start: 0.9088 (mt) cc_final: 0.8794 (tt) REVERT: F 116 ASP cc_start: 0.8087 (p0) cc_final: 0.7679 (p0) REVERT: F 170 GLN cc_start: 0.7882 (tt0) cc_final: 0.7557 (tt0) REVERT: G 203 MET cc_start: 0.9014 (mtp) cc_final: 0.8752 (mtm) REVERT: G 255 GLU cc_start: 0.8469 (tp30) cc_final: 0.8015 (tp30) REVERT: G 257 GLU cc_start: 0.8424 (mp0) cc_final: 0.8063 (mp0) REVERT: H 224 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7856 (mmmt) REVERT: H 227 TYR cc_start: 0.9140 (p90) cc_final: 0.8915 (p90) REVERT: H 244 LYS cc_start: 0.8060 (tttm) cc_final: 0.7838 (ttmm) REVERT: f 10 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8022 (tm-30) REVERT: f 11 GLU cc_start: 0.8223 (tt0) cc_final: 0.7812 (tt0) REVERT: f 20 LYS cc_start: 0.8596 (mttt) cc_final: 0.7518 (pttp) outliers start: 45 outliers final: 37 residues processed: 349 average time/residue: 0.1781 time to fit residues: 89.2195 Evaluate side-chains 365 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 327 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 251 LEU 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 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 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 65 CYS 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 202 ASN Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 31 ILE 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 45 VAL Chi-restraints excluded: chain f residue 46 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 103 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 117 ASN F 163 GLN G 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.068312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.048873 restraints weight = 79944.988| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 3.38 r_work: 0.2365 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2367 r_free = 0.2367 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2367 r_free = 0.2367 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 19462 Z= 0.207 Angle : 0.602 7.759 26650 Z= 0.321 Chirality : 0.043 0.296 3014 Planarity : 0.006 0.075 3188 Dihedral : 9.175 59.819 3218 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.78 % Allowed : 19.70 % Favored : 77.52 % 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: 1.23 (0.18), residues: 2156 helix: 2.22 (0.16), residues: 1016 sheet: 1.11 (0.24), residues: 424 loop : -1.54 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 95 TYR 0.034 0.002 TYR C 171 PHE 0.015 0.002 PHE H 1 TRP 0.013 0.002 TRP H 131 HIS 0.007 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (19422) covalent geometry : angle 0.59748 / 0.32 (26632) hydrogen bonds : bond 0.05310 / 3.60 ( 985) hydrogen bonds : angle 4.07308 / 2.86 ( 2815) metal coordination : bond 0.01504 / 0.91 ( 40) metal coordination : angle 2.73728 / 1.84 ( 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 : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9084 (mt) cc_final: 0.8728 (tt) REVERT: B 92 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7689 (tm-30) REVERT: C 203 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8708 (mtm) REVERT: D 227 TYR cc_start: 0.9181 (p90) cc_final: 0.8781 (p90) REVERT: b 4 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7378 (mm110) REVERT: b 7 GLU cc_start: 0.8401 (tp30) cc_final: 0.7740 (tp30) REVERT: b 10 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7841 (tm-30) REVERT: b 20 LYS cc_start: 0.8979 (tttt) cc_final: 0.7795 (pttm) REVERT: b 38 GLU cc_start: 0.8472 (tp30) cc_final: 0.8166 (tp30) REVERT: F 116 ASP cc_start: 0.8137 (p0) cc_final: 0.7750 (p0) REVERT: F 170 GLN cc_start: 0.8060 (tt0) cc_final: 0.7749 (tt0) REVERT: G 203 MET cc_start: 0.9008 (mtp) cc_final: 0.8750 (mtm) REVERT: G 255 GLU cc_start: 0.8377 (tp30) cc_final: 0.7863 (tp30) REVERT: G 257 GLU cc_start: 0.8423 (mp0) cc_final: 0.8047 (mp0) REVERT: H 224 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7903 (mmmt) REVERT: H 227 TYR cc_start: 0.9190 (p90) cc_final: 0.8869 (p90) REVERT: f 10 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8065 (tm-30) REVERT: f 20 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7484 (pttm) outliers start: 52 outliers final: 42 residues processed: 351 average time/residue: 0.1791 time to fit residues: 89.3892 Evaluate side-chains 371 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 326 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 203 MET 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 138 THR 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 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 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 163 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 59 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.069672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.050901 restraints weight = 67649.234| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 2.96 r_work: 0.2425 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2427 r_free = 0.2427 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2427 r_free = 0.2427 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: 0.2427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19462 Z= 0.124 Angle : 0.566 8.169 26650 Z= 0.297 Chirality : 0.040 0.164 3014 Planarity : 0.005 0.070 3188 Dihedral : 9.111 59.955 3218 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 2.14 % Allowed : 20.34 % Favored : 77.52 % 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: 1.39 (0.18), residues: 2156 helix: 2.39 (0.17), residues: 1016 sheet: 1.12 (0.24), residues: 426 loop : -1.48 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 91 TYR 0.044 0.001 TYR C 171 PHE 0.033 0.001 PHE E 220 TRP 0.015 0.001 TRP A 19 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (19422) covalent geometry : angle 0.56002 / 0.30 (26632) hydrogen bonds : bond 0.04109 / 2.77 ( 985) hydrogen bonds : angle 3.90943 / 2.75 ( 2815) metal coordination : bond 0.01122 / 0.69 ( 40) metal coordination : angle 3.11268 / 2.30 ( 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 369 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ILE cc_start: 0.9065 (mt) cc_final: 0.8699 (tt) REVERT: B 92 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7614 (tm-30) REVERT: C 203 MET cc_start: 0.8940 (mtm) cc_final: 0.8710 (mtm) REVERT: D 19 TRP cc_start: 0.8403 (p-90) cc_final: 0.7327 (p-90) REVERT: D 34 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8378 (mppt) REVERT: D 227 TYR cc_start: 0.9165 (p90) cc_final: 0.8748 (p90) REVERT: b 4 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7414 (mm110) REVERT: b 10 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7961 (tm-30) REVERT: b 11 GLU cc_start: 0.8111 (tt0) cc_final: 0.7857 (tt0) REVERT: b 20 LYS cc_start: 0.8905 (tttt) cc_final: 0.7789 (pttm) REVERT: b 38 GLU cc_start: 0.8512 (tp30) cc_final: 0.8290 (tp30) REVERT: b 45 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8375 (p) REVERT: F 116 ASP cc_start: 0.8032 (p0) cc_final: 0.7642 (p0) REVERT: F 170 GLN cc_start: 0.7889 (tt0) cc_final: 0.7558 (tt0) REVERT: G 203 MET cc_start: 0.9004 (mtp) cc_final: 0.8738 (mtm) REVERT: G 255 GLU cc_start: 0.8276 (tp30) cc_final: 0.7772 (tp30) REVERT: G 257 GLU cc_start: 0.8378 (mp0) cc_final: 0.8040 (mp0) REVERT: H 224 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7882 (mmmt) REVERT: H 227 TYR cc_start: 0.9184 (p90) cc_final: 0.8929 (p90) REVERT: f 10 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8034 (tm-30) REVERT: f 11 GLU cc_start: 0.8214 (tt0) cc_final: 0.7925 (tt0) REVERT: f 20 LYS cc_start: 0.8695 (mttt) cc_final: 0.7561 (pttm) outliers start: 40 outliers final: 36 residues processed: 350 average time/residue: 0.1795 time to fit residues: 89.6913 Evaluate side-chains 363 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 325 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain C residue 9 GLN 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 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 253 THR Chi-restraints excluded: chain H residue 260 THR 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: 0.0970 chunk 155 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 101 optimal weight: 0.2980 chunk 174 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.0020 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN F 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.070151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.050026 restraints weight = 107222.679| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 4.07 r_work: 0.2394 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2397 r_free = 0.2397 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 = 0.2397 r_free = 0.2397 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: 0.2397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19462 Z= 0.118 Angle : 0.571 8.783 26650 Z= 0.299 Chirality : 0.039 0.140 3014 Planarity : 0.005 0.065 3188 Dihedral : 9.045 59.578 3218 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 2.14 % Allowed : 20.50 % Favored : 77.36 % 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: 1.45 (0.18), residues: 2156 helix: 2.43 (0.17), residues: 1020 sheet: 1.14 (0.23), residues: 446 loop : -1.53 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 91 TYR 0.043 0.001 TYR G 171 PHE 0.035 0.001 PHE E 220 TRP 0.029 0.001 TRP D 131 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (19422) covalent geometry : angle 0.56603 / 0.30 (26632) hydrogen bonds : bond 0.03747 / 2.52 ( 985) hydrogen bonds : angle 3.83312 / 2.70 ( 2815) metal coordination : bond 0.01030 / 0.68 ( 40) metal coordination : angle 2.86572 / 1.98 ( 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 372 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 332 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8126 (mp0) cc_final: 0.7920 (mp0) REVERT: B 84 ILE cc_start: 0.9086 (mt) cc_final: 0.8722 (tt) REVERT: B 92 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7882 (tm-30) REVERT: C 203 MET cc_start: 0.8965 (mtm) cc_final: 0.8733 (mtm) REVERT: D 19 TRP cc_start: 0.8422 (p-90) cc_final: 0.7801 (p-90) REVERT: D 34 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8428 (mmtt) REVERT: D 227 TYR cc_start: 0.9172 (p90) cc_final: 0.8673 (p90) REVERT: b 4 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7410 (mm110) REVERT: b 10 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8096 (tm-30) REVERT: b 20 LYS cc_start: 0.8901 (tttt) cc_final: 0.7768 (pttm) REVERT: b 38 GLU cc_start: 0.8590 (tp30) cc_final: 0.8376 (tp30) REVERT: b 45 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8524 (p) REVERT: F 84 ILE cc_start: 0.9087 (mt) cc_final: 0.8793 (tt) REVERT: F 116 ASP cc_start: 0.8116 (p0) cc_final: 0.7696 (p0) REVERT: F 170 GLN cc_start: 0.7998 (tt0) cc_final: 0.7703 (tt0) REVERT: G 203 MET cc_start: 0.9015 (mtp) cc_final: 0.8767 (mtm) REVERT: G 255 GLU cc_start: 0.8465 (tp30) cc_final: 0.7948 (tp30) REVERT: G 257 GLU cc_start: 0.8556 (mp0) cc_final: 0.8193 (mp0) REVERT: H 224 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7881 (mmmt) REVERT: H 227 TYR cc_start: 0.9174 (p90) cc_final: 0.8871 (p90) REVERT: f 10 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8100 (tm-30) REVERT: f 20 LYS cc_start: 0.8656 (mttt) cc_final: 0.7531 (pttp) outliers start: 40 outliers final: 36 residues processed: 353 average time/residue: 0.1782 time to fit residues: 89.9845 Evaluate side-chains 365 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 327 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 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 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 30 THR 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 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 179 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 136 optimal weight: 0.0070 chunk 4 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 F 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.070022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.050749 restraints weight = 79686.686| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 3.41 r_work: 0.2416 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19462 Z= 0.129 Angle : 0.580 8.464 26650 Z= 0.303 Chirality : 0.040 0.151 3014 Planarity : 0.005 0.065 3188 Dihedral : 9.054 58.982 3218 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 2.25 % Allowed : 20.50 % Favored : 77.25 % 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: 1.43 (0.18), residues: 2156 helix: 2.41 (0.17), residues: 1020 sheet: 1.04 (0.23), residues: 474 loop : -1.59 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 91 TYR 0.038 0.002 TYR C 171 PHE 0.036 0.001 PHE E 220 TRP 0.034 0.001 TRP H 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (19422) covalent geometry : angle 0.57606 / 0.30 (26632) hydrogen bonds : bond 0.03892 / 2.61 ( 985) hydrogen bonds : angle 3.83893 / 2.70 ( 2815) metal coordination : bond 0.01021 / 0.63 ( 40) metal coordination : angle 2.77193 / 1.93 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4622.85 seconds wall clock time: 79 minutes 59.32 seconds (4799.32 seconds total)