Starting phenix.real_space_refine on Sun May 25 13:26:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qbk_18313/05_2025/8qbk_18313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qbk_18313/05_2025/8qbk_18313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qbk_18313/05_2025/8qbk_18313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qbk_18313/05_2025/8qbk_18313.map" model { file = "/net/cci-nas-00/data/ceres_data/8qbk_18313/05_2025/8qbk_18313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qbk_18313/05_2025/8qbk_18313.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 6} 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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 6} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} 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: {'GLN:plan1': 3, 'ASP:plan': 14, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6} 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: 24.39, per 1000 atoms: 0.89 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: 7.21 Conformation dependent library (CDL) restraints added in 3.8 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: 12.48 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: 11.22 Time building geometry restraints manager: 8.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3277 1.32 - 1.44: 10982 1.44 - 1.57: 13731 1.57 - 1.69: 1083 1.69 - 1.81: 72 Bond restraints: 29145 Sorted by residual: bond pdb=" CA LYS A 231 " pdb=" C LYS A 231 " ideal model delta sigma weight residual 1.526 1.588 -0.062 1.23e-02 6.61e+03 2.58e+01 bond pdb=" CD GLU E 106 " pdb=" OE2 GLU E 106 " ideal model delta sigma weight residual 1.249 1.342 -0.093 1.90e-02 2.77e+03 2.38e+01 bond pdb=" CD GLU T 106 " pdb=" OE2 GLU T 106 " ideal model delta sigma weight residual 1.249 1.341 -0.092 1.90e-02 2.77e+03 2.35e+01 bond pdb=" N ILE P 94 " pdb=" CA ILE P 94 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N TYR E 137 " pdb=" CA TYR E 137 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.26e+00 ... (remaining 29140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.09: 41973 6.09 - 12.18: 39 12.18 - 18.26: 5 18.26 - 24.35: 2 24.35 - 30.44: 1 Bond angle restraints: 42020 Sorted by residual: angle pdb=" O GLU E 106 " pdb=" C GLU E 106 " pdb=" N LEU E 107 " ideal model delta sigma weight residual 122.15 91.71 30.44 1.14e+00 7.69e-01 7.13e+02 angle pdb=" O GLU T 106 " pdb=" C GLU T 106 " pdb=" N LEU T 107 " ideal model delta sigma weight residual 122.15 99.70 22.45 1.14e+00 7.69e-01 3.88e+02 angle pdb=" C3' G W 64 " pdb=" O3' G W 64 " pdb=" P C W 65 " ideal model delta sigma weight residual 120.20 99.14 21.06 1.50e+00 4.44e-01 1.97e+02 angle pdb=" C3' G C 64 " pdb=" O3' G C 64 " pdb=" P C C 65 " ideal model delta sigma weight residual 120.20 102.81 17.39 1.50e+00 4.44e-01 1.34e+02 angle pdb=" C3' G M 64 " pdb=" O3' G M 64 " pdb=" P C M 65 " ideal model delta sigma weight residual 120.20 103.89 16.31 1.50e+00 4.44e-01 1.18e+02 ... (remaining 42015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 15241 35.95 - 71.90: 1942 71.90 - 107.85: 108 107.85 - 143.80: 3 143.80 - 179.75: 22 Dihedral angle restraints: 17316 sinusoidal: 11130 harmonic: 6186 Sorted by residual: dihedral pdb=" O4' U C 74 " pdb=" C1' U C 74 " pdb=" N1 U C 74 " pdb=" C2 U C 74 " ideal model delta sinusoidal sigma weight residual -160.00 19.42 -179.42 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U W 74 " pdb=" C1' U W 74 " pdb=" N1 U W 74 " pdb=" C2 U W 74 " ideal model delta sinusoidal sigma weight residual -160.00 17.49 -177.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 74 " pdb=" C1' U M 74 " pdb=" N1 U M 74 " pdb=" C2 U M 74 " ideal model delta sinusoidal sigma weight residual -160.00 16.73 -176.73 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 17313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4886 0.098 - 0.196: 181 0.196 - 0.294: 9 0.294 - 0.392: 11 0.392 - 0.490: 15 Chirality restraints: 5102 Sorted by residual: chirality pdb=" P G W 69 " pdb=" OP1 G W 69 " pdb=" OP2 G W 69 " pdb=" O5' G W 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" P G R 69 " pdb=" OP1 G R 69 " pdb=" OP2 G R 69 " pdb=" O5' G R 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" P G C 69 " pdb=" OP1 G C 69 " pdb=" OP2 G C 69 " pdb=" O5' G C 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 5099 not shown) Planarity restraints: 3322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 106 " -0.122 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" C GLU E 106 " 0.355 2.00e-02 2.50e+03 pdb=" O GLU E 106 " -0.121 2.00e-02 2.50e+03 pdb=" N LEU E 107 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 106 " -0.102 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C GLU T 106 " 0.312 2.00e-02 2.50e+03 pdb=" O GLU T 106 " -0.109 2.00e-02 2.50e+03 pdb=" N LEU T 107 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 252 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LYS K 252 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS K 252 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL K 253 " 0.021 2.00e-02 2.50e+03 ... (remaining 3319 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.02: 1 2.02 - 2.74: 3224 2.74 - 3.46: 39100 3.46 - 4.18: 78313 4.18 - 4.90: 121315 Nonbonded interactions: 241953 Sorted by model distance: nonbonded pdb=" NZ LYS A 231 " pdb=" OP1 G C 69 " model vdw 1.306 3.120 nonbonded pdb=" O2' C W 55 " pdb=" OP2 G W 56 " model vdw 2.132 3.040 nonbonded pdb=" O2' G W 16 " pdb=" O5' A W 17 " model vdw 2.173 3.040 nonbonded pdb=" NZ LYS A 231 " pdb=" P G C 69 " model vdw 2.204 3.480 nonbonded pdb=" O ARG U 238 " pdb=" N2 G W 44 " model vdw 2.205 3.120 ... (remaining 241948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 23 or resid 25 through 206 or (resid 207 through \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throu \ gh 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) or \ resid 232 through 237 or (resid 238 and (name N or name CA or name C or name O \ or name CB )) or resid 239 through 257 or (resid 258 through 259 and (name N or \ name CA or name C or name O or name CB )) or resid 260 or (resid 261 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 3 \ 11)) selection = (chain 'K' and (resid 3 through 23 or resid 25 through 206 or (resid 207 through \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throu \ gh 210 or (resid 211 through 212 and (name N or name CA or name C or name O or n \ ame CB )) or resid 213 through 237 or (resid 238 and (name N or name CA or name \ C or name O or name CB )) or resid 239 through 311)) selection = (chain 'P' and (resid 3 through 23 or resid 25 through 210 or (resid 211 through \ 212 and (name N or name CA or name C or name O or name CB )) or resid 213 throu \ gh 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) or \ resid 232 through 257 or (resid 258 through 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 or (resid 261 through 262 and (name N or \ name CA or name C or name O or name CB )) or resid 263 through 311)) selection = (chain 'U' and (resid 3 through 23 or resid 25 through 206 or (resid 207 through \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throu \ gh 210 or (resid 211 through 212 and (name N or name CA or name C or name O or n \ ame CB )) or resid 213 through 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 232 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 257 or (resid 258 \ through 259 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 60 or (resid 261 through 262 and (name N or name CA or name C or name O or name \ CB )) or resid 263 through 311)) } ncs_group { reference = chain 'B' selection = (chain 'Q' and resid 1 through 85) } ncs_group { reference = chain 'C' selection = chain 'M' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'S' selection = chain 'X' } ncs_group { reference = (chain 'E' and (resid 3 through 41 or (resid 42 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 179 or (resid 180 throug \ h 181 and (name N or name CA or name C or name O or name CB )) or resid 182 thro \ ugh 304 or resid 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: 21.180 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 77.880 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 29147 Z= 0.243 Angle : 0.731 30.441 42020 Z= 0.458 Chirality : 0.049 0.490 5102 Planarity : 0.006 0.205 3322 Dihedral : 24.714 179.747 13324 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.69 % Allowed : 25.11 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 PHE 0.040 0.001 PHE E 5 TYR 0.021 0.001 TYR E 137 ARG 0.011 0.000 ARG K 238 Details of bonding type rmsd hydrogen bonds : bond 0.15028 ( 1441) hydrogen bonds : angle 5.75972 ( 3694) covalent geometry : bond 0.00419 (29145) covalent geometry : angle 0.73137 (42020) Misc. bond : bond 0.05467 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 246 ARG cc_start: 0.7542 (ttp-170) cc_final: 0.6573 (tpt90) REVERT: G 252 LYS cc_start: 0.6287 (mmtp) cc_final: 0.6041 (mmmt) REVERT: K 233 CYS cc_start: 0.6539 (t) cc_final: 0.5732 (p) REVERT: P 261 LYS cc_start: 0.6597 (tmtt) cc_final: 0.5776 (tmtt) REVERT: T 65 GLU cc_start: 0.8330 (pm20) cc_final: 0.8016 (mp0) REVERT: E 106 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8081 (mt-10) outliers start: 11 outliers final: 5 residues processed: 227 average time/residue: 1.4474 time to fit residues: 379.8996 Evaluate side-chains 189 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain E residue 69 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 30.0000 chunk 232 optimal weight: 0.1980 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 10 GLN F 249 ASN E 12 GLN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 255 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.192127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142567 restraints weight = 89031.138| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.89 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 29147 Z= 0.252 Angle : 0.632 7.992 42020 Z= 0.337 Chirality : 0.040 0.222 5102 Planarity : 0.005 0.065 3322 Dihedral : 25.635 177.298 9942 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.89 % Allowed : 22.79 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2098 helix: 1.21 (0.15), residues: 1180 sheet: 0.31 (0.33), residues: 192 loop : -0.18 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 78 HIS 0.005 0.001 HIS E 16 PHE 0.020 0.002 PHE E 134 TYR 0.028 0.002 TYR A 260 ARG 0.007 0.001 ARG K 238 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 1441) hydrogen bonds : angle 4.33926 ( 3694) covalent geometry : bond 0.00582 (29145) covalent geometry : angle 0.63245 (42020) Misc. bond : bond 0.00055 ( 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 273 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 252 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8222 (mptm) REVERT: F 265 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8182 (mp) REVERT: G 246 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7384 (tpt90) REVERT: K 211 LYS cc_start: 0.7436 (mtpp) cc_final: 0.7191 (mttm) REVERT: P 11 ARG cc_start: 0.7305 (ttp80) cc_final: 0.7059 (ttm-80) REVERT: T 294 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7161 (mttt) REVERT: U 206 MET cc_start: 0.7977 (tpt) cc_final: 0.7728 (tpt) outliers start: 62 outliers final: 23 residues processed: 251 average time/residue: 1.3000 time to fit residues: 382.5882 Evaluate side-chains 210 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 250 GLU 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 F residue 265 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 262 VAL Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 233 CYS Chi-restraints excluded: chain U residue 293 SER Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 98 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 209 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN T 112 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.196397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147588 restraints weight = 100812.322| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 5.18 r_work (final): 0.3862 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29147 Z= 0.143 Angle : 0.535 7.581 42020 Z= 0.289 Chirality : 0.035 0.236 5102 Planarity : 0.004 0.059 3322 Dihedral : 25.474 179.448 9933 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.64 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2098 helix: 1.49 (0.15), residues: 1190 sheet: 0.12 (0.33), residues: 200 loop : -0.08 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 PHE 0.017 0.001 PHE T 134 TYR 0.018 0.001 TYR A 260 ARG 0.009 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 1441) hydrogen bonds : angle 3.97258 ( 3694) covalent geometry : bond 0.00318 (29145) covalent geometry : angle 0.53533 (42020) Misc. bond : bond 0.00086 ( 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 265 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 204 ARG cc_start: 0.7049 (mtt90) cc_final: 0.6710 (mtt90) REVERT: G 277 LYS cc_start: 0.7859 (mttt) cc_final: 0.6818 (mppt) REVERT: K 206 MET cc_start: 0.8015 (tpp) cc_final: 0.7802 (tpp) REVERT: K 211 LYS cc_start: 0.7307 (mtpp) cc_final: 0.7079 (mttm) REVERT: K 279 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6738 (pt0) REVERT: P 11 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6998 (ttm-80) REVERT: T 294 LYS cc_start: 0.7446 (mtmp) cc_final: 0.7170 (mttt) REVERT: U 206 MET cc_start: 0.7764 (tpt) cc_final: 0.7475 (tpt) outliers start: 58 outliers final: 19 residues processed: 249 average time/residue: 1.3757 time to fit residues: 398.3121 Evaluate side-chains 202 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 100 GLN 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 93 VAL Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 69 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 250 optimal weight: 0.2980 chunk 231 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN E 249 ASN E 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.193501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145017 restraints weight = 112907.831| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 5.22 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 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 = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 29147 Z= 0.195 Angle : 0.563 7.634 42020 Z= 0.303 Chirality : 0.037 0.214 5102 Planarity : 0.004 0.061 3322 Dihedral : 25.477 177.903 9933 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.45 % Allowed : 22.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.18), residues: 2098 helix: 1.46 (0.15), residues: 1180 sheet: 0.16 (0.33), residues: 200 loop : -0.09 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.004 0.001 HIS U 280 PHE 0.017 0.002 PHE A 10 TYR 0.029 0.002 TYR U 184 ARG 0.007 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 1441) hydrogen bonds : angle 4.01742 ( 3694) covalent geometry : bond 0.00453 (29145) covalent geometry : angle 0.56295 (42020) Misc. bond : bond 0.00063 ( 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 251 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 24 ARG cc_start: 0.7293 (mtt90) cc_final: 0.6810 (mtt90) REVERT: G 204 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6859 (mtt90) REVERT: G 252 LYS cc_start: 0.7666 (mmmt) cc_final: 0.7275 (mttt) REVERT: G 277 LYS cc_start: 0.7874 (mttt) cc_final: 0.6835 (mppt) REVERT: K 206 MET cc_start: 0.8081 (tpp) cc_final: 0.7827 (tpp) REVERT: K 279 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6737 (pt0) REVERT: P 11 ARG cc_start: 0.7270 (ttp80) cc_final: 0.6961 (ttm-80) REVERT: T 11 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8723 (mm-40) REVERT: T 294 LYS cc_start: 0.7397 (mtmp) cc_final: 0.7139 (mttt) outliers start: 55 outliers final: 29 residues processed: 231 average time/residue: 1.2740 time to fit residues: 345.7960 Evaluate side-chains 209 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 52 THR 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 249 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 218 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 287 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 212 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 237 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 47 optimal weight: 0.0040 chunk 50 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 37 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.195843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146977 restraints weight = 99881.557| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 5.13 r_work (final): 0.3855 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29147 Z= 0.144 Angle : 0.535 8.069 42020 Z= 0.288 Chirality : 0.035 0.208 5102 Planarity : 0.004 0.057 3322 Dihedral : 25.444 178.654 9933 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.76 % Allowed : 23.67 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.18), residues: 2098 helix: 1.59 (0.15), residues: 1188 sheet: 0.22 (0.33), residues: 200 loop : -0.10 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 PHE 0.013 0.001 PHE U 92 TYR 0.027 0.002 TYR U 184 ARG 0.007 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 1441) hydrogen bonds : angle 3.88299 ( 3694) covalent geometry : bond 0.00322 (29145) covalent geometry : angle 0.53501 (42020) Misc. bond : bond 0.00035 ( 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 242 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 24 ARG cc_start: 0.7298 (mtt90) cc_final: 0.6782 (mtt90) REVERT: G 252 LYS cc_start: 0.7604 (mmmt) cc_final: 0.7267 (mttt) REVERT: G 254 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8565 (tt) REVERT: G 277 LYS cc_start: 0.7857 (mttt) cc_final: 0.6874 (mppt) REVERT: G 288 ASN cc_start: 0.9058 (t0) cc_final: 0.8788 (t0) REVERT: K 206 MET cc_start: 0.8089 (tpp) cc_final: 0.7789 (tpp) REVERT: K 211 LYS cc_start: 0.7423 (mtpp) cc_final: 0.7127 (mttm) REVERT: K 279 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6796 (pt0) REVERT: P 11 ARG cc_start: 0.7232 (ttp80) cc_final: 0.6947 (ttm-80) REVERT: T 294 LYS cc_start: 0.7396 (mtmp) cc_final: 0.7135 (mttt) REVERT: U 206 MET cc_start: 0.7854 (tpt) cc_final: 0.7498 (tpt) outliers start: 44 outliers final: 27 residues processed: 230 average time/residue: 1.3516 time to fit residues: 362.8641 Evaluate side-chains 210 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 293 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 265 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 225 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN T 124 GLN ** E 47 HIS ** 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 = 0.4393 r_free = 0.4393 target = 0.193053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.144889 restraints weight = 100080.678| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 4.74 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 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 = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29147 Z= 0.197 Angle : 0.561 7.722 42020 Z= 0.301 Chirality : 0.037 0.220 5102 Planarity : 0.004 0.070 3322 Dihedral : 25.465 179.770 9933 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.20 % Allowed : 23.98 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2098 helix: 1.53 (0.15), residues: 1180 sheet: 0.12 (0.33), residues: 200 loop : -0.10 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.006 0.001 HIS T 16 PHE 0.017 0.002 PHE P 10 TYR 0.029 0.002 TYR A 302 ARG 0.010 0.001 ARG K 238 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 1441) hydrogen bonds : angle 3.98158 ( 3694) covalent geometry : bond 0.00457 (29145) covalent geometry : angle 0.56123 (42020) Misc. bond : bond 0.00069 ( 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 243 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 252 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7357 (mttt) REVERT: G 254 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8541 (tt) REVERT: G 288 ASN cc_start: 0.9099 (t0) cc_final: 0.8807 (t0) REVERT: K 31 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8126 (mtm-85) REVERT: K 35 GLU cc_start: 0.7435 (pm20) cc_final: 0.7201 (mp0) REVERT: K 206 MET cc_start: 0.8164 (tpp) cc_final: 0.7893 (tpp) REVERT: K 279 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6817 (pt0) REVERT: T 294 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7202 (mttt) REVERT: E 293 ARG cc_start: 0.6603 (ttp-170) cc_final: 0.6290 (mtm-85) outliers start: 51 outliers final: 32 residues processed: 227 average time/residue: 1.3638 time to fit residues: 361.2531 Evaluate side-chains 215 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 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 249 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 218 SER 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 55 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 92 optimal weight: 0.0970 chunk 171 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 223 optimal weight: 8.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN E 47 HIS 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 = 0.4414 r_free = 0.4414 target = 0.195157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147021 restraints weight = 106394.748| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 4.87 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 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 = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29147 Z= 0.143 Angle : 0.540 9.289 42020 Z= 0.291 Chirality : 0.035 0.200 5102 Planarity : 0.004 0.055 3322 Dihedral : 25.457 179.317 9933 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.82 % Allowed : 24.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2098 helix: 1.58 (0.15), residues: 1188 sheet: 0.12 (0.33), residues: 200 loop : -0.11 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 PHE 0.014 0.001 PHE U 92 TYR 0.027 0.002 TYR A 302 ARG 0.011 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 1441) hydrogen bonds : angle 3.88464 ( 3694) covalent geometry : bond 0.00320 (29145) covalent geometry : angle 0.54040 (42020) Misc. bond : bond 0.00039 ( 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 234 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 235 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8046 (mp) REVERT: G 252 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7354 (mttt) REVERT: G 276 ARG cc_start: 0.7063 (ttp80) cc_final: 0.6708 (ttp80) REVERT: G 288 ASN cc_start: 0.9083 (t0) cc_final: 0.8816 (t0) REVERT: K 31 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8128 (mtm-85) REVERT: K 35 GLU cc_start: 0.7426 (pm20) cc_final: 0.7166 (mp0) REVERT: K 206 MET cc_start: 0.8144 (tpp) cc_final: 0.7829 (tpp) REVERT: K 279 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6819 (pt0) REVERT: P 211 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7319 (mmtt) REVERT: T 294 LYS cc_start: 0.7417 (mtmp) cc_final: 0.7134 (mttt) REVERT: E 176 TYR cc_start: 0.7743 (t80) cc_final: 0.7428 (t80) REVERT: E 293 ARG cc_start: 0.6730 (ttp-170) cc_final: 0.6423 (mtm-85) outliers start: 45 outliers final: 28 residues processed: 224 average time/residue: 1.3249 time to fit residues: 345.6042 Evaluate side-chains 214 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 218 SER Chi-restraints excluded: chain U residue 293 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 265 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 150 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 194 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4410 r_free = 0.4410 target = 0.195007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145971 restraints weight = 98516.753| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 5.21 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2089 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= 0.146 Angle : 0.536 8.937 42020 Z= 0.288 Chirality : 0.035 0.197 5102 Planarity : 0.004 0.054 3322 Dihedral : 25.422 179.819 9933 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.51 % Allowed : 25.24 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2098 helix: 1.65 (0.15), residues: 1188 sheet: 0.18 (0.32), residues: 208 loop : -0.13 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 PHE 0.015 0.001 PHE U 215 TYR 0.034 0.002 TYR A 302 ARG 0.010 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 1441) hydrogen bonds : angle 3.84056 ( 3694) covalent geometry : bond 0.00328 (29145) covalent geometry : angle 0.53579 (42020) Misc. bond : bond 0.00048 ( 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 235 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 252 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7432 (mttt) REVERT: G 276 ARG cc_start: 0.6945 (ttp80) cc_final: 0.6556 (ttp80) REVERT: G 288 ASN cc_start: 0.9119 (t0) cc_final: 0.8900 (t0) REVERT: K 31 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8170 (mtm-85) REVERT: K 35 GLU cc_start: 0.7328 (pm20) cc_final: 0.7067 (mp0) REVERT: K 206 MET cc_start: 0.8141 (tpp) cc_final: 0.7854 (tpp) REVERT: K 211 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7103 (mttm) REVERT: K 279 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6804 (pt0) REVERT: P 211 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7248 (mmtt) REVERT: T 294 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7189 (mttt) REVERT: E 176 TYR cc_start: 0.7870 (t80) cc_final: 0.7555 (t80) REVERT: E 293 ARG cc_start: 0.6756 (ttp-170) cc_final: 0.6442 (mtm-85) outliers start: 40 outliers final: 29 residues processed: 224 average time/residue: 1.4334 time to fit residues: 381.9229 Evaluate side-chains 216 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 26 MET 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 P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 249 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 148 SER Chi-restraints excluded: chain T residue 169 VAL 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 7 LEU 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 141 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 248 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4411 r_free = 0.4411 target = 0.195065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146039 restraints weight = 95249.249| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 5.15 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 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 = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29147 Z= 0.146 Angle : 0.536 9.787 42020 Z= 0.288 Chirality : 0.035 0.197 5102 Planarity : 0.004 0.054 3322 Dihedral : 25.417 179.909 9933 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.57 % Allowed : 25.55 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2098 helix: 1.66 (0.15), residues: 1188 sheet: 0.19 (0.32), residues: 208 loop : -0.13 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 PHE 0.018 0.001 PHE U 215 TYR 0.032 0.001 TYR A 302 ARG 0.010 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 1441) hydrogen bonds : angle 3.84111 ( 3694) covalent geometry : bond 0.00328 (29145) covalent geometry : angle 0.53634 (42020) Misc. bond : bond 0.00043 ( 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 232 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 252 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7578 (mttt) REVERT: G 288 ASN cc_start: 0.9117 (t0) cc_final: 0.8834 (t0) REVERT: K 31 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8159 (mtm-85) REVERT: K 35 GLU cc_start: 0.7293 (pm20) cc_final: 0.7059 (mp0) REVERT: K 206 MET cc_start: 0.8129 (tpp) cc_final: 0.7853 (tpp) REVERT: K 211 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7067 (mttm) REVERT: K 279 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6812 (pt0) REVERT: P 211 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7266 (mmtt) REVERT: T 294 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7182 (mttt) REVERT: E 30 ILE cc_start: 0.8881 (mm) cc_final: 0.8623 (tp) REVERT: E 176 TYR cc_start: 0.7863 (t80) cc_final: 0.7546 (t80) REVERT: E 293 ARG cc_start: 0.6755 (ttp-170) cc_final: 0.6446 (mtm-85) outliers start: 41 outliers final: 29 residues processed: 219 average time/residue: 1.2872 time to fit residues: 329.8524 Evaluate side-chains 219 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 26 MET 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 P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 249 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 148 SER Chi-restraints excluded: chain T residue 169 VAL 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 7 LEU 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 239 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 172 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 112 optimal weight: 0.0870 chunk 38 optimal weight: 0.0670 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN T 112 ASN 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 = 0.195822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.147215 restraints weight = 101136.616| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 5.21 r_work (final): 0.3856 ------------------------------------------------------------------------------- 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29147 Z= 0.132 Angle : 0.531 9.808 42020 Z= 0.287 Chirality : 0.035 0.197 5102 Planarity : 0.004 0.053 3322 Dihedral : 25.404 179.837 9933 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.20 % Allowed : 25.86 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 2098 helix: 1.68 (0.15), residues: 1188 sheet: 0.25 (0.33), residues: 208 loop : -0.11 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 PHE 0.019 0.001 PHE U 215 TYR 0.033 0.001 TYR U 184 ARG 0.010 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1441) hydrogen bonds : angle 3.81429 ( 3694) covalent geometry : bond 0.00292 (29145) covalent geometry : angle 0.53125 (42020) Misc. bond : bond 0.00035 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 252 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7460 (mttt) REVERT: G 277 LYS cc_start: 0.7563 (mtmt) cc_final: 0.6754 (mppt) REVERT: G 288 ASN cc_start: 0.9087 (t0) cc_final: 0.8812 (t0) REVERT: K 31 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8143 (mtm-85) REVERT: K 206 MET cc_start: 0.8150 (tpp) cc_final: 0.7887 (tpp) REVERT: K 211 LYS cc_start: 0.7561 (mtpt) cc_final: 0.7011 (mttm) REVERT: K 279 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6827 (pt0) REVERT: P 211 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7260 (mmtt) REVERT: T 294 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7162 (mttt) REVERT: E 30 ILE cc_start: 0.8904 (mm) cc_final: 0.8657 (tp) REVERT: E 176 TYR cc_start: 0.7900 (t80) cc_final: 0.7551 (t80) REVERT: E 293 ARG cc_start: 0.6750 (ttp-170) cc_final: 0.6450 (mtm-85) outliers start: 35 outliers final: 28 residues processed: 215 average time/residue: 1.3032 time to fit residues: 335.3769 Evaluate side-chains 213 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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 5 PHE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain P residue 233 CYS Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 249 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 148 SER Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain 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 55 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN E 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.194537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145531 restraints weight = 100959.882| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 5.24 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29147 Z= 0.165 Angle : 0.550 10.484 42020 Z= 0.295 Chirality : 0.036 0.196 5102 Planarity : 0.004 0.055 3322 Dihedral : 25.406 179.216 9933 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.20 % Allowed : 25.86 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.18), residues: 2098 helix: 1.62 (0.15), residues: 1184 sheet: 0.21 (0.33), residues: 208 loop : -0.16 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS P 280 PHE 0.022 0.001 PHE U 215 TYR 0.033 0.002 TYR U 184 ARG 0.009 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 1441) hydrogen bonds : angle 3.87786 ( 3694) covalent geometry : bond 0.00378 (29145) covalent geometry : angle 0.55031 (42020) Misc. bond : bond 0.00058 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14859.31 seconds wall clock time: 258 minutes 2.11 seconds (15482.11 seconds total)