Starting phenix.real_space_refine on Thu Feb 5 17:48:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmu_54068/02_2026/9rmu_54068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmu_54068/02_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_54068/02_2026/9rmu_54068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmu_54068/02_2026/9rmu_54068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rmu_54068/02_2026/9rmu_54068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmu_54068/02_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-2.0-5952/lib/python3.9/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: 5.62, per 1000 atoms: 0.30 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: 1.49 Conformation dependent library (CDL) restraints added in 961.3 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: 2.46 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: 3.35 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5909 1.34 - 1.45: 2961 1.45 - 1.57: 10321 1.57 - 1.69: 123 1.69 - 1.81: 108 Bond restraints: 19422 Sorted by residual: bond pdb=" CB GLN H 216 " pdb=" CG GLN H 216 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.08e+00 bond pdb=" CB GLN D 216 " pdb=" CG GLN D 216 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CB ASP E 193 " pdb=" CG ASP E 193 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.73e+00 bond pdb=" CB ASP A 193 " pdb=" CG ASP A 193 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.71e+00 bond pdb=" C ILE C 5 " pdb=" N PRO C 6 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.69e+00 ... (remaining 19417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 26360 1.64 - 3.29: 210 3.29 - 4.93: 49 4.93 - 6.58: 11 6.58 - 8.22: 2 Bond angle restraints: 26632 Sorted by residual: angle pdb=" CB GLN H 216 " pdb=" CG GLN H 216 " pdb=" CD GLN H 216 " ideal model delta sigma weight residual 112.60 118.66 -6.06 1.70e+00 3.46e-01 1.27e+01 angle pdb=" CA GLN H 216 " pdb=" CB GLN H 216 " pdb=" CG GLN H 216 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA GLU G 246 " pdb=" CB GLU G 246 " pdb=" CG GLU G 246 " ideal model delta sigma weight residual 114.10 119.82 -5.72 2.00e+00 2.50e-01 8.17e+00 angle pdb=" CA GLN D 216 " pdb=" CB GLN D 216 " pdb=" CG GLN D 216 " ideal model delta sigma weight residual 114.10 119.68 -5.58 2.00e+00 2.50e-01 7.78e+00 angle pdb=" C GLN H 216 " pdb=" CA GLN H 216 " pdb=" CB GLN H 216 " ideal model delta sigma weight residual 110.42 115.69 -5.27 1.99e+00 2.53e-01 7.02e+00 ... (remaining 26627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10189 17.76 - 35.53: 1078 35.53 - 53.29: 244 53.29 - 71.05: 86 71.05 - 88.82: 27 Dihedral angle restraints: 11624 sinusoidal: 5266 harmonic: 6358 Sorted by residual: dihedral pdb=" CB GLU G 10 " pdb=" CG GLU G 10 " pdb=" CD GLU G 10 " pdb=" OE1 GLU G 10 " ideal model delta sinusoidal sigma weight residual 0.00 87.35 -87.35 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU C 10 " pdb=" CG GLU C 10 " pdb=" CD GLU C 10 " pdb=" OE1 GLU C 10 " ideal model delta sinusoidal sigma weight residual 0.00 87.04 -87.04 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU H 38 " pdb=" CG GLU H 38 " pdb=" CD GLU H 38 " pdb=" OE1 GLU H 38 " ideal model delta sinusoidal sigma weight residual 0.00 85.92 -85.92 1 3.00e+01 1.11e-03 9.91e+00 ... (remaining 11621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1863 0.025 - 0.051: 728 0.051 - 0.076: 218 0.076 - 0.101: 108 0.101 - 0.126: 97 Chirality restraints: 3014 Sorted by residual: chirality pdb=" CA ILE D 269 " pdb=" N ILE D 269 " pdb=" C ILE D 269 " pdb=" CB ILE D 269 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL H 141 " pdb=" N VAL H 141 " pdb=" C VAL H 141 " pdb=" CB VAL H 141 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL H 250 " pdb=" N VAL H 250 " pdb=" C VAL H 250 " pdb=" CB VAL H 250 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 3011 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 193 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ASP A 193 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A 193 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 194 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 193 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C ASP E 193 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP E 193 " 0.013 2.00e-02 2.50e+03 pdb=" N MET E 194 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU f 28 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO f 29 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO f 29 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO f 29 " -0.022 5.00e-02 4.00e+02 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 8379 2.97 - 3.45: 17833 3.45 - 3.93: 30128 3.93 - 4.42: 32732 4.42 - 4.90: 54276 Nonbonded interactions: 143348 Sorted by model distance: nonbonded pdb=" N GLU G 246 " pdb=" OE1 GLU G 246 " model vdw 2.484 3.120 nonbonded pdb=" O ASP A 193 " pdb=" OD1 ASP A 193 " model vdw 2.490 3.040 nonbonded pdb=" O ASP E 193 " pdb=" OD1 ASP E 193 " model vdw 2.492 3.040 nonbonded pdb=" N GLU C 246 " pdb=" OE1 GLU C 246 " model vdw 2.537 3.120 nonbonded pdb=" N GLN G 170 " pdb=" OE1 GLN G 170 " model vdw 2.547 3.120 ... (remaining 143343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 141 \ or resid 148 through 301)) selection = (chain 'B' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 269 \ or resid 301)) selection = (chain 'C' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 141 \ or resid 148 through 269 or resid 301)) selection = (chain 'D' and (resid 1 through 8 or resid 10 through 141 or resid 148 through 2 \ 69 or resid 301)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 141 \ or resid 148 through 301)) selection = (chain 'F' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 269 \ or resid 301)) selection = (chain 'G' and (resid 1 through 8 or resid 10 through 44 or resid 56 through 141 \ or resid 148 through 269 or resid 301)) selection = (chain 'H' and (resid 1 through 8 or resid 10 through 141 or resid 148 through 2 \ 69 or resid 301)) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.360 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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= 0.214 Angle : 0.481 10.692 26650 Z= 0.230 Chirality : 0.037 0.126 3014 Planarity : 0.003 0.039 3188 Dihedral : 15.866 88.816 7496 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.12 % Allowed : 18.15 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 2156 helix: 2.65 (0.17), residues: 994 sheet: 0.58 (0.25), residues: 446 loop : -0.93 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 91 TYR 0.008 0.001 TYR E 205 PHE 0.011 0.001 PHE B 220 TRP 0.011 0.001 TRP D 19 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00200 (19422) covalent geometry : angle 0.43957 (26632) hydrogen bonds : bond 0.12789 ( 985) hydrogen bonds : angle 4.92023 ( 2815) metal coordination : bond 0.19591 ( 40) metal coordination : angle 7.50233 ( 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 : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 SER cc_start: 0.8601 (t) cc_final: 0.8133 (p) REVERT: A 170 GLN cc_start: 0.7721 (tt0) cc_final: 0.7418 (tt0) REVERT: A 171 TYR cc_start: 0.8728 (m-80) cc_final: 0.8142 (m-80) REVERT: B 3 GLU cc_start: 0.8364 (tp30) cc_final: 0.7542 (mm-30) REVERT: B 15 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6019 (p90) REVERT: B 46 GLN cc_start: 0.8612 (pt0) cc_final: 0.8395 (pt0) REVERT: B 83 TYR cc_start: 0.8846 (t80) cc_final: 0.8636 (t80) REVERT: B 84 ILE cc_start: 0.9166 (mt) cc_final: 0.8815 (tt) REVERT: B 255 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7815 (mp0) REVERT: B 257 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8030 (mp0) REVERT: C 110 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8782 (tt) REVERT: C 203 MET cc_start: 0.8598 (mtp) cc_final: 0.8335 (mtm) REVERT: C 257 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8267 (mp0) REVERT: D 27 LYS cc_start: 0.8844 (mttt) cc_final: 0.8430 (mmtt) REVERT: b 10 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7320 (tm-30) REVERT: b 11 GLU cc_start: 0.7768 (tt0) cc_final: 0.7349 (tt0) REVERT: b 20 LYS cc_start: 0.8686 (tttt) cc_final: 0.7534 (pttm) REVERT: b 43 CYS cc_start: 0.5861 (m) cc_final: 0.5661 (m) REVERT: E 28 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8487 (pt) REVERT: E 170 GLN cc_start: 0.8058 (tt0) cc_final: 0.7678 (tt0) REVERT: F 15 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.6279 (p90) REVERT: F 46 GLN cc_start: 0.8685 (pt0) cc_final: 0.8223 (pp30) REVERT: F 84 ILE cc_start: 0.9203 (mt) cc_final: 0.8882 (tt) REVERT: F 246 GLU cc_start: 0.7880 (mp0) cc_final: 0.7570 (mp0) REVERT: G 10 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7369 (mt-10) REVERT: G 203 MET cc_start: 0.8691 (mtp) cc_final: 0.8432 (mtm) REVERT: G 257 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8138 (mp0) REVERT: G 264 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8223 (ptt-90) REVERT: H 19 TRP cc_start: 0.7843 (p-90) cc_final: 0.7595 (p-90) REVERT: H 23 LYS cc_start: 0.8516 (mttt) cc_final: 0.8254 (mttp) REVERT: H 34 LYS cc_start: 0.8351 (mtpp) cc_final: 0.7937 (mmtt) REVERT: H 63 MET cc_start: 0.8847 (ttm) cc_final: 0.8542 (ttm) REVERT: H 227 TYR cc_start: 0.8434 (p90) cc_final: 0.8132 (p90) REVERT: H 228 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7351 (tpp80) REVERT: H 257 GLU cc_start: 0.8002 (tp30) cc_final: 0.7677 (tt0) REVERT: f 20 LYS cc_start: 0.8093 (mttt) cc_final: 0.7302 (pttt) outliers start: 21 outliers final: 7 residues processed: 403 average time/residue: 0.1872 time to fit residues: 106.5794 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 : 0.729 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 114 HIS A 117 ASN A 202 ASN D 17 ASN D 114 HIS D 240 HIS E 67 HIS E 114 HIS E 117 ASN ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3069 r_free = 0.3069 target = 0.071427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.052030 restraints weight = 77889.160| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 3.30 r_work: 0.2451 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19462 Z= 0.146 Angle : 0.518 8.394 26650 Z= 0.274 Chirality : 0.040 0.175 3014 Planarity : 0.004 0.043 3188 Dihedral : 8.812 58.976 3226 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.94 % Allowed : 17.13 % Favored : 79.93 % 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: 2.55 (0.17), residues: 1010 sheet: 0.67 (0.23), residues: 482 loop : -1.14 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 91 TYR 0.016 0.002 TYR G 272 PHE 0.011 0.001 PHE H 220 TRP 0.015 0.001 TRP A 19 HIS 0.006 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00336 (19422) covalent geometry : angle 0.51343 (26632) hydrogen bonds : bond 0.04484 ( 985) hydrogen bonds : angle 4.05280 ( 2815) metal coordination : bond 0.01150 ( 40) metal coordination : angle 2.58803 ( 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 402 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 347 time to evaluate : 0.734 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: A 171 TYR cc_start: 0.8964 (m-80) cc_final: 0.8675 (m-80) REVERT: B 46 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8241 (pp30) REVERT: B 84 ILE cc_start: 0.9064 (mt) cc_final: 0.8750 (tt) REVERT: C 64 ASP cc_start: 0.8543 (m-30) cc_final: 0.8315 (m-30) REVERT: C 203 MET cc_start: 0.8973 (mtp) cc_final: 0.8764 (mtm) REVERT: D 25 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8118 (tpp80) REVERT: D 125 GLU cc_start: 0.8229 (mp0) cc_final: 0.7952 (mp0) REVERT: D 227 TYR cc_start: 0.9110 (p90) cc_final: 0.8829 (p90) REVERT: b 10 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7865 (tm-30) REVERT: b 11 GLU cc_start: 0.8159 (tt0) cc_final: 0.7682 (tp30) REVERT: b 20 LYS cc_start: 0.8878 (tttt) cc_final: 0.7785 (pttt) REVERT: F 23 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8862 (tptp) REVERT: F 46 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8469 (pp30) REVERT: F 116 ASP cc_start: 0.8073 (p0) cc_final: 0.7656 (p0) REVERT: F 136 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7427 (tm-30) REVERT: G 203 MET cc_start: 0.8984 (mtp) cc_final: 0.8763 (mtm) REVERT: G 264 ARG cc_start: 0.8942 (mtm-85) cc_final: 0.8562 (ptt-90) REVERT: H 224 LYS cc_start: 0.8279 (mmmt) cc_final: 0.8060 (mmmt) REVERT: H 226 TYR cc_start: 0.7721 (m-10) cc_final: 0.7482 (m-10) REVERT: H 227 TYR cc_start: 0.9074 (p90) cc_final: 0.8848 (p90) REVERT: f 10 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7911 (tm-30) REVERT: f 20 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7517 (pttp) outliers start: 55 outliers final: 34 residues processed: 378 average time/residue: 0.1829 time to fit residues: 97.9593 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 : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 15 TYR 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 22 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 HIS 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 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 23 LYS 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 31 ILE 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: 1.9990 chunk 160 optimal weight: 0.4980 chunk 115 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 117 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 ASN D 114 HIS b 46 GLN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 114 HIS H 155 ASN f 46 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.070346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.050232 restraints weight = 98368.962| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 3.79 r_work: 0.2390 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19462 Z= 0.142 Angle : 0.514 7.635 26650 Z= 0.273 Chirality : 0.040 0.163 3014 Planarity : 0.005 0.054 3188 Dihedral : 8.932 59.861 3218 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.84 % Allowed : 17.51 % Favored : 79.66 % 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: 1.37 (0.18), residues: 2156 helix: 2.39 (0.17), residues: 1016 sheet: 0.86 (0.24), residues: 452 loop : -1.42 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 91 TYR 0.013 0.001 TYR G 272 PHE 0.014 0.001 PHE E 1 TRP 0.014 0.001 TRP D 19 HIS 0.006 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00331 (19422) covalent geometry : angle 0.50838 (26632) hydrogen bonds : bond 0.04458 ( 985) hydrogen bonds : angle 3.99123 ( 2815) metal coordination : bond 0.01630 ( 40) metal coordination : angle 3.01320 ( 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 393 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 340 time to evaluate : 0.778 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: 0.9067 (mt) cc_final: 0.8731 (tt) REVERT: B 92 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 255 GLU cc_start: 0.8265 (mp0) cc_final: 0.7987 (pm20) REVERT: C 64 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: D 25 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8058 (tpp80) REVERT: D 27 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8487 (mmtt) REVERT: D 63 MET cc_start: 0.9070 (ttm) cc_final: 0.8506 (ttm) REVERT: D 227 TYR cc_start: 0.9170 (p90) cc_final: 0.8801 (p90) REVERT: b 4 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7356 (mm110) REVERT: b 7 GLU cc_start: 0.8494 (tp30) cc_final: 0.8160 (tp30) REVERT: b 10 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7934 (tm-30) REVERT: b 11 GLU cc_start: 0.8152 (tt0) cc_final: 0.7732 (tp30) REVERT: b 20 LYS cc_start: 0.8942 (tttt) cc_final: 0.7853 (pttt) REVERT: F 116 ASP cc_start: 0.8051 (p0) cc_final: 0.7645 (p0) REVERT: G 255 GLU cc_start: 0.8434 (tp30) cc_final: 0.8062 (tp30) REVERT: G 257 GLU cc_start: 0.8609 (mp0) cc_final: 0.8387 (mp0) REVERT: H 63 MET cc_start: 0.9026 (ttm) cc_final: 0.8476 (ttm) REVERT: H 227 TYR cc_start: 0.9109 (p90) cc_final: 0.8877 (p90) REVERT: f 10 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8118 (tm-30) REVERT: f 20 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7581 (pttm) outliers start: 53 outliers final: 38 residues processed: 371 average time/residue: 0.1826 time to fit residues: 96.2160 Evaluate side-chains 371 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 330 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 2 VAL 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 141 VAL Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 64 ASP 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 45 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 44 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 G residue 269 ILE Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 153 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 0.5980 chunk 193 optimal weight: 0.3980 chunk 22 optimal weight: 0.0030 chunk 205 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 157 optimal weight: 0.0870 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 117 ASN B 163 GLN D 219 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN F 163 GLN H 17 ASN H 114 HIS H 219 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.071844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.051708 restraints weight = 100572.750| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 3.85 r_work: 0.2439 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 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 = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19462 Z= 0.098 Angle : 0.484 7.598 26650 Z= 0.253 Chirality : 0.039 0.160 3014 Planarity : 0.004 0.052 3188 Dihedral : 8.813 59.926 3218 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 2.41 % Allowed : 18.58 % Favored : 79.01 % 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: 1.55 (0.19), residues: 2156 helix: 2.53 (0.17), residues: 1014 sheet: 0.94 (0.24), residues: 450 loop : -1.29 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 91 TYR 0.025 0.001 TYR A 171 PHE 0.013 0.001 PHE A 1 TRP 0.011 0.001 TRP E 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00215 (19422) covalent geometry : angle 0.47776 (26632) hydrogen bonds : bond 0.03367 ( 985) hydrogen bonds : angle 3.79532 ( 2815) metal coordination : bond 0.01016 ( 40) metal coordination : angle 2.91183 ( 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 380 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 335 time to evaluate : 0.781 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 46 GLN cc_start: 0.8665 (pt0) cc_final: 0.8388 (pt0) REVERT: B 84 ILE cc_start: 0.9057 (mt) cc_final: 0.8713 (tt) REVERT: B 92 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 255 GLU cc_start: 0.8279 (mp0) cc_final: 0.7907 (mp0) REVERT: C 64 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: D 19 TRP cc_start: 0.8234 (p-90) cc_final: 0.7609 (p-90) REVERT: D 25 ARG cc_start: 0.8464 (tpp80) cc_final: 0.8094 (tpp80) REVERT: D 34 LYS cc_start: 0.8896 (mtpp) cc_final: 0.8395 (mmtt) REVERT: D 131 TRP cc_start: 0.9132 (t60) cc_final: 0.8921 (t60) REVERT: D 216 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6518 (mm-40) REVERT: D 227 TYR cc_start: 0.9176 (p90) cc_final: 0.8763 (p90) REVERT: D 244 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7877 (ttmm) REVERT: b 4 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7310 (mm110) REVERT: b 7 GLU cc_start: 0.8509 (tp30) cc_final: 0.8196 (tp30) REVERT: b 10 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7917 (tm-30) REVERT: b 11 GLU cc_start: 0.8132 (tt0) cc_final: 0.7880 (tt0) REVERT: b 20 LYS cc_start: 0.8902 (tttt) cc_final: 0.7849 (pttt) REVERT: F 84 ILE cc_start: 0.9088 (mt) cc_final: 0.8800 (tt) REVERT: F 116 ASP cc_start: 0.8021 (p0) cc_final: 0.7586 (p0) REVERT: G 255 GLU cc_start: 0.8457 (tp30) cc_final: 0.8008 (tp30) REVERT: G 257 GLU cc_start: 0.8445 (mp0) cc_final: 0.8167 (mp0) REVERT: H 19 TRP cc_start: 0.8505 (p-90) cc_final: 0.8187 (p-90) REVERT: f 10 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8041 (tm-30) REVERT: f 11 GLU cc_start: 0.8142 (tt0) cc_final: 0.7733 (tt0) REVERT: f 20 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7538 (pttp) outliers start: 45 outliers final: 25 residues processed: 357 average time/residue: 0.1884 time to fit residues: 94.3373 Evaluate side-chains 352 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 222 ASP 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 216 GLN 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 234 LEU Chi-restraints excluded: chain G residue 9 GLN 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 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: 1.9990 chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 170 GLN F 163 GLN G 117 ASN H 114 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.068115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.048354 restraints weight = 91859.050| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 3.69 r_work: 0.2346 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2348 r_free = 0.2348 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2348 r_free = 0.2348 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19462 Z= 0.182 Angle : 0.574 7.584 26650 Z= 0.304 Chirality : 0.042 0.191 3014 Planarity : 0.005 0.058 3188 Dihedral : 9.089 58.925 3218 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 3.16 % Allowed : 18.20 % Favored : 78.64 % 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: 1.24 (0.18), residues: 2156 helix: 2.24 (0.17), residues: 1016 sheet: 1.14 (0.24), residues: 422 loop : -1.56 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 91 TYR 0.028 0.002 TYR A 171 PHE 0.014 0.002 PHE H 1 TRP 0.015 0.001 TRP A 19 HIS 0.007 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00436 (19422) covalent geometry : angle 0.56899 (26632) hydrogen bonds : bond 0.05163 ( 985) hydrogen bonds : angle 4.07486 ( 2815) metal coordination : bond 0.01461 ( 40) metal coordination : angle 2.91892 ( 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 397 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.8730 (m90) cc_final: 0.8300 (m-70) REVERT: B 46 GLN cc_start: 0.8742 (pt0) cc_final: 0.8505 (pt0) REVERT: B 92 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7683 (tm-30) REVERT: D 19 TRP cc_start: 0.8329 (p-90) cc_final: 0.7291 (p-90) REVERT: D 25 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8136 (tpp80) REVERT: D 34 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8326 (mppt) REVERT: D 171 TYR cc_start: 0.8213 (m-10) cc_final: 0.7929 (m-10) REVERT: D 216 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6487 (mm-40) REVERT: D 227 TYR cc_start: 0.9212 (p90) cc_final: 0.8786 (p90) REVERT: D 244 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7963 (ttmm) REVERT: b 4 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7404 (mm110) REVERT: b 7 GLU cc_start: 0.8441 (tp30) cc_final: 0.7906 (tp30) REVERT: b 10 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7916 (tm-30) REVERT: b 11 GLU cc_start: 0.8181 (tt0) cc_final: 0.7767 (tp30) REVERT: b 20 LYS cc_start: 0.8979 (tttt) cc_final: 0.7808 (pttm) REVERT: E 225 VAL cc_start: 0.8742 (t) cc_final: 0.8537 (p) REVERT: F 46 GLN cc_start: 0.8959 (pt0) cc_final: 0.8685 (pp30) REVERT: G 255 GLU cc_start: 0.8427 (tp30) cc_final: 0.7982 (tp30) REVERT: G 257 GLU cc_start: 0.8444 (mp0) cc_final: 0.8103 (mp0) REVERT: H 19 TRP cc_start: 0.8586 (p-90) cc_final: 0.7960 (p-90) REVERT: H 34 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8589 (mmtt) REVERT: f 10 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8136 (tm-30) REVERT: f 20 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.7575 (pttm) outliers start: 59 outliers final: 43 residues processed: 369 average time/residue: 0.1823 time to fit residues: 95.5143 Evaluate side-chains 369 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 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 A residue 159 LYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 2 VAL 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 211 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 269 ILE 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 216 GLN 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 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 31 ILE 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 269 ILE Chi-restraints excluded: chain H residue 5 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 260 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 42 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 184 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 159 optimal weight: 0.4980 chunk 215 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 ASN D 240 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN H 114 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.069508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.049621 restraints weight = 96733.331| |-----------------------------------------------------------------------------| r_work (start): 0.2531 rms_B_bonded: 3.78 r_work: 0.2382 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19462 Z= 0.119 Angle : 0.532 7.186 26650 Z= 0.277 Chirality : 0.040 0.189 3014 Planarity : 0.004 0.055 3188 Dihedral : 8.966 58.897 3218 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Rotamer: Outliers : 2.73 % Allowed : 19.86 % Favored : 77.41 % 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: 1.38 (0.18), residues: 2156 helix: 2.41 (0.17), residues: 1018 sheet: 1.12 (0.24), residues: 424 loop : -1.55 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 91 TYR 0.033 0.001 TYR A 171 PHE 0.014 0.001 PHE A 1 TRP 0.013 0.001 TRP A 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00275 (19422) covalent geometry : angle 0.52692 (26632) hydrogen bonds : bond 0.03905 ( 985) hydrogen bonds : angle 3.87768 ( 2815) metal coordination : bond 0.01094 ( 40) metal coordination : angle 2.90148 ( 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 383 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 332 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.8763 (pt0) cc_final: 0.8532 (pt0) REVERT: B 92 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 19 TRP cc_start: 0.8383 (p-90) cc_final: 0.7509 (p-90) REVERT: D 34 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8441 (mmtt) REVERT: D 216 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6655 (mm-40) REVERT: D 227 TYR cc_start: 0.9205 (p90) cc_final: 0.8746 (p90) REVERT: D 244 LYS cc_start: 0.8202 (tmtt) cc_final: 0.8001 (ttmm) REVERT: b 4 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7395 (mm110) REVERT: b 10 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8054 (tm-30) REVERT: b 11 GLU cc_start: 0.8263 (tt0) cc_final: 0.7793 (tp30) REVERT: b 20 LYS cc_start: 0.8957 (tttt) cc_final: 0.7838 (pttm) REVERT: b 34 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8172 (mppt) REVERT: F 46 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8692 (pp30) REVERT: G 10 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7736 (mt-10) REVERT: G 255 GLU cc_start: 0.8420 (tp30) cc_final: 0.7960 (tp30) REVERT: G 257 GLU cc_start: 0.8488 (mp0) cc_final: 0.8148 (mp0) REVERT: H 19 TRP cc_start: 0.8569 (p-90) cc_final: 0.7939 (p-90) REVERT: H 34 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8615 (mmtt) REVERT: f 10 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8131 (tm-30) REVERT: f 20 LYS cc_start: 0.8806 (mttt) cc_final: 0.7608 (pttp) outliers start: 51 outliers final: 39 residues processed: 362 average time/residue: 0.1877 time to fit residues: 95.6773 Evaluate side-chains 369 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 326 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 2 VAL 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 251 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 216 GLN 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 34 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 31 ILE Chi-restraints excluded: chain F residue 46 GLN 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 5 ILE 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 23 LYS Chi-restraints excluded: chain f residue 42 LYS 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: 1.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 125 optimal weight: 0.0010 chunk 154 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 117 ASN ** D 16 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.070379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.050671 restraints weight = 95434.464| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 3.67 r_work: 0.2416 rms_B_bonded: 3.95 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 = 0.25 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 = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3236 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= 0.111 Angle : 0.529 7.174 26650 Z= 0.274 Chirality : 0.039 0.267 3014 Planarity : 0.004 0.055 3188 Dihedral : 8.899 58.870 3218 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 2.62 % Allowed : 20.02 % 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: 1.47 (0.18), residues: 2156 helix: 2.50 (0.17), residues: 1020 sheet: 1.11 (0.24), residues: 442 loop : -1.58 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 91 TYR 0.020 0.001 TYR H 227 PHE 0.015 0.001 PHE E 1 TRP 0.018 0.001 TRP D 131 HIS 0.004 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00254 (19422) covalent geometry : angle 0.52477 (26632) hydrogen bonds : bond 0.03588 ( 985) hydrogen bonds : angle 3.79678 ( 2815) metal coordination : bond 0.00966 ( 40) metal coordination : angle 2.74613 ( 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 378 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 329 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.8713 (pt0) cc_final: 0.8442 (pt0) REVERT: B 92 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 255 GLU cc_start: 0.8478 (pm20) cc_final: 0.8262 (pm20) REVERT: B 257 GLU cc_start: 0.7935 (mp0) cc_final: 0.7732 (mp0) REVERT: D 19 TRP cc_start: 0.8367 (p-90) cc_final: 0.7501 (p-90) REVERT: D 34 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8403 (mmtt) REVERT: D 216 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6542 (mm-40) REVERT: D 227 TYR cc_start: 0.9190 (p90) cc_final: 0.8688 (p90) REVERT: D 244 LYS cc_start: 0.8184 (tmtt) cc_final: 0.7976 (ttmm) REVERT: b 4 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7379 (mm110) REVERT: b 10 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7980 (tm-30) REVERT: b 11 GLU cc_start: 0.8226 (tt0) cc_final: 0.7994 (tt0) REVERT: b 20 LYS cc_start: 0.8925 (tttt) cc_final: 0.7797 (pttm) REVERT: F 46 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8596 (pp30) REVERT: F 84 ILE cc_start: 0.9087 (mt) cc_final: 0.8796 (tt) REVERT: F 116 ASP cc_start: 0.8084 (p0) cc_final: 0.7665 (p0) REVERT: G 255 GLU cc_start: 0.8386 (tp30) cc_final: 0.7847 (tp30) REVERT: G 257 GLU cc_start: 0.8459 (mp0) cc_final: 0.8082 (mp0) REVERT: H 19 TRP cc_start: 0.8562 (p-90) cc_final: 0.7999 (p-90) REVERT: H 34 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8575 (mmtt) REVERT: f 10 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8087 (tm-30) REVERT: f 11 GLU cc_start: 0.8236 (tt0) cc_final: 0.7880 (tt0) REVERT: f 20 LYS cc_start: 0.8770 (mttt) cc_final: 0.7620 (pttp) outliers start: 49 outliers final: 37 residues processed: 357 average time/residue: 0.1861 time to fit residues: 94.1164 Evaluate side-chains 364 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 324 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 2 VAL 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 153 ASN Chi-restraints excluded: chain D residue 167 ASP 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 216 GLN 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 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 5 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 42 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 187 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 117 ASN B 163 GLN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 117 ASN H 240 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.069688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.050237 restraints weight = 81016.917| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 3.41 r_work: 0.2406 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3313 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= 0.124 Angle : 0.546 9.146 26650 Z= 0.283 Chirality : 0.039 0.193 3014 Planarity : 0.004 0.057 3188 Dihedral : 8.916 58.861 3218 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 2.46 % Allowed : 20.13 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.18), residues: 2156 helix: 2.51 (0.17), residues: 1020 sheet: 1.10 (0.23), residues: 462 loop : -1.65 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 91 TYR 0.024 0.001 TYR C 171 PHE 0.015 0.001 PHE A 1 TRP 0.014 0.001 TRP D 131 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00291 (19422) covalent geometry : angle 0.54168 (26632) hydrogen bonds : bond 0.03824 ( 985) hydrogen bonds : angle 3.83594 ( 2815) metal coordination : bond 0.01011 ( 40) metal coordination : angle 2.59098 ( 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 373 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.8736 (pt0) cc_final: 0.8494 (pt0) REVERT: B 84 ILE cc_start: 0.9075 (mt) cc_final: 0.8788 (tt) REVERT: B 92 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 163 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8334 (tp40) REVERT: D 19 TRP cc_start: 0.8357 (p-90) cc_final: 0.7521 (p-90) REVERT: D 34 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8464 (mmtt) REVERT: D 216 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6680 (mm-40) REVERT: D 227 TYR cc_start: 0.9208 (p90) cc_final: 0.8724 (p90) REVERT: b 4 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7373 (mm110) REVERT: b 10 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8039 (tm-30) REVERT: b 11 GLU cc_start: 0.8230 (tt0) cc_final: 0.8010 (tt0) REVERT: b 20 LYS cc_start: 0.8944 (tttt) cc_final: 0.7836 (pttm) REVERT: b 34 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8135 (mppt) REVERT: F 46 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8604 (pp30) REVERT: F 84 ILE cc_start: 0.9079 (mt) cc_final: 0.8802 (tt) REVERT: F 116 ASP cc_start: 0.8091 (p0) cc_final: 0.7675 (p0) REVERT: G 255 GLU cc_start: 0.8393 (tp30) cc_final: 0.7831 (tp30) REVERT: G 257 GLU cc_start: 0.8488 (mp0) cc_final: 0.8102 (mp0) REVERT: H 19 TRP cc_start: 0.8518 (p-90) cc_final: 0.7995 (p-90) REVERT: H 34 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8598 (mmtt) REVERT: f 10 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8122 (tm-30) REVERT: f 20 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.7639 (pttp) outliers start: 46 outliers final: 36 residues processed: 352 average time/residue: 0.1822 time to fit residues: 90.5165 Evaluate side-chains 367 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 216 GLN 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 34 LYS Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 15 TYR Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 64 ASP 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 251 LEU Chi-restraints excluded: chain H residue 5 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 20 LYS Chi-restraints excluded: chain f residue 23 LYS Chi-restraints excluded: chain f residue 42 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 59 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 84 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 163 GLN ** D 16 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 H 240 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.070011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.051145 restraints weight = 67445.219| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 2.97 r_work: 0.2434 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 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 = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3348 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= 0.121 Angle : 0.563 8.992 26650 Z= 0.292 Chirality : 0.040 0.290 3014 Planarity : 0.005 0.064 3188 Dihedral : 8.912 58.843 3218 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Rotamer: Outliers : 2.36 % Allowed : 20.29 % 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: 1.48 (0.18), residues: 2156 helix: 2.52 (0.17), residues: 1020 sheet: 1.13 (0.23), residues: 442 loop : -1.60 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 91 TYR 0.047 0.002 TYR C 171 PHE 0.016 0.001 PHE E 1 TRP 0.014 0.001 TRP D 131 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00283 (19422) covalent geometry : angle 0.55949 (26632) hydrogen bonds : bond 0.03699 ( 985) hydrogen bonds : angle 3.80615 ( 2815) metal coordination : bond 0.00961 ( 40) metal coordination : angle 2.58362 ( 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 374 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 330 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.8675 (pt0) cc_final: 0.8433 (pt0) REVERT: B 84 ILE cc_start: 0.9060 (mt) cc_final: 0.8790 (tt) REVERT: B 92 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7689 (tm-30) REVERT: D 19 TRP cc_start: 0.8320 (p-90) cc_final: 0.7517 (p-90) REVERT: D 34 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8519 (mmtt) REVERT: D 216 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6589 (mm-40) REVERT: D 224 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8241 (mmtm) REVERT: D 227 TYR cc_start: 0.9181 (p90) cc_final: 0.8677 (p90) REVERT: b 4 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7377 (mm110) REVERT: b 10 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7947 (tm-30) REVERT: b 11 GLU cc_start: 0.8171 (tt0) cc_final: 0.7938 (tt0) REVERT: b 20 LYS cc_start: 0.8916 (tttt) cc_final: 0.7843 (pttm) REVERT: F 46 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8545 (pp30) REVERT: F 84 ILE cc_start: 0.9072 (mt) cc_final: 0.8792 (tt) REVERT: F 116 ASP cc_start: 0.7995 (p0) cc_final: 0.7605 (p0) REVERT: G 257 GLU cc_start: 0.8419 (mp0) cc_final: 0.8141 (mp0) REVERT: f 10 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8080 (tm-30) REVERT: f 20 LYS cc_start: 0.8729 (mttt) cc_final: 0.7660 (pttp) REVERT: f 25 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7843 (ttm170) outliers start: 44 outliers final: 39 residues processed: 356 average time/residue: 0.1942 time to fit residues: 97.5134 Evaluate side-chains 368 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 326 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 234 LEU 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 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 216 GLN 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 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 46 GLN 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 30 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 5 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 23 LYS Chi-restraints excluded: chain f residue 42 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 136 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** D 16 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 H 240 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.069294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.049333 restraints weight = 105096.608| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 3.91 r_work: 0.2370 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19462 Z= 0.140 Angle : 0.581 8.818 26650 Z= 0.302 Chirality : 0.041 0.286 3014 Planarity : 0.005 0.064 3188 Dihedral : 8.976 58.836 3218 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 2.41 % Allowed : 19.86 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.18), residues: 2156 helix: 2.48 (0.17), residues: 1018 sheet: 1.03 (0.22), residues: 492 loop : -1.68 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 91 TYR 0.032 0.002 TYR A 171 PHE 0.017 0.001 PHE A 1 TRP 0.014 0.001 TRP D 131 HIS 0.004 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00336 (19422) covalent geometry : angle 0.57750 (26632) hydrogen bonds : bond 0.04125 ( 985) hydrogen bonds : angle 3.87635 ( 2815) metal coordination : bond 0.01104 ( 40) metal coordination : angle 2.56359 ( 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 369 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.8766 (pt0) cc_final: 0.8521 (pt0) REVERT: B 84 ILE cc_start: 0.9063 (mt) cc_final: 0.8796 (tt) REVERT: D 19 TRP cc_start: 0.8367 (p-90) cc_final: 0.7588 (p-90) REVERT: D 34 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8582 (mmtt) REVERT: D 95 ARG cc_start: 0.8750 (ptm160) cc_final: 0.8484 (ptm-80) REVERT: D 216 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6768 (mm-40) REVERT: D 224 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8261 (mmtm) REVERT: D 227 TYR cc_start: 0.9155 (p90) cc_final: 0.8633 (p90) REVERT: D 244 LYS cc_start: 0.8214 (tmtt) cc_final: 0.8005 (ttmm) REVERT: b 4 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7450 (mm110) REVERT: b 10 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8055 (tm-30) REVERT: b 11 GLU cc_start: 0.8270 (tt0) cc_final: 0.7840 (tp30) REVERT: b 20 LYS cc_start: 0.8960 (tttt) cc_final: 0.7882 (pttm) REVERT: b 34 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8201 (mppt) REVERT: F 46 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8586 (pp30) REVERT: F 84 ILE cc_start: 0.9075 (mt) cc_final: 0.8792 (tt) REVERT: G 10 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7728 (mt-10) REVERT: G 257 GLU cc_start: 0.8552 (mp0) cc_final: 0.8260 (mp0) REVERT: H 19 TRP cc_start: 0.8591 (p-90) cc_final: 0.7963 (p-90) REVERT: H 34 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8573 (mmtt) REVERT: f 10 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8196 (tm-30) REVERT: f 20 LYS cc_start: 0.8806 (mttt) cc_final: 0.7675 (pttp) outliers start: 45 outliers final: 39 residues processed: 352 average time/residue: 0.1910 time to fit residues: 94.5057 Evaluate side-chains 364 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 234 LEU 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 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 216 GLN Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 34 LYS 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 46 GLN Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 141 VAL 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 30 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 5 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 23 LYS Chi-restraints excluded: chain f residue 42 LYS Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 179 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 136 optimal weight: 0.0040 chunk 4 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 99 optimal weight: 0.0040 chunk 3 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 170 GLN B 127 GLN ** D 16 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 H 240 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.050738 restraints weight = 78199.965| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 3.25 r_work: 0.2421 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19462 Z= 0.121 Angle : 0.572 9.020 26650 Z= 0.296 Chirality : 0.040 0.290 3014 Planarity : 0.005 0.079 3188 Dihedral : 8.947 58.822 3218 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.70 % Rotamer: Outliers : 2.30 % Allowed : 20.29 % Favored : 77.41 % 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 (0.18), residues: 2156 helix: 2.52 (0.17), residues: 1020 sheet: 1.04 (0.22), residues: 484 loop : -1.64 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 91 TYR 0.033 0.001 TYR A 171 PHE 0.016 0.001 PHE E 1 TRP 0.013 0.001 TRP D 131 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00286 (19422) covalent geometry : angle 0.56864 (26632) hydrogen bonds : bond 0.03685 ( 985) hydrogen bonds : angle 3.79686 ( 2815) metal coordination : bond 0.00961 ( 40) metal coordination : angle 2.60555 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4914.00 seconds wall clock time: 85 minutes 10.93 seconds (5110.93 seconds total)