Starting phenix.real_space_refine on Sat Aug 8 08:05:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qbk_18313/08_2026/8qbk_18313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qbk_18313/08_2026/8qbk_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_2026/8qbk_18313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qbk_18313/08_2026/8qbk_18313.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qbk_18313/08_2026/8qbk_18313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qbk_18313/08_2026/8qbk_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.57, per 1000 atoms: 0.28 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: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.94 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: 5.90 Time building geometry restraints manager: 3.36 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=" C1' DC B 12 " pdb=" N1 DC B 12 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.95e+01 bond pdb=" C1' DC V 12 " pdb=" N1 DC V 12 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.73e+01 ... (remaining 29140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.09: 41976 6.09 - 12.18: 38 12.18 - 18.26: 3 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 119.70 99.14 20.56 1.20e+00 6.94e-01 2.93e+02 angle pdb=" C3' G C 64 " pdb=" O3' G C 64 " pdb=" P C C 65 " ideal model delta sigma weight residual 119.70 102.81 16.89 1.20e+00 6.94e-01 1.98e+02 angle pdb=" C3' G M 64 " pdb=" O3' G M 64 " pdb=" P C M 65 " ideal model delta sigma weight residual 119.70 103.89 15.81 1.20e+00 6.94e-01 1.74e+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: 4487 0.098 - 0.196: 580 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: 19.390 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.850 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.005 0.093 29147 Z= 0.400 Angle : 0.830 30.441 42020 Z= 0.662 Chirality : 0.060 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 are 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/Z covalent geometry : bond 0.00504 / 0.40 (29145) covalent geometry : angle 0.82971 / 0.66 (42020) hydrogen bonds : bond 0.15028 / 10.08 ( 1441) hydrogen bonds : angle 5.75972 / 4.14 ( 3694) Misc. bond : bond 0.05467 / 2.74 ( 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 : 0.800 Fit side-chains 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: A 231 LYS cc_start: 0.6532 (mtpp) cc_final: 0.6304 (mtpp) 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: 0.5770 (tmtt) REVERT: T 65 GLU cc_start: 0.8330 (pm20) cc_final: 0.8016 (mp0) REVERT: U 231 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.6129 (mtpp) 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: 0.6956 time to fit residues: 183.7466 Evaluate side-chains 189 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 U residue 231 LYS 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: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 20.0000 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: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 10 GLN F 249 ASN E 12 GLN E 47 HIS 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 = 0.4419 r_free = 0.4419 target = 0.195750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146739 restraints weight = 102426.442| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 5.12 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 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 = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29147 Z= 0.162 Angle : 0.592 10.430 42020 Z= 0.342 Chirality : 0.042 0.349 5102 Planarity : 0.005 0.056 3322 Dihedral : 25.697 178.366 9946 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.95 % Allowed : 23.41 % Favored : 73.63 % 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 are not related in a simple way. whole: 1.33 (0.18), residues: 2098 helix: 1.58 (0.15), residues: 1176 sheet: 0.45 (0.33), residues: 192 loop : -0.02 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 204 TYR 0.020 0.002 TYR E 137 PHE 0.025 0.002 PHE T 134 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (29145) covalent geometry : angle 0.59176 / 0.34 (42020) hydrogen bonds : bond 0.05617 / 3.80 ( 1441) hydrogen bonds : angle 4.37501 / 3.14 ( 3694) Misc. bond : bond 0.00080 / 0.04 ( 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 253 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 231 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7774 (mttt) REVERT: K 211 LYS cc_start: 0.7369 (mtpp) cc_final: 0.7129 (mttm) REVERT: P 11 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6942 (ttm-80) outliers start: 47 outliers final: 12 residues processed: 235 average time/residue: 0.6504 time to fit residues: 179.6373 Evaluate side-chains 192 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 218 SER 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 77 GLN Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 218 SER Chi-restraints excluded: chain U residue 293 SER Chi-restraints excluded: chain E residue 69 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 7.9990 chunk 61 optimal weight: 30.0000 chunk 128 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN K 280 HIS P 113 ASN T 9 GLN T 112 ASN E 249 ASN E 255 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.195499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146716 restraints weight = 102070.485| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.79 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3855 r_free = 0.3855 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 = 0.3855 r_free = 0.3855 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29147 Z= 0.155 Angle : 0.545 8.240 42020 Z= 0.317 Chirality : 0.040 0.306 5102 Planarity : 0.004 0.055 3322 Dihedral : 25.581 177.719 9935 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.45 % Allowed : 23.16 % Favored : 73.38 % 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 are not related in a simple way. whole: 1.20 (0.18), residues: 2098 helix: 1.47 (0.15), residues: 1180 sheet: 0.38 (0.32), residues: 192 loop : -0.08 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 257 TYR 0.023 0.002 TYR K 66 PHE 0.018 0.002 PHE G 274 TRP 0.005 0.001 TRP A 78 HIS 0.006 0.001 HIS P 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (29145) covalent geometry : angle 0.54454 / 0.32 (42020) hydrogen bonds : bond 0.05039 / 3.40 ( 1441) hydrogen bonds : angle 4.17663 / 3.00 ( 3694) Misc. bond : bond 0.00034 / 0.02 ( 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 263 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 204 ARG cc_start: 0.7225 (mtt90) cc_final: 0.6949 (mtt90) REVERT: G 252 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7388 (mttt) REVERT: A 231 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7756 (mtpt) REVERT: K 206 MET cc_start: 0.8079 (tpp) cc_final: 0.7876 (tpp) REVERT: K 279 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6761 (pt0) REVERT: P 11 ARG cc_start: 0.7152 (ttp80) cc_final: 0.6924 (ttm-80) REVERT: T 294 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7120 (mttt) REVERT: E 249 ASN cc_start: 0.7964 (m-40) cc_final: 0.7760 (m110) outliers start: 55 outliers final: 22 residues processed: 241 average time/residue: 0.6546 time to fit residues: 185.3375 Evaluate side-chains 210 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL 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 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 K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain T residue 257 THR 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 213 LEU 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: 2.9990 chunk 109 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 249 ASN P 113 ASN T 112 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 = 0.4399 r_free = 0.4399 target = 0.193552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144472 restraints weight = 99058.570| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 5.08 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1531 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= 0.193 Angle : 0.567 9.129 42020 Z= 0.324 Chirality : 0.041 0.310 5102 Planarity : 0.005 0.058 3322 Dihedral : 25.611 177.974 9933 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.45 % Allowed : 22.85 % 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 are not related in a simple way. whole: 1.09 (0.18), residues: 2098 helix: 1.39 (0.15), residues: 1182 sheet: 0.19 (0.32), residues: 208 loop : -0.13 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 257 TYR 0.026 0.002 TYR A 260 PHE 0.019 0.002 PHE A 10 TRP 0.006 0.001 TRP A 78 HIS 0.004 0.001 HIS U 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (29145) covalent geometry : angle 0.56714 / 0.32 (42020) hydrogen bonds : bond 0.04965 / 3.36 ( 1441) hydrogen bonds : angle 4.12219 / 2.96 ( 3694) Misc. bond : bond 0.00039 / 0.02 ( 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 249 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 204 ARG cc_start: 0.7204 (mtt90) cc_final: 0.6993 (mtt90) REVERT: G 252 LYS cc_start: 0.7918 (mmmt) cc_final: 0.7575 (mttt) REVERT: A 231 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7921 (mtpt) REVERT: K 206 MET cc_start: 0.8171 (tpp) cc_final: 0.7897 (tpp) REVERT: K 279 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6721 (pt0) REVERT: P 11 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6898 (ttm-80) REVERT: P 204 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6591 (mm110) REVERT: T 294 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7170 (mttt) outliers start: 55 outliers final: 28 residues processed: 230 average time/residue: 0.6224 time to fit residues: 167.7225 Evaluate side-chains 213 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 6 THR 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 A residue 53 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain P residue 204 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 50 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 218 SER Chi-restraints excluded: chain U residue 233 CYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 244 VAL 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: 9.9990 chunk 184 optimal weight: 0.3980 chunk 249 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 95 optimal weight: 0.4980 chunk 114 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 112 ASN 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 = 0.4419 r_free = 0.4419 target = 0.195555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146260 restraints weight = 104538.948| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 5.16 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 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 = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29147 Z= 0.144 Angle : 0.530 8.976 42020 Z= 0.307 Chirality : 0.039 0.316 5102 Planarity : 0.004 0.054 3322 Dihedral : 25.577 178.184 9933 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.82 % Allowed : 23.73 % Favored : 73.45 % 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 are not related in a simple way. whole: 1.23 (0.18), residues: 2098 helix: 1.54 (0.15), residues: 1180 sheet: 0.19 (0.32), residues: 208 loop : -0.09 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 24 TYR 0.022 0.001 TYR A 260 PHE 0.013 0.001 PHE A 96 TRP 0.006 0.001 TRP P 78 HIS 0.004 0.001 HIS P 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (29145) covalent geometry : angle 0.53046 / 0.31 (42020) hydrogen bonds : bond 0.04646 / 3.16 ( 1441) hydrogen bonds : angle 4.00096 / 2.87 ( 3694) Misc. bond : bond 0.00031 / 0.02 ( 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 235 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8189 (mptm) REVERT: G 252 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7521 (mttt) REVERT: A 231 LYS cc_start: 0.8123 (mtpp) cc_final: 0.7908 (mtpt) REVERT: K 62 MET cc_start: 0.6572 (pmm) cc_final: 0.6360 (ppp) REVERT: K 206 MET cc_start: 0.8093 (tpp) cc_final: 0.7823 (tpp) REVERT: K 279 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6753 (pt0) REVERT: P 11 ARG cc_start: 0.7201 (ttp80) cc_final: 0.6907 (ttm-80) REVERT: P 204 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.6459 (mm110) REVERT: T 294 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7172 (mttt) outliers start: 45 outliers final: 23 residues processed: 223 average time/residue: 0.6907 time to fit residues: 179.6907 Evaluate side-chains 208 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 213 LEU Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain P residue 204 GLN Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 257 THR 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 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 142 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 222 optimal weight: 20.0000 chunk 128 optimal weight: 0.5980 chunk 95 optimal weight: 0.0070 chunk 147 optimal weight: 40.0000 chunk 244 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 112 ASN ** T 124 GLN ** 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 = 0.4423 r_free = 0.4423 target = 0.195931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147024 restraints weight = 99279.386| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 5.10 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 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 = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29147 Z= 0.137 Angle : 0.522 9.007 42020 Z= 0.302 Chirality : 0.039 0.317 5102 Planarity : 0.004 0.054 3322 Dihedral : 25.547 178.576 9933 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.01 % Allowed : 23.79 % Favored : 73.20 % 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 are not related in a simple way. whole: 1.30 (0.18), residues: 2098 helix: 1.62 (0.15), residues: 1188 sheet: 0.25 (0.32), residues: 208 loop : -0.14 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 24 TYR 0.026 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 E 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (29145) covalent geometry : angle 0.52213 / 0.30 (42020) hydrogen bonds : bond 0.04502 / 3.06 ( 1441) hydrogen bonds : angle 3.91768 / 2.81 ( 3694) Misc. bond : bond 0.00027 / 0.01 ( 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 236 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8182 (mptm) REVERT: G 252 LYS cc_start: 0.7800 (mmmt) cc_final: 0.7521 (mttt) REVERT: A 206 MET cc_start: 0.8219 (tpt) cc_final: 0.7705 (tpt) REVERT: A 231 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7877 (mtpt) REVERT: K 31 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7754 (mtm-85) REVERT: K 206 MET cc_start: 0.8120 (tpp) cc_final: 0.7834 (tpp) REVERT: K 211 LYS cc_start: 0.7440 (mtpp) cc_final: 0.7206 (mttm) REVERT: K 279 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6732 (pt0) REVERT: P 11 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6883 (ttm-80) REVERT: P 204 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6438 (mm110) REVERT: P 261 LYS cc_start: 0.7761 (tmtt) cc_final: 0.7526 (tmtt) REVERT: T 294 LYS cc_start: 0.7376 (mtmp) cc_final: 0.7102 (mttt) outliers start: 48 outliers final: 25 residues processed: 222 average time/residue: 0.5945 time to fit residues: 154.7902 Evaluate side-chains 209 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 53 VAL Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 204 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 34 LEU Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 218 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 106 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 184 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 298 ASN T 112 ASN ** T 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4411 r_free = 0.4411 target = 0.194811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145299 restraints weight = 88128.154| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 4.93 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 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 = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29147 Z= 0.166 Angle : 0.544 9.718 42020 Z= 0.310 Chirality : 0.040 0.317 5102 Planarity : 0.004 0.056 3322 Dihedral : 25.556 179.432 9933 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.33 % Allowed : 23.54 % Favored : 73.13 % 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 are not related in a simple way. whole: 1.23 (0.18), residues: 2098 helix: 1.56 (0.15), residues: 1184 sheet: 0.26 (0.33), residues: 208 loop : -0.17 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 24 TYR 0.029 0.002 TYR A 302 PHE 0.015 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/Z covalent geometry : bond 0.00353 / 0.17 (29145) covalent geometry : angle 0.54362 / 0.31 (42020) hydrogen bonds : bond 0.04611 / 3.13 ( 1441) hydrogen bonds : angle 3.95715 / 2.84 ( 3694) Misc. bond : bond 0.00044 / 0.02 ( 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 243 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8223 (mptm) REVERT: G 252 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7577 (mttt) REVERT: A 206 MET cc_start: 0.8278 (tpt) cc_final: 0.7708 (tpt) REVERT: A 231 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7963 (mtpt) REVERT: K 31 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7712 (mtm-85) REVERT: K 62 MET cc_start: 0.6556 (pmm) cc_final: 0.6083 (ppp) REVERT: K 206 MET cc_start: 0.8122 (tpp) cc_final: 0.7829 (tpp) REVERT: K 279 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6775 (pt0) REVERT: P 261 LYS cc_start: 0.7813 (tmtt) cc_final: 0.7600 (tmtt) REVERT: T 294 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7133 (mttt) REVERT: U 51 TYR cc_start: 0.8693 (p90) cc_final: 0.8467 (p90) REVERT: U 231 LYS cc_start: 0.7346 (mmmm) cc_final: 0.6947 (mtpt) outliers start: 53 outliers final: 34 residues processed: 225 average time/residue: 0.6572 time to fit residues: 173.9973 Evaluate side-chains 225 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 14 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 VAL 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 K residue 299 LEU 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 P residue 289 LEU Chi-restraints excluded: chain T residue 6 THR 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 215 SER Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 218 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 141 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.0070 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 10 GLN G 298 ASN T 112 ASN ** T 124 GLN ** 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 = 0.4420 r_free = 0.4420 target = 0.195656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.146548 restraints weight = 93844.612| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 5.06 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 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 = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29147 Z= 0.144 Angle : 0.535 9.337 42020 Z= 0.305 Chirality : 0.039 0.319 5102 Planarity : 0.004 0.054 3322 Dihedral : 25.549 179.310 9933 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.95 % Allowed : 24.17 % Favored : 72.88 % 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 are not related in a simple way. whole: 1.27 (0.18), residues: 2098 helix: 1.57 (0.15), residues: 1188 sheet: 0.30 (0.33), residues: 208 loop : -0.13 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 24 TYR 0.028 0.002 TYR A 302 PHE 0.012 0.001 PHE P 92 TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS T 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (29145) covalent geometry : angle 0.53452 / 0.30 (42020) hydrogen bonds : bond 0.04502 / 3.06 ( 1441) hydrogen bonds : angle 3.92990 / 2.82 ( 3694) Misc. bond : bond 0.00039 / 0.02 ( 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 240 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8185 (mptm) REVERT: G 252 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7517 (mttt) REVERT: A 206 MET cc_start: 0.8235 (tpt) cc_final: 0.7665 (tpt) REVERT: A 231 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7940 (mtpt) REVERT: K 31 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7733 (mtm-85) REVERT: K 62 MET cc_start: 0.6640 (pmm) cc_final: 0.6434 (ppp) REVERT: K 206 MET cc_start: 0.8137 (tpp) cc_final: 0.7846 (tpp) REVERT: K 279 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6771 (pt0) REVERT: P 11 ARG cc_start: 0.7201 (ttm170) cc_final: 0.6916 (ttp-170) REVERT: T 294 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7124 (mttt) REVERT: U 51 TYR cc_start: 0.8708 (p90) cc_final: 0.8491 (p90) REVERT: U 231 LYS cc_start: 0.7431 (mmmm) cc_final: 0.7004 (mtpt) REVERT: E 176 TYR cc_start: 0.7360 (t80) cc_final: 0.6940 (t80) REVERT: E 180 MET cc_start: 0.7644 (mmt) cc_final: 0.7356 (mpt) outliers start: 47 outliers final: 31 residues processed: 224 average time/residue: 0.6665 time to fit residues: 174.8634 Evaluate side-chains 222 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 6 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 VAL 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 K residue 299 LEU 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 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 218 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 158 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 175 optimal weight: 0.0030 chunk 228 optimal weight: 2.9990 chunk 60 optimal weight: 40.0000 chunk 248 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 86 optimal weight: 0.0060 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 298 ASN A 130 ASN T 112 ASN ** T 124 GLN ** 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 = 0.4424 r_free = 0.4424 target = 0.196307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147663 restraints weight = 101075.860| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 5.22 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 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 = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29147 Z= 0.126 Angle : 0.517 8.991 42020 Z= 0.297 Chirality : 0.038 0.319 5102 Planarity : 0.004 0.053 3322 Dihedral : 25.516 179.308 9933 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.39 % Allowed : 24.67 % Favored : 72.94 % 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 are not related in a simple way. whole: 1.40 (0.18), residues: 2098 helix: 1.69 (0.15), residues: 1188 sheet: 0.35 (0.33), residues: 208 loop : -0.12 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 24 TYR 0.030 0.001 TYR A 302 PHE 0.013 0.001 PHE P 92 TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (29145) covalent geometry : angle 0.51730 / 0.30 (42020) hydrogen bonds : bond 0.04336 / 2.95 ( 1441) hydrogen bonds : angle 3.84866 / 2.77 ( 3694) Misc. bond : bond 0.00027 / 0.01 ( 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 235 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8138 (mptm) REVERT: G 252 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7621 (mttt) REVERT: G 277 LYS cc_start: 0.7790 (mttt) cc_final: 0.6805 (mppt) REVERT: G 288 ASN cc_start: 0.9116 (t0) cc_final: 0.8871 (t0) REVERT: A 206 MET cc_start: 0.8054 (tpt) cc_final: 0.7504 (tpt) REVERT: K 31 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7654 (mtm-85) REVERT: K 206 MET cc_start: 0.8106 (tpp) cc_final: 0.7852 (tpp) REVERT: K 279 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6873 (pt0) REVERT: T 294 LYS cc_start: 0.7430 (mtmp) cc_final: 0.7159 (mttt) REVERT: U 51 TYR cc_start: 0.8664 (p90) cc_final: 0.8420 (p90) REVERT: U 238 ARG cc_start: 0.6662 (tpt170) cc_final: 0.6422 (ttm-80) REVERT: E 176 TYR cc_start: 0.7547 (t80) cc_final: 0.7010 (t80) REVERT: E 180 MET cc_start: 0.7722 (mmt) cc_final: 0.7427 (mpt) outliers start: 38 outliers final: 22 residues processed: 222 average time/residue: 0.6747 time to fit residues: 175.2104 Evaluate side-chains 211 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 6 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 53 VAL 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 K residue 299 LEU 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 34 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain E residue 34 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: 1.9990 chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 33 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 298 ASN ** T 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.195494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.146837 restraints weight = 97619.199| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 5.19 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 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 = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2096 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= 0.140 Angle : 0.525 9.936 42020 Z= 0.300 Chirality : 0.039 0.318 5102 Planarity : 0.004 0.053 3322 Dihedral : 25.508 179.984 9933 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.76 % Allowed : 25.36 % Favored : 72.88 % 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 are not related in a simple way. whole: 1.39 (0.18), residues: 2098 helix: 1.68 (0.15), residues: 1188 sheet: 0.37 (0.34), residues: 208 loop : -0.12 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 24 TYR 0.031 0.002 TYR A 302 PHE 0.013 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/Z covalent geometry : bond 0.00285 / 0.14 (29145) covalent geometry : angle 0.52490 / 0.30 (42020) hydrogen bonds : bond 0.04395 / 2.99 ( 1441) hydrogen bonds : angle 3.86125 / 2.78 ( 3694) Misc. bond : bond 0.00040 / 0.02 ( 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 215 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8117 (mptm) REVERT: G 252 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7637 (mttt) REVERT: G 288 ASN cc_start: 0.9130 (t0) cc_final: 0.8909 (t0) REVERT: A 206 MET cc_start: 0.8081 (tpt) cc_final: 0.7525 (tpt) REVERT: K 31 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7677 (mtm-85) REVERT: K 35 GLU cc_start: 0.7286 (pm20) cc_final: 0.7052 (mp0) REVERT: K 206 MET cc_start: 0.8099 (tpp) cc_final: 0.7856 (tpp) REVERT: K 211 LYS cc_start: 0.7481 (mmmt) cc_final: 0.7130 (mttm) REVERT: K 279 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6882 (pt0) REVERT: P 261 LYS cc_start: 0.7597 (tmtt) cc_final: 0.7396 (tmtt) REVERT: T 294 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7182 (mttt) REVERT: U 51 TYR cc_start: 0.8687 (p90) cc_final: 0.8448 (p90) REVERT: E 30 ILE cc_start: 0.8873 (mm) cc_final: 0.8662 (tp) REVERT: E 176 TYR cc_start: 0.7577 (t80) cc_final: 0.7339 (t80) outliers start: 28 outliers final: 22 residues processed: 205 average time/residue: 0.6765 time to fit residues: 162.1046 Evaluate side-chains 208 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 6 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 299 LEU 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 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 50 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 255 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 62 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 253 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 298 ASN ** T 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.193923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.144671 restraints weight = 86726.440| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 4.99 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2090 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= 0.184 Angle : 0.558 12.827 42020 Z= 0.315 Chirality : 0.040 0.317 5102 Planarity : 0.004 0.057 3322 Dihedral : 25.536 179.386 9933 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.13 % Allowed : 25.36 % Favored : 72.50 % 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 are not related in a simple way. whole: 1.20 (0.18), residues: 2098 helix: 1.54 (0.15), residues: 1184 sheet: 0.11 (0.32), residues: 232 loop : -0.17 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 24 TYR 0.031 0.002 TYR A 302 PHE 0.017 0.002 PHE A 10 TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS T 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (29145) covalent geometry : angle 0.55817 / 0.31 (42020) hydrogen bonds : bond 0.04629 / 3.13 ( 1441) hydrogen bonds : angle 3.96241 / 2.86 ( 3694) Misc. bond : bond 0.00072 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7688.96 seconds wall clock time: 132 minutes 30.24 seconds (7950.24 seconds total)