Starting phenix.real_space_refine on Mon Aug 25 09:28:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qbk_18313/08_2025/8qbk_18313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qbk_18313/08_2025/8qbk_18313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qbk_18313/08_2025/8qbk_18313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qbk_18313/08_2025/8qbk_18313.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qbk_18313/08_2025/8qbk_18313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qbk_18313/08_2025/8qbk_18313.map" } resolution = 2.99 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= 0.000 sd= 1.000 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 P 552 5.49 5 Mg 4 5.21 5 S 51 5.16 5 C 15514 2.51 5 N 4953 2.21 5 O 6398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27472 Number of models: 1 Model: "" Number of chains: 26 Chain: "F" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 2349 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2339 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 78 Conformer: "B" Number of residues, atoms: 309, 2339 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 78 bond proxies already assigned to first conformer: 2373 Chain: "B" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1752 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "C" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna2p': 11, 'rna3p': 49} Chain breaks: 2 Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "K" Number of atoms: 2333 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2323 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 309, 2323 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 2357 Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "M" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 2 Chain: "N" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "P" Number of atoms: 2339 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2329 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 83 Conformer: "B" Number of residues, atoms: 309, 2329 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 83 bond proxies already assigned to first conformer: 2363 Chain: "Q" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1752 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "R" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 2 Chain: "S" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "T" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2223 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 133 Chain: "U" Number of atoms: 2353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2343 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 78 Conformer: "B" Number of residues, atoms: 309, 2343 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 78 bond proxies already assigned to first conformer: 2377 Chain: "V" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "W" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 2 Chain: "X" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "E" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2231 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS A 24 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 24 " occ=0.50 residue: pdb=" N AHIS K 24 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS K 24 " occ=0.50 residue: pdb=" N AHIS P 24 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS P 24 " occ=0.50 residue: pdb=" N AHIS U 24 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS U 24 " occ=0.50 Time building chain proxies: 8.00, per 1000 atoms: 0.29 Number of scatterers: 27472 At special positions: 0 Unit cell: (129.792, 137.28, 242.944, 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) S 51 16.00 P 552 15.00 Mg 4 11.99 O 6398 8.00 N 4953 7.00 C 15514 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3992 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 18 sheets defined 65.1% alpha, 8.4% beta 185 base pairs and 321 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 198 through 201 Processing helix chain 'F' and resid 202 through 213 Proline residue: F 208 - end of helix Processing helix chain 'F' and resid 217 through 230 Processing helix chain 'F' and resid 232 through 250 Processing helix chain 'F' and resid 263 through 274 Processing helix chain 'F' and resid 275 through 292 removed outlier: 3.564A pdb=" N LEU F 279 " --> pdb=" O ASP F 275 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG F 292 " --> pdb=" O ASN F 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 18 Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.528A pdb=" N TYR G 201 " --> pdb=" O ASN G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 202 through 213 Proline residue: G 208 - end of helix Processing helix chain 'G' and resid 217 through 230 Processing helix chain 'G' and resid 232 through 250 Processing helix chain 'G' and resid 263 through 274 Processing helix chain 'G' and resid 275 through 292 removed outlier: 3.537A pdb=" N LEU G 279 " --> pdb=" O ASP G 275 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG G 292 " --> pdb=" O ASN G 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.856A pdb=" N LEU A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 43 through 46 removed outlier: 3.611A pdb=" N PHE A 46 " --> pdb=" O THR A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.544A pdb=" N LEU A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 101 through 107 removed outlier: 3.721A pdb=" N ASN A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.912A pdb=" N VAL A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 187 removed outlier: 4.485A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.579A pdb=" N THR A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 294 through 311 Processing helix chain 'K' and resid 4 through 16 removed outlier: 3.699A pdb=" N LEU K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 31 Processing helix chain 'K' and resid 33 through 43 Processing helix chain 'K' and resid 44 through 46 No H-bonds generated for 'chain 'K' and resid 44 through 46' Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 84 through 87 Processing helix chain 'K' and resid 101 through 107 removed outlier: 3.742A pdb=" N ASN K 105 " --> pdb=" O SER K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 122 through 127 removed outlier: 3.531A pdb=" N LEU K 127 " --> pdb=" O PHE K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 139 removed outlier: 3.846A pdb=" N VAL K 132 " --> pdb=" O THR K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 153 Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'K' and resid 174 through 188 removed outlier: 4.716A pdb=" N SER K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG K 188 " --> pdb=" O TYR K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 220 Processing helix chain 'K' and resid 221 through 224 Processing helix chain 'K' and resid 228 through 232 Processing helix chain 'K' and resid 256 through 272 Processing helix chain 'K' and resid 277 through 292 Processing helix chain 'K' and resid 292 through 311 removed outlier: 3.695A pdb=" N HIS K 296 " --> pdb=" O ASP K 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 16 removed outlier: 3.995A pdb=" N LEU P 15 " --> pdb=" O ARG P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 31 Processing helix chain 'P' and resid 33 through 43 Processing helix chain 'P' and resid 44 through 46 No H-bonds generated for 'chain 'P' and resid 44 through 46' Processing helix chain 'P' and resid 69 through 83 Processing helix chain 'P' and resid 84 through 87 Processing helix chain 'P' and resid 101 through 107 removed outlier: 3.714A pdb=" N ASN P 105 " --> pdb=" O SER P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'P' and resid 122 through 127 removed outlier: 3.545A pdb=" N LEU P 127 " --> pdb=" O PHE P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 139 removed outlier: 3.807A pdb=" N VAL P 132 " --> pdb=" O THR P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 153 Processing helix chain 'P' and resid 165 through 174 Processing helix chain 'P' and resid 174 through 188 removed outlier: 4.592A pdb=" N SER P 187 " --> pdb=" O GLY P 183 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG P 188 " --> pdb=" O TYR P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 220 Processing helix chain 'P' and resid 221 through 224 Processing helix chain 'P' and resid 228 through 232 Processing helix chain 'P' and resid 256 through 272 Processing helix chain 'P' and resid 277 through 292 Processing helix chain 'P' and resid 292 through 311 removed outlier: 3.552A pdb=" N HIS P 296 " --> pdb=" O ASP P 292 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 18 Processing helix chain 'T' and resid 44 through 55 Processing helix chain 'T' and resid 67 through 75 Processing helix chain 'T' and resid 79 through 91 Processing helix chain 'T' and resid 100 through 112 removed outlier: 3.501A pdb=" N PHE T 110 " --> pdb=" O GLU T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 118 removed outlier: 3.666A pdb=" N ARG T 118 " --> pdb=" O GLU T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 129 No H-bonds generated for 'chain 'T' and resid 127 through 129' Processing helix chain 'T' and resid 133 through 138 Processing helix chain 'T' and resid 138 through 147 Processing helix chain 'T' and resid 155 through 164 Processing helix chain 'T' and resid 166 through 171 Processing helix chain 'T' and resid 173 through 190 Processing helix chain 'T' and resid 198 through 201 Processing helix chain 'T' and resid 202 through 213 Proline residue: T 208 - end of helix Processing helix chain 'T' and resid 217 through 230 removed outlier: 3.750A pdb=" N LYS T 230 " --> pdb=" O PHE T 226 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 250 Processing helix chain 'T' and resid 263 through 274 Processing helix chain 'T' and resid 275 through 291 Processing helix chain 'U' and resid 4 through 16 removed outlier: 3.718A pdb=" N LEU U 15 " --> pdb=" O ARG U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 31 Processing helix chain 'U' and resid 33 through 43 Processing helix chain 'U' and resid 44 through 47 Processing helix chain 'U' and resid 69 through 83 Processing helix chain 'U' and resid 101 through 107 removed outlier: 3.671A pdb=" N ASN U 105 " --> pdb=" O SER U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 122 through 127 Processing helix chain 'U' and resid 128 through 139 removed outlier: 4.073A pdb=" N VAL U 132 " --> pdb=" O THR U 128 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 154 Processing helix chain 'U' and resid 165 through 174 Processing helix chain 'U' and resid 174 through 188 removed outlier: 4.518A pdb=" N SER U 187 " --> pdb=" O GLY U 183 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG U 188 " --> pdb=" O TYR U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 205 through 220 Processing helix chain 'U' and resid 221 through 224 Processing helix chain 'U' and resid 228 through 232 Processing helix chain 'U' and resid 256 through 272 Processing helix chain 'U' and resid 277 through 292 Processing helix chain 'U' and resid 292 through 311 Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 100 through 112 removed outlier: 3.549A pdb=" N PHE E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 119 removed outlier: 3.579A pdb=" N ARG E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'E' and resid 155 through 164 Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 173 through 190 Processing helix chain 'E' and resid 198 through 201 Processing helix chain 'E' and resid 202 through 213 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 217 through 230 removed outlier: 3.936A pdb=" N LYS E 230 " --> pdb=" O PHE E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 250 Processing helix chain 'E' and resid 263 through 274 Processing helix chain 'E' and resid 275 through 291 Processing sheet with id=AA1, first strand: chain 'F' and resid 253 through 255 Processing sheet with id=AA2, first strand: chain 'G' and resid 253 through 255 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA6, first strand: chain 'K' and resid 48 through 54 Processing sheet with id=AA7, first strand: chain 'K' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'K' and resid 242 through 243 Processing sheet with id=AA9, first strand: chain 'P' and resid 48 through 54 Processing sheet with id=AB1, first strand: chain 'P' and resid 93 through 94 Processing sheet with id=AB2, first strand: chain 'P' and resid 247 through 248 Processing sheet with id=AB3, first strand: chain 'T' and resid 59 through 62 removed outlier: 6.329A pdb=" N THR T 31 " --> pdb=" O VAL T 93 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE T 95 " --> pdb=" O THR T 31 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE T 33 " --> pdb=" O ILE T 95 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE T 94 " --> pdb=" O ILE T 121 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE T 123 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU T 96 " --> pdb=" O ILE T 123 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASP T 125 " --> pdb=" O LEU T 96 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU T 152 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS T 122 " --> pdb=" O LEU T 152 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N CYS T 154 " --> pdb=" O CYS T 122 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN T 124 " --> pdb=" O CYS T 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 253 through 255 Processing sheet with id=AB5, first strand: chain 'U' and resid 49 through 53 Processing sheet with id=AB6, first strand: chain 'U' and resid 93 through 94 Processing sheet with id=AB7, first strand: chain 'U' and resid 247 through 248 Processing sheet with id=AB8, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.569A pdb=" N LEU E 34 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR E 31 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE E 95 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE E 33 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE E 94 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE E 123 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU E 96 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASP E 125 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU E 152 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS E 122 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS E 154 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN E 124 " --> pdb=" O CYS E 154 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 253 through 255 969 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 472 hydrogen bonds 904 hydrogen bond angles 0 basepair planarities 185 basepair parallelities 321 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3277 1.32 - 1.44: 10982 1.44 - 1.57: 13731 1.57 - 1.69: 1083 1.69 - 1.81: 72 Bond restraints: 29145 Sorted by residual: bond pdb=" CA LYS A 231 " pdb=" C LYS A 231 " ideal model delta sigma weight residual 1.526 1.588 -0.062 1.23e-02 6.61e+03 2.58e+01 bond pdb=" CD GLU E 106 " pdb=" OE2 GLU E 106 " ideal model delta sigma weight residual 1.249 1.342 -0.093 1.90e-02 2.77e+03 2.38e+01 bond pdb=" CD GLU T 106 " pdb=" OE2 GLU T 106 " ideal model delta sigma weight residual 1.249 1.341 -0.092 1.90e-02 2.77e+03 2.35e+01 bond pdb=" N ILE P 94 " pdb=" CA ILE P 94 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N TYR E 137 " pdb=" CA TYR E 137 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.26e+00 ... (remaining 29140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.09: 41973 6.09 - 12.18: 39 12.18 - 18.26: 5 18.26 - 24.35: 2 24.35 - 30.44: 1 Bond angle restraints: 42020 Sorted by residual: angle pdb=" O GLU E 106 " pdb=" C GLU E 106 " pdb=" N LEU E 107 " ideal model delta sigma weight residual 122.15 91.71 30.44 1.14e+00 7.69e-01 7.13e+02 angle pdb=" O GLU T 106 " pdb=" C GLU T 106 " pdb=" N LEU T 107 " ideal model delta sigma weight residual 122.15 99.70 22.45 1.14e+00 7.69e-01 3.88e+02 angle pdb=" C3' G W 64 " pdb=" O3' G W 64 " pdb=" P C W 65 " ideal model delta sigma weight residual 120.20 99.14 21.06 1.50e+00 4.44e-01 1.97e+02 angle pdb=" C3' G C 64 " pdb=" O3' G C 64 " pdb=" P C C 65 " ideal model delta sigma weight residual 120.20 102.81 17.39 1.50e+00 4.44e-01 1.34e+02 angle pdb=" C3' G M 64 " pdb=" O3' G M 64 " pdb=" P C M 65 " ideal model delta sigma weight residual 120.20 103.89 16.31 1.50e+00 4.44e-01 1.18e+02 ... (remaining 42015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 15241 35.95 - 71.90: 1942 71.90 - 107.85: 108 107.85 - 143.80: 3 143.80 - 179.75: 22 Dihedral angle restraints: 17316 sinusoidal: 11130 harmonic: 6186 Sorted by residual: dihedral pdb=" O4' U C 74 " pdb=" C1' U C 74 " pdb=" N1 U C 74 " pdb=" C2 U C 74 " ideal model delta sinusoidal sigma weight residual -160.00 19.42 -179.42 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U W 74 " pdb=" C1' U W 74 " pdb=" N1 U W 74 " pdb=" C2 U W 74 " ideal model delta sinusoidal sigma weight residual -160.00 17.49 -177.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 74 " pdb=" C1' U M 74 " pdb=" N1 U M 74 " pdb=" C2 U M 74 " ideal model delta sinusoidal sigma weight residual -160.00 16.73 -176.73 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 17313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4886 0.098 - 0.196: 181 0.196 - 0.294: 9 0.294 - 0.392: 11 0.392 - 0.490: 15 Chirality restraints: 5102 Sorted by residual: chirality pdb=" P G W 69 " pdb=" OP1 G W 69 " pdb=" OP2 G W 69 " pdb=" O5' G W 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" P G R 69 " pdb=" OP1 G R 69 " pdb=" OP2 G R 69 " pdb=" O5' G R 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" P G C 69 " pdb=" OP1 G C 69 " pdb=" OP2 G C 69 " pdb=" O5' G C 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 5099 not shown) Planarity restraints: 3322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 106 " -0.122 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" C GLU E 106 " 0.355 2.00e-02 2.50e+03 pdb=" O GLU E 106 " -0.121 2.00e-02 2.50e+03 pdb=" N LEU E 107 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 106 " -0.102 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C GLU T 106 " 0.312 2.00e-02 2.50e+03 pdb=" O GLU T 106 " -0.109 2.00e-02 2.50e+03 pdb=" N LEU T 107 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 252 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LYS K 252 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS K 252 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL K 253 " 0.021 2.00e-02 2.50e+03 ... (remaining 3319 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.02: 1 2.02 - 2.74: 3224 2.74 - 3.46: 39100 3.46 - 4.18: 78313 4.18 - 4.90: 121315 Nonbonded interactions: 241953 Sorted by model distance: nonbonded pdb=" NZ LYS A 231 " pdb=" OP1 G C 69 " model vdw 1.306 3.120 nonbonded pdb=" O2' C W 55 " pdb=" OP2 G W 56 " model vdw 2.132 3.040 nonbonded pdb=" O2' G W 16 " pdb=" O5' A W 17 " model vdw 2.173 3.040 nonbonded pdb=" NZ LYS A 231 " pdb=" P G C 69 " model vdw 2.204 3.480 nonbonded pdb=" O ARG U 238 " pdb=" N2 G W 44 " model vdw 2.205 3.120 ... (remaining 241948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 23 or resid 25 through 206 or (resid 207 through \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throu \ gh 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) or \ resid 232 through 237 or (resid 238 and (name N or name CA or name C or name O \ or name CB )) or resid 239 through 257 or (resid 258 through 259 and (name N or \ name CA or name C or name O or name CB )) or resid 260 or (resid 261 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 3 \ 11)) selection = (chain 'K' and (resid 3 through 23 or resid 25 through 206 or (resid 207 through \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throu \ gh 210 or (resid 211 through 212 and (name N or name CA or name C or name O or n \ ame CB )) or resid 213 through 237 or (resid 238 and (name N or name CA or name \ C or name O or name CB )) or resid 239 through 311)) selection = (chain 'P' and (resid 3 through 23 or resid 25 through 210 or (resid 211 through \ 212 and (name N or name CA or name C or name O or name CB )) or resid 213 throu \ gh 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) or \ resid 232 through 257 or (resid 258 through 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 or (resid 261 through 262 and (name N or \ name CA or name C or name O or name CB )) or resid 263 through 311)) selection = (chain 'U' and (resid 3 through 23 or resid 25 through 206 or (resid 207 through \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throu \ gh 210 or (resid 211 through 212 and (name N or name CA or name C or name O or n \ ame CB )) or resid 213 through 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 232 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 257 or (resid 258 \ through 259 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 60 or (resid 261 through 262 and (name N or name CA or name C or name O or name \ CB )) or resid 263 through 311)) } ncs_group { reference = chain 'B' selection = (chain 'Q' and resid 1 through 85) } ncs_group { reference = chain 'C' selection = chain 'M' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'S' selection = chain 'X' } ncs_group { reference = (chain 'E' and (resid 3 through 41 or (resid 42 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 179 or (resid 180 throug \ h 181 and (name N or name CA or name C or name O or name CB )) or resid 182 thro \ ugh 401)) selection = chain 'T' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'L' and resid 1 through 85) selection = chain 'V' } 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: 17.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.220 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 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 : 0.004 0.093 29147 Z= 0.243 Angle : 0.731 30.441 42020 Z= 0.458 Chirality : 0.049 0.490 5102 Planarity : 0.006 0.205 3322 Dihedral : 24.714 179.747 13324 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.69 % Allowed : 25.11 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.22 (0.19), residues: 2098 helix: 1.51 (0.16), residues: 1166 sheet: 0.57 (0.36), residues: 200 loop : -0.17 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 238 TYR 0.021 0.001 TYR E 137 PHE 0.040 0.001 PHE E 5 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00419 (29145) covalent geometry : angle 0.73137 (42020) hydrogen bonds : bond 0.15028 ( 1441) hydrogen bonds : angle 5.75972 ( 3694) Misc. bond : bond 0.05467 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 246 ARG cc_start: 0.7542 (ttp-170) cc_final: 0.6574 (tpt90) REVERT: G 252 LYS cc_start: 0.6287 (mmtp) cc_final: 0.6041 (mmmt) REVERT: K 233 CYS cc_start: 0.6539 (t) cc_final: 0.5732 (p) REVERT: P 261 LYS cc_start: 0.6597 (tmtt) cc_final: 0.5776 (tmtt) REVERT: T 65 GLU cc_start: 0.8330 (pm20) cc_final: 0.8016 (mp0) REVERT: E 106 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8081 (mt-10) outliers start: 11 outliers final: 5 residues processed: 227 average time/residue: 0.6976 time to fit residues: 182.3877 Evaluate side-chains 189 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain E residue 69 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 10 GLN F 249 ASN K 280 HIS E 12 GLN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 255 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.196637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.147955 restraints weight = 102813.550| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 5.16 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29147 Z= 0.150 Angle : 0.577 7.900 42020 Z= 0.309 Chirality : 0.036 0.235 5102 Planarity : 0.004 0.056 3322 Dihedral : 25.542 179.636 9942 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.95 % Allowed : 23.35 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.30 (0.18), residues: 2098 helix: 1.57 (0.15), residues: 1188 sheet: 0.37 (0.33), residues: 192 loop : -0.09 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 204 TYR 0.022 0.001 TYR E 137 PHE 0.021 0.002 PHE E 134 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00328 (29145) covalent geometry : angle 0.57668 (42020) hydrogen bonds : bond 0.04688 ( 1441) hydrogen bonds : angle 4.16539 ( 3694) Misc. bond : bond 0.00090 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 211 LYS cc_start: 0.7266 (mtpp) cc_final: 0.7058 (mttm) REVERT: K 279 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6707 (pt0) REVERT: K 300 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7294 (pp) REVERT: P 11 ARG cc_start: 0.7186 (ttp80) cc_final: 0.6889 (ttm-80) REVERT: U 206 MET cc_start: 0.7806 (tpt) cc_final: 0.7595 (tpt) outliers start: 47 outliers final: 11 residues processed: 252 average time/residue: 0.6511 time to fit residues: 190.7535 Evaluate side-chains 193 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 293 SER Chi-restraints excluded: chain E residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 186 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 117 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: F 249 ASN A 204 GLN T 9 GLN T 112 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 255 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.194556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145806 restraints weight = 101566.638| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 5.05 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29147 Z= 0.179 Angle : 0.561 7.728 42020 Z= 0.301 Chirality : 0.037 0.230 5102 Planarity : 0.004 0.058 3322 Dihedral : 25.452 176.680 9933 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.95 % Allowed : 22.03 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.24 (0.18), residues: 2098 helix: 1.50 (0.15), residues: 1184 sheet: 0.14 (0.33), residues: 200 loop : 0.02 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 31 TYR 0.024 0.002 TYR K 66 PHE 0.016 0.002 PHE U 10 TRP 0.005 0.001 TRP A 78 HIS 0.004 0.001 HIS U 280 Details of bonding type rmsd covalent geometry : bond 0.00411 (29145) covalent geometry : angle 0.56118 (42020) hydrogen bonds : bond 0.04612 ( 1441) hydrogen bonds : angle 4.07315 ( 3694) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 235 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8213 (mp) REVERT: G 204 ARG cc_start: 0.7214 (mtt90) cc_final: 0.6975 (mtt90) REVERT: G 246 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7568 (tpt90) REVERT: G 277 LYS cc_start: 0.7807 (mttt) cc_final: 0.6844 (mppt) REVERT: K 31 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7949 (mtm-85) REVERT: K 206 MET cc_start: 0.8088 (tpp) cc_final: 0.7884 (tpp) REVERT: K 211 LYS cc_start: 0.7342 (mtpp) cc_final: 0.7017 (mttm) REVERT: K 279 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6749 (pt0) REVERT: P 11 ARG cc_start: 0.7284 (ttp80) cc_final: 0.7022 (ttm-80) REVERT: T 294 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7087 (mttt) outliers start: 63 outliers final: 24 residues processed: 240 average time/residue: 0.6517 time to fit residues: 181.6597 Evaluate side-chains 206 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain P residue 26 MET Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 233 CYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.194465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146194 restraints weight = 99558.424| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 5.13 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29147 Z= 0.179 Angle : 0.552 7.525 42020 Z= 0.297 Chirality : 0.036 0.212 5102 Planarity : 0.004 0.058 3322 Dihedral : 25.446 177.446 9933 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.77 % Allowed : 22.22 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.26 (0.18), residues: 2098 helix: 1.52 (0.15), residues: 1184 sheet: 0.24 (0.33), residues: 200 loop : -0.03 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 238 TYR 0.029 0.002 TYR U 184 PHE 0.016 0.002 PHE P 10 TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00414 (29145) covalent geometry : angle 0.55199 (42020) hydrogen bonds : bond 0.04422 ( 1441) hydrogen bonds : angle 3.97687 ( 3694) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8248 (mptm) REVERT: G 277 LYS cc_start: 0.7792 (mttt) cc_final: 0.6813 (mppt) REVERT: K 31 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8034 (mtm-85) REVERT: K 206 MET cc_start: 0.8047 (tpp) cc_final: 0.7803 (tpp) REVERT: K 279 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6816 (pt0) REVERT: P 11 ARG cc_start: 0.7231 (ttp80) cc_final: 0.6931 (ttm-80) REVERT: T 294 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7113 (mttt) REVERT: U 206 MET cc_start: 0.7921 (tpt) cc_final: 0.7593 (tpt) outliers start: 60 outliers final: 29 residues processed: 233 average time/residue: 0.6525 time to fit residues: 176.5458 Evaluate side-chains 213 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 26 MET Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 68 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 95 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN E 249 ASN E 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.195641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.147122 restraints weight = 104796.976| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 5.25 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29147 Z= 0.153 Angle : 0.538 7.592 42020 Z= 0.290 Chirality : 0.035 0.203 5102 Planarity : 0.004 0.056 3322 Dihedral : 25.417 178.249 9933 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.58 % Allowed : 22.85 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.29 (0.18), residues: 2098 helix: 1.59 (0.15), residues: 1188 sheet: 0.21 (0.33), residues: 200 loop : -0.10 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 118 TYR 0.024 0.001 TYR A 302 PHE 0.013 0.001 PHE U 92 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00348 (29145) covalent geometry : angle 0.53844 (42020) hydrogen bonds : bond 0.04274 ( 1441) hydrogen bonds : angle 3.89720 ( 3694) Misc. bond : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 235 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8130 (mp) REVERT: F 252 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8242 (mptm) REVERT: G 277 LYS cc_start: 0.7772 (mttt) cc_final: 0.6761 (mppt) REVERT: K 31 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8077 (mtm-85) REVERT: K 35 GLU cc_start: 0.7292 (pm20) cc_final: 0.7031 (mp0) REVERT: K 206 MET cc_start: 0.8123 (tpp) cc_final: 0.7827 (tpp) REVERT: K 211 LYS cc_start: 0.7429 (mtpp) cc_final: 0.7138 (mttm) REVERT: K 279 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6828 (pt0) REVERT: P 11 ARG cc_start: 0.7235 (ttp80) cc_final: 0.6935 (ttm-80) REVERT: T 294 LYS cc_start: 0.7355 (mtmp) cc_final: 0.7079 (mttt) REVERT: U 206 MET cc_start: 0.7870 (tpt) cc_final: 0.7522 (tpt) REVERT: E 293 ARG cc_start: 0.6607 (ttp-170) cc_final: 0.6312 (mtm-85) outliers start: 57 outliers final: 30 residues processed: 229 average time/residue: 0.7042 time to fit residues: 187.0897 Evaluate side-chains 209 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 26 MET Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 233 CYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 142 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 183 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 222 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 95 optimal weight: 0.0980 chunk 147 optimal weight: 10.0000 chunk 244 optimal weight: 0.4980 chunk 230 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 10 GLN T 112 ASN T 124 GLN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 255 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.196320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148465 restraints weight = 99121.319| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 4.83 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29147 Z= 0.135 Angle : 0.530 9.040 42020 Z= 0.284 Chirality : 0.035 0.199 5102 Planarity : 0.004 0.054 3322 Dihedral : 25.384 179.511 9933 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.76 % Allowed : 23.98 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.45 (0.18), residues: 2098 helix: 1.74 (0.15), residues: 1186 sheet: 0.28 (0.33), residues: 200 loop : -0.06 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 276 TYR 0.027 0.001 TYR A 302 PHE 0.013 0.001 PHE P 92 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00299 (29145) covalent geometry : angle 0.53008 (42020) hydrogen bonds : bond 0.04101 ( 1441) hydrogen bonds : angle 3.81730 ( 3694) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8187 (mptm) REVERT: G 288 ASN cc_start: 0.9073 (t0) cc_final: 0.8744 (t0) REVERT: K 31 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8024 (mtm-85) REVERT: K 206 MET cc_start: 0.8116 (tpp) cc_final: 0.7827 (tpp) REVERT: K 279 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6857 (pt0) REVERT: P 11 ARG cc_start: 0.7171 (ttp80) cc_final: 0.6845 (ttp-170) REVERT: P 211 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7378 (mmtt) REVERT: T 294 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7063 (mttt) REVERT: U 51 TYR cc_start: 0.8680 (p90) cc_final: 0.8359 (p90) REVERT: E 293 ARG cc_start: 0.6596 (ttp-170) cc_final: 0.6314 (mtm-85) outliers start: 44 outliers final: 27 residues processed: 229 average time/residue: 0.6847 time to fit residues: 182.7547 Evaluate side-chains 210 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN T 112 ASN T 124 GLN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 255 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.194863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145377 restraints weight = 88845.122| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 4.92 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29147 Z= 0.158 Angle : 0.541 7.827 42020 Z= 0.291 Chirality : 0.036 0.213 5102 Planarity : 0.004 0.055 3322 Dihedral : 25.379 179.852 9933 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.01 % Allowed : 24.36 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.37 (0.18), residues: 2098 helix: 1.67 (0.15), residues: 1190 sheet: 0.29 (0.33), residues: 208 loop : -0.11 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 118 TYR 0.027 0.002 TYR A 302 PHE 0.014 0.001 PHE P 10 TRP 0.005 0.001 TRP A 78 HIS 0.004 0.001 HIS U 280 Details of bonding type rmsd covalent geometry : bond 0.00359 (29145) covalent geometry : angle 0.54113 (42020) hydrogen bonds : bond 0.04226 ( 1441) hydrogen bonds : angle 3.88004 ( 3694) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8201 (mptm) REVERT: G 288 ASN cc_start: 0.9115 (t0) cc_final: 0.8829 (t0) REVERT: K 31 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7945 (mtm-85) REVERT: K 206 MET cc_start: 0.8139 (tpp) cc_final: 0.7887 (tpp) REVERT: K 211 LYS cc_start: 0.7538 (mmmt) cc_final: 0.6998 (mttm) REVERT: K 279 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6897 (pt0) REVERT: P 11 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6931 (ttp-170) REVERT: P 211 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7311 (mmtt) REVERT: T 294 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7141 (mttt) REVERT: U 51 TYR cc_start: 0.8645 (p90) cc_final: 0.8364 (p90) REVERT: U 206 MET cc_start: 0.7868 (tpt) cc_final: 0.7495 (tpt) REVERT: E 176 TYR cc_start: 0.7760 (t80) cc_final: 0.7458 (t80) REVERT: E 293 ARG cc_start: 0.6621 (ttp-170) cc_final: 0.6357 (mtm-85) outliers start: 48 outliers final: 31 residues processed: 222 average time/residue: 0.6788 time to fit residues: 175.7561 Evaluate side-chains 219 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 233 CYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN T 124 GLN E 47 HIS E 249 ASN E 255 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.194818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.145803 restraints weight = 94513.821| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 5.12 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29147 Z= 0.163 Angle : 0.544 9.824 42020 Z= 0.291 Chirality : 0.036 0.199 5102 Planarity : 0.004 0.056 3322 Dihedral : 25.384 179.906 9933 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.89 % Allowed : 24.92 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.35 (0.18), residues: 2098 helix: 1.65 (0.15), residues: 1188 sheet: 0.29 (0.33), residues: 208 loop : -0.10 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 24 TYR 0.025 0.002 TYR A 302 PHE 0.014 0.001 PHE A 10 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00372 (29145) covalent geometry : angle 0.54393 (42020) hydrogen bonds : bond 0.04215 ( 1441) hydrogen bonds : angle 3.88222 ( 3694) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8179 (mptm) REVERT: G 288 ASN cc_start: 0.9116 (t0) cc_final: 0.8839 (t0) REVERT: K 31 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7974 (mtm-85) REVERT: K 206 MET cc_start: 0.8154 (tpp) cc_final: 0.7897 (tpp) REVERT: K 211 LYS cc_start: 0.7532 (mmmt) cc_final: 0.6975 (mttm) REVERT: K 279 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6874 (pt0) REVERT: P 11 ARG cc_start: 0.7247 (ttp80) cc_final: 0.6886 (ttp-170) REVERT: P 211 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7289 (mmtt) REVERT: T 294 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7166 (mttt) REVERT: U 51 TYR cc_start: 0.8667 (p90) cc_final: 0.8356 (p90) REVERT: E 176 TYR cc_start: 0.7890 (t80) cc_final: 0.7605 (t80) REVERT: E 293 ARG cc_start: 0.6630 (ttp-170) cc_final: 0.6357 (mtm-85) outliers start: 46 outliers final: 31 residues processed: 221 average time/residue: 0.7058 time to fit residues: 181.9231 Evaluate side-chains 216 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 233 CYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 158 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 248 optimal weight: 0.0020 chunk 79 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN T 124 GLN E 249 ASN E 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.195449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146563 restraints weight = 100838.350| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 5.22 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29147 Z= 0.141 Angle : 0.534 7.920 42020 Z= 0.287 Chirality : 0.035 0.211 5102 Planarity : 0.004 0.055 3322 Dihedral : 25.381 180.000 9933 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.51 % Allowed : 25.36 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.41 (0.18), residues: 2098 helix: 1.70 (0.15), residues: 1186 sheet: 0.34 (0.33), residues: 208 loop : -0.11 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 24 TYR 0.028 0.001 TYR A 302 PHE 0.013 0.001 PHE P 92 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00316 (29145) covalent geometry : angle 0.53426 (42020) hydrogen bonds : bond 0.04121 ( 1441) hydrogen bonds : angle 3.84985 ( 3694) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8160 (mptm) REVERT: G 288 ASN cc_start: 0.9103 (t0) cc_final: 0.8828 (t0) REVERT: K 31 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7966 (mtm-85) REVERT: K 206 MET cc_start: 0.8158 (tpp) cc_final: 0.7897 (tpp) REVERT: K 211 LYS cc_start: 0.7545 (mmmt) cc_final: 0.6981 (mttm) REVERT: K 279 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6860 (pt0) REVERT: P 11 ARG cc_start: 0.7226 (ttp80) cc_final: 0.6869 (ttp-170) REVERT: P 211 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7239 (mmtt) REVERT: T 294 LYS cc_start: 0.7382 (mtmp) cc_final: 0.7121 (mttt) REVERT: U 51 TYR cc_start: 0.8669 (p90) cc_final: 0.8405 (p90) REVERT: E 30 ILE cc_start: 0.8878 (mm) cc_final: 0.8648 (tp) REVERT: E 176 TYR cc_start: 0.7866 (t80) cc_final: 0.7570 (t80) REVERT: E 293 ARG cc_start: 0.6695 (ttp-170) cc_final: 0.6414 (mtm-85) outliers start: 40 outliers final: 30 residues processed: 211 average time/residue: 0.7197 time to fit residues: 175.6517 Evaluate side-chains 214 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 233 CYS Chi-restraints excluded: chain U residue 293 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 254 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 248 optimal weight: 0.0470 chunk 176 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 47 optimal weight: 0.0000 overall best weight: 0.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN T 124 GLN E 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.196037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147418 restraints weight = 97798.135| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 5.30 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29147 Z= 0.132 Angle : 0.537 12.994 42020 Z= 0.287 Chirality : 0.035 0.195 5102 Planarity : 0.004 0.054 3322 Dihedral : 25.371 179.938 9933 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.51 % Allowed : 25.24 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.46 (0.18), residues: 2098 helix: 1.75 (0.15), residues: 1186 sheet: 0.36 (0.33), residues: 208 loop : -0.10 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 24 TYR 0.031 0.001 TYR A 302 PHE 0.012 0.001 PHE U 92 TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00290 (29145) covalent geometry : angle 0.53661 (42020) hydrogen bonds : bond 0.04060 ( 1441) hydrogen bonds : angle 3.82122 ( 3694) Misc. bond : bond 0.00036 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8143 (mptm) REVERT: G 288 ASN cc_start: 0.9108 (t0) cc_final: 0.8828 (t0) REVERT: K 31 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7961 (mtm-85) REVERT: K 206 MET cc_start: 0.8169 (tpp) cc_final: 0.7903 (tpp) REVERT: K 211 LYS cc_start: 0.7518 (mmmt) cc_final: 0.6970 (mttm) REVERT: K 279 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6850 (pt0) REVERT: P 11 ARG cc_start: 0.7247 (ttp80) cc_final: 0.6909 (ttp-170) REVERT: P 211 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7227 (mmtt) REVERT: T 294 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7126 (mttt) REVERT: U 51 TYR cc_start: 0.8646 (p90) cc_final: 0.8374 (p90) REVERT: E 30 ILE cc_start: 0.8887 (mm) cc_final: 0.8659 (tp) REVERT: E 176 TYR cc_start: 0.7865 (t80) cc_final: 0.7570 (t80) REVERT: E 293 ARG cc_start: 0.6716 (ttp-170) cc_final: 0.6432 (mtm-85) outliers start: 40 outliers final: 30 residues processed: 211 average time/residue: 0.6954 time to fit residues: 170.6617 Evaluate side-chains 216 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 233 CYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 255 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 214 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN E 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.195120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.145693 restraints weight = 87131.691| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 5.03 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29147 Z= 0.160 Angle : 0.541 8.021 42020 Z= 0.291 Chirality : 0.036 0.213 5102 Planarity : 0.004 0.055 3322 Dihedral : 25.365 179.514 9933 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.13 % Allowed : 25.61 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.39 (0.18), residues: 2098 helix: 1.70 (0.15), residues: 1186 sheet: 0.32 (0.33), residues: 208 loop : -0.12 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 24 TYR 0.032 0.002 TYR A 302 PHE 0.014 0.001 PHE A 10 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd covalent geometry : bond 0.00364 (29145) covalent geometry : angle 0.54140 (42020) hydrogen bonds : bond 0.04172 ( 1441) hydrogen bonds : angle 3.85995 ( 3694) Misc. bond : bond 0.00053 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7778.28 seconds wall clock time: 133 minutes 54.42 seconds (8034.42 seconds total)