Starting phenix.real_space_refine on Wed Mar 4 11:15:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ux4_20929/03_2026/6ux4_20929.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ux4_20929/03_2026/6ux4_20929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ux4_20929/03_2026/6ux4_20929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ux4_20929/03_2026/6ux4_20929.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ux4_20929/03_2026/6ux4_20929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ux4_20929/03_2026/6ux4_20929.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Ca 24 9.91 5 S 56 5.16 5 C 8302 2.51 5 N 2374 2.21 5 O 2501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13257 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "E" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 9, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "G" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 9, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 241 " occ=0.50 residue: pdb=" N AARG C 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 241 " occ=0.50 Time building chain proxies: 4.05, per 1000 atoms: 0.31 Number of scatterers: 13257 At special positions: 0 Unit cell: (138.03, 133.75, 66.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 24 19.99 S 56 16.00 O 2501 8.00 N 2374 7.00 C 8302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 749.2 milliseconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 16 sheets defined 43.5% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.711A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.798A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.572A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.969A pdb=" N LEU A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'E' and resid 124 through 133 removed outlier: 3.882A pdb=" N GLU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 148 through 155 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.947A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.624A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.668A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.693A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.629A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.596A pdb=" N VAL E 288 " --> pdb=" O ASP E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 134 removed outlier: 3.632A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 removed outlier: 3.616A pdb=" N ARG B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.745A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.580A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.807A pdb=" N LEU B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.526A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 removed outlier: 3.790A pdb=" N GLU F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.562A pdb=" N THR F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 223 Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.727A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.756A pdb=" N ASP F 254 " --> pdb=" O MET F 250 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.539A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 132 removed outlier: 3.620A pdb=" N GLU C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 156 removed outlier: 3.583A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.564A pdb=" N GLU C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.573A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.610A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.738A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 332 removed outlier: 3.515A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.528A pdb=" N GLU G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 147 No H-bonds generated for 'chain 'G' and resid 145 through 147' Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.580A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.530A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.761A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.573A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 256 removed outlier: 3.657A pdb=" N GLN G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 removed outlier: 3.610A pdb=" N VAL G 288 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 334 removed outlier: 3.543A pdb=" N ASN G 332 " --> pdb=" O GLU G 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.623A pdb=" N GLU D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.617A pdb=" N ARG D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.743A pdb=" N ILE D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 230 through 241 removed outlier: 3.581A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.809A pdb=" N LEU D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.526A pdb=" N ASN D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 removed outlier: 3.794A pdb=" N GLU H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 155 Processing helix chain 'H' and resid 166 through 171 Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.557A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 223 Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.511A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.756A pdb=" N ASP H 254 " --> pdb=" O MET H 250 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.556A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.398A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 207 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE A 229 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA A 209 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY A 295 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.519A pdb=" N ALA E 143 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 3.664A pdb=" N GLY E 322 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY E 295 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.654A pdb=" N ALA B 143 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 119 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 207 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 209 " --> pdb=" O ILE B 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.577A pdb=" N GLY B 322 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 317 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 296 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 296 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.245A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 119 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL F 181 " --> pdb=" O ILE F 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.695A pdb=" N GLY F 322 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE F 317 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL F 296 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.402A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA C 209 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 263 through 268 removed outlier: 3.516A pdb=" N GLY C 295 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 157 through 161 removed outlier: 3.520A pdb=" N ALA G 143 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 3.695A pdb=" N GLY G 322 " --> pdb=" O ARG G 263 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 295 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.650A pdb=" N ALA D 143 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 119 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE D 229 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA D 209 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.580A pdb=" N GLY D 322 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE D 317 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL D 296 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 296 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.245A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL H 119 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.731A pdb=" N GLY H 322 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE H 317 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL H 296 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU H 319 " --> pdb=" O ILE H 294 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3364 1.33 - 1.45: 2169 1.45 - 1.57: 7779 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 13400 Sorted by residual: bond pdb=" CG GLN A 227 " pdb=" CD GLN A 227 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.91e+00 bond pdb=" CG LEU E 220 " pdb=" CD2 LEU E 220 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.74e+00 bond pdb=" CG LEU D 220 " pdb=" CD2 LEU D 220 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.73e+00 bond pdb=" CG GLN C 227 " pdb=" CD GLN C 227 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.66e+00 bond pdb=" CG LEU B 220 " pdb=" CD2 LEU B 220 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.61e+00 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 17136 1.63 - 3.26: 871 3.26 - 4.89: 135 4.89 - 6.52: 7 6.52 - 8.16: 3 Bond angle restraints: 18152 Sorted by residual: angle pdb=" C GLU B 266 " pdb=" N VAL B 267 " pdb=" CA VAL B 267 " ideal model delta sigma weight residual 123.33 119.66 3.67 8.70e-01 1.32e+00 1.77e+01 angle pdb=" N GLU D 259 " pdb=" CA GLU D 259 " pdb=" C GLU D 259 " ideal model delta sigma weight residual 114.56 109.45 5.11 1.27e+00 6.20e-01 1.62e+01 angle pdb=" N GLU B 259 " pdb=" CA GLU B 259 " pdb=" C GLU B 259 " ideal model delta sigma weight residual 114.56 109.46 5.10 1.27e+00 6.20e-01 1.61e+01 angle pdb=" C GLU D 266 " pdb=" N VAL D 267 " pdb=" CA VAL D 267 " ideal model delta sigma weight residual 123.33 119.84 3.49 8.70e-01 1.32e+00 1.61e+01 angle pdb=" C VAL B 267 " pdb=" CA VAL B 267 " pdb=" CB VAL B 267 " ideal model delta sigma weight residual 110.13 113.16 -3.03 9.70e-01 1.06e+00 9.74e+00 ... (remaining 18147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7441 17.54 - 35.09: 624 35.09 - 52.63: 83 52.63 - 70.18: 19 70.18 - 87.72: 13 Dihedral angle restraints: 8180 sinusoidal: 3108 harmonic: 5072 Sorted by residual: dihedral pdb=" CA ASN B 147 " pdb=" C ASN B 147 " pdb=" N VAL B 148 " pdb=" CA VAL B 148 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN D 147 " pdb=" C ASN D 147 " pdb=" N VAL D 148 " pdb=" CA VAL D 148 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CB GLU A 171 " pdb=" CG GLU A 171 " pdb=" CD GLU A 171 " pdb=" OE1 GLU A 171 " ideal model delta sinusoidal sigma weight residual 0.00 87.72 -87.72 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1791 0.077 - 0.155: 360 0.155 - 0.232: 19 0.232 - 0.310: 2 0.310 - 0.387: 2 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB ILE C 293 " pdb=" CA ILE C 293 " pdb=" CG1 ILE C 293 " pdb=" CG2 ILE C 293 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB ILE A 293 " pdb=" CA ILE A 293 " pdb=" CG1 ILE A 293 " pdb=" CG2 ILE A 293 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL B 205 " pdb=" CA VAL B 205 " pdb=" CG1 VAL B 205 " pdb=" CG2 VAL B 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2171 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 267 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C VAL A 267 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 267 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 268 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 267 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C VAL C 267 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL C 267 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO C 268 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 267 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO C 268 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " -0.031 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3224 2.78 - 3.31: 10984 3.31 - 3.84: 21168 3.84 - 4.37: 24208 4.37 - 4.90: 44003 Nonbonded interactions: 103587 Sorted by model distance: nonbonded pdb=" OD1 ASP A 184 " pdb=" O HOH A 501 " model vdw 2.254 3.040 nonbonded pdb=" O ILE D 285 " pdb=" OG1 THR D 289 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 185 " pdb=" O HOH A 501 " model vdw 2.263 3.040 nonbonded pdb=" OG SER E 124 " pdb=" OD2 ASP E 184 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 124 " pdb=" OD2 ASP A 184 " model vdw 2.268 3.040 ... (remaining 103582 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 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 401)) \ selection = (chain 'B' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 401)) selection = (chain 'C' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 401)) \ selection = (chain 'D' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 401)) selection = (chain 'E' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 401)) selection = (chain 'F' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 401)) selection = (chain 'G' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 401)) selection = (chain 'H' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 401)) } 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 group one per residue 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.060 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.011 0.071 13400 Z= 0.435 Angle : 0.832 8.155 18152 Z= 0.481 Chirality : 0.060 0.387 2174 Planarity : 0.005 0.056 2360 Dihedral : 13.470 87.723 4912 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.29 % Allowed : 6.02 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.15), residues: 1766 helix: -4.39 (0.08), residues: 790 sheet: 0.19 (0.23), residues: 384 loop : -2.71 (0.20), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 135 TYR 0.012 0.002 TYR F 333 PHE 0.011 0.002 PHE B 312 TRP 0.008 0.001 TRP H 123 HIS 0.013 0.002 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.01072 (13400) covalent geometry : angle 0.83176 (18152) hydrogen bonds : bond 0.28530 ( 503) hydrogen bonds : angle 9.11414 ( 1417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 265 time to evaluate : 0.524 Fit side-chains REVERT: A 184 ASP cc_start: 0.8774 (t0) cc_final: 0.7848 (t70) REVERT: A 210 GLU cc_start: 0.7824 (tt0) cc_final: 0.7228 (tt0) REVERT: A 298 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7363 (ptp-110) REVERT: A 316 ASP cc_start: 0.8592 (m-30) cc_final: 0.8372 (m-30) REVERT: E 213 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8068 (mtt90) REVERT: E 309 ASP cc_start: 0.7295 (p0) cc_final: 0.6714 (p0) REVERT: B 174 ASN cc_start: 0.8637 (m-40) cc_final: 0.8314 (m-40) REVERT: B 254 ASP cc_start: 0.8053 (t0) cc_final: 0.7787 (t0) REVERT: F 153 LEU cc_start: 0.7660 (mt) cc_final: 0.7454 (mt) REVERT: F 184 ASP cc_start: 0.8926 (t70) cc_final: 0.8526 (t0) REVERT: F 262 ARG cc_start: 0.7884 (mmt-90) cc_final: 0.7624 (mmt90) REVERT: C 210 GLU cc_start: 0.7723 (tt0) cc_final: 0.7488 (tt0) REVERT: C 247 TYR cc_start: 0.9033 (m-80) cc_final: 0.8451 (m-80) REVERT: C 298 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7369 (ptp-110) REVERT: G 213 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8073 (mtt90) REVERT: G 309 ASP cc_start: 0.7301 (p0) cc_final: 0.6717 (p0) REVERT: D 174 ASN cc_start: 0.8634 (m-40) cc_final: 0.8315 (m-40) REVERT: D 254 ASP cc_start: 0.8062 (t0) cc_final: 0.7812 (t0) REVERT: H 153 LEU cc_start: 0.7649 (mt) cc_final: 0.7442 (mt) REVERT: H 184 ASP cc_start: 0.8817 (t70) cc_final: 0.8408 (t0) outliers start: 2 outliers final: 2 residues processed: 265 average time/residue: 0.1609 time to fit residues: 56.4180 Evaluate side-chains 202 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN F 286 HIS F 332 ASN C 219 GLN C 332 ASN H 286 HIS H 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.140717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.110214 restraints weight = 29738.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.111372 restraints weight = 15426.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.113493 restraints weight = 12022.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.114177 restraints weight = 8101.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.117402 restraints weight = 7095.633| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.003 0.023 13400 Z= 0.114 Angle : 0.447 5.013 18152 Z= 0.242 Chirality : 0.046 0.138 2174 Planarity : 0.004 0.043 2360 Dihedral : 3.908 15.268 1944 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.60 % Allowed : 10.96 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.17), residues: 1766 helix: -2.58 (0.14), residues: 798 sheet: 0.81 (0.26), residues: 336 loop : -1.89 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 132 TYR 0.010 0.001 TYR D 247 PHE 0.006 0.001 PHE A 251 TRP 0.004 0.001 TRP G 123 HIS 0.004 0.001 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00266 (13400) covalent geometry : angle 0.44730 (18152) hydrogen bonds : bond 0.03778 ( 503) hydrogen bonds : angle 4.92318 ( 1417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.490 Fit side-chains REVERT: A 184 ASP cc_start: 0.8658 (t0) cc_final: 0.7879 (t70) REVERT: A 210 GLU cc_start: 0.7394 (tt0) cc_final: 0.6763 (tt0) REVERT: A 298 ARG cc_start: 0.7431 (ttm110) cc_final: 0.7186 (ptp-110) REVERT: E 153 LEU cc_start: 0.8178 (mt) cc_final: 0.7930 (mm) REVERT: E 266 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8243 (mt-10) REVERT: E 309 ASP cc_start: 0.7025 (p0) cc_final: 0.6586 (p0) REVERT: B 174 ASN cc_start: 0.8813 (m-40) cc_final: 0.8490 (m-40) REVERT: B 254 ASP cc_start: 0.8140 (t0) cc_final: 0.7846 (t0) REVERT: F 262 ARG cc_start: 0.7783 (mmt-90) cc_final: 0.7498 (mmt90) REVERT: C 210 GLU cc_start: 0.7457 (tt0) cc_final: 0.6993 (tt0) REVERT: C 298 ARG cc_start: 0.7461 (ttm110) cc_final: 0.7208 (ptp-110) REVERT: G 309 ASP cc_start: 0.7016 (p0) cc_final: 0.6581 (p0) REVERT: D 174 ASN cc_start: 0.8796 (m-40) cc_final: 0.8495 (m-40) REVERT: D 254 ASP cc_start: 0.8159 (t0) cc_final: 0.7877 (t0) outliers start: 20 outliers final: 16 residues processed: 236 average time/residue: 0.1330 time to fit residues: 43.1134 Evaluate side-chains 213 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 190 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 94 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN E 332 ASN B 253 GLN F 286 HIS C 253 GLN D 253 GLN H 286 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.140732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.109167 restraints weight = 27047.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111188 restraints weight = 14185.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.113148 restraints weight = 10576.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.113913 restraints weight = 7704.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.117321 restraints weight = 6736.371| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13400 Z= 0.117 Angle : 0.424 4.894 18152 Z= 0.224 Chirality : 0.046 0.145 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.498 17.365 1944 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.60 % Allowed : 13.57 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.19), residues: 1766 helix: -1.37 (0.17), residues: 798 sheet: 0.92 (0.26), residues: 336 loop : -1.46 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.016 0.001 TYR H 333 PHE 0.004 0.001 PHE A 251 TRP 0.003 0.000 TRP C 123 HIS 0.005 0.001 HIS H 286 Details of bonding type rmsd covalent geometry : bond 0.00285 (13400) covalent geometry : angle 0.42430 (18152) hydrogen bonds : bond 0.03444 ( 503) hydrogen bonds : angle 4.31848 ( 1417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7958 (t0) cc_final: 0.7671 (t0) REVERT: A 298 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7222 (ptp-110) REVERT: E 153 LEU cc_start: 0.8184 (mt) cc_final: 0.7943 (mm) REVERT: E 309 ASP cc_start: 0.6985 (p0) cc_final: 0.6571 (p0) REVERT: B 174 ASN cc_start: 0.8833 (m-40) cc_final: 0.8532 (m-40) REVERT: B 218 GLU cc_start: 0.8151 (tp30) cc_final: 0.7842 (mm-30) REVERT: B 254 ASP cc_start: 0.8077 (t0) cc_final: 0.7721 (t0) REVERT: B 262 ARG cc_start: 0.8433 (mmt-90) cc_final: 0.8207 (mmt-90) REVERT: B 285 ILE cc_start: 0.7863 (mm) cc_final: 0.7656 (mm) REVERT: F 144 GLU cc_start: 0.7267 (tm-30) cc_final: 0.7002 (tm-30) REVERT: F 262 ARG cc_start: 0.7733 (mmt-90) cc_final: 0.7486 (mmt90) REVERT: F 267 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8440 (m) REVERT: C 151 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8039 (mmmm) REVERT: C 200 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8027 (mtpp) REVERT: C 210 GLU cc_start: 0.7479 (tt0) cc_final: 0.6964 (tt0) REVERT: C 298 ARG cc_start: 0.7478 (ttm110) cc_final: 0.7241 (ptp-110) REVERT: G 309 ASP cc_start: 0.6979 (p0) cc_final: 0.6566 (p0) REVERT: D 174 ASN cc_start: 0.8840 (m-40) cc_final: 0.8549 (m-40) REVERT: D 218 GLU cc_start: 0.8131 (tp30) cc_final: 0.7791 (mm-30) REVERT: D 254 ASP cc_start: 0.8098 (t0) cc_final: 0.7783 (t0) REVERT: H 144 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7008 (tm-30) REVERT: H 267 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8423 (m) outliers start: 20 outliers final: 11 residues processed: 214 average time/residue: 0.1360 time to fit residues: 39.9257 Evaluate side-chains 204 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 135 optimal weight: 0.0470 chunk 172 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN C 253 GLN C 332 ASN D 253 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.139606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.107353 restraints weight = 26014.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.110039 restraints weight = 14966.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.112316 restraints weight = 10143.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.113465 restraints weight = 7657.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.114106 restraints weight = 6205.031| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13400 Z= 0.145 Angle : 0.426 4.367 18152 Z= 0.224 Chirality : 0.047 0.136 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.419 17.402 1944 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.10 % Allowed : 14.59 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.19), residues: 1766 helix: -0.75 (0.18), residues: 798 sheet: 0.98 (0.27), residues: 336 loop : -1.17 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 213 TYR 0.018 0.001 TYR H 333 PHE 0.006 0.001 PHE G 251 TRP 0.002 0.000 TRP E 123 HIS 0.004 0.001 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00359 (13400) covalent geometry : angle 0.42570 (18152) hydrogen bonds : bond 0.03293 ( 503) hydrogen bonds : angle 4.16198 ( 1417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.428 Fit side-chains REVERT: A 210 GLU cc_start: 0.7710 (tt0) cc_final: 0.6800 (tt0) REVERT: A 284 ASP cc_start: 0.7886 (t0) cc_final: 0.7458 (t0) REVERT: A 298 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7272 (ptp-110) REVERT: E 309 ASP cc_start: 0.7039 (p0) cc_final: 0.6673 (p0) REVERT: B 174 ASN cc_start: 0.8780 (m-40) cc_final: 0.8468 (m-40) REVERT: B 218 GLU cc_start: 0.8177 (tp30) cc_final: 0.7860 (mm-30) REVERT: B 254 ASP cc_start: 0.8063 (t0) cc_final: 0.7726 (t0) REVERT: F 144 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6981 (tm-30) REVERT: F 262 ARG cc_start: 0.7766 (mmt-90) cc_final: 0.7386 (mmt180) REVERT: F 267 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8457 (m) REVERT: C 151 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8021 (mmmm) REVERT: C 200 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8056 (mtpp) REVERT: C 210 GLU cc_start: 0.7509 (tt0) cc_final: 0.7040 (tt0) REVERT: C 298 ARG cc_start: 0.7571 (ttm110) cc_final: 0.7316 (ptp-110) REVERT: G 309 ASP cc_start: 0.7035 (p0) cc_final: 0.6658 (p0) REVERT: D 174 ASN cc_start: 0.8780 (m-40) cc_final: 0.8477 (m-40) REVERT: D 218 GLU cc_start: 0.8182 (tp30) cc_final: 0.7851 (mm-30) REVERT: D 254 ASP cc_start: 0.8035 (t0) cc_final: 0.7750 (t0) REVERT: H 144 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6986 (tm-30) REVERT: H 262 ARG cc_start: 0.7752 (mmt-90) cc_final: 0.7419 (mmt180) REVERT: H 267 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8440 (m) outliers start: 27 outliers final: 22 residues processed: 212 average time/residue: 0.1367 time to fit residues: 40.3290 Evaluate side-chains 211 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 157 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 163 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 127 optimal weight: 0.0470 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN C 253 GLN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.143705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.112453 restraints weight = 35721.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.116349 restraints weight = 18587.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.116687 restraints weight = 11552.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.120025 restraints weight = 6748.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.120744 restraints weight = 5032.566| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13400 Z= 0.078 Angle : 0.378 4.389 18152 Z= 0.201 Chirality : 0.045 0.136 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.089 14.426 1944 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.31 % Allowed : 15.60 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1766 helix: -0.19 (0.19), residues: 798 sheet: 1.14 (0.27), residues: 336 loop : -0.89 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 213 TYR 0.016 0.001 TYR F 333 PHE 0.003 0.001 PHE H 232 TRP 0.003 0.001 TRP A 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00184 (13400) covalent geometry : angle 0.37829 (18152) hydrogen bonds : bond 0.02566 ( 503) hydrogen bonds : angle 3.88349 ( 1417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7810 (t0) cc_final: 0.7320 (t0) REVERT: A 298 ARG cc_start: 0.7419 (ttm110) cc_final: 0.7139 (ptp-110) REVERT: E 153 LEU cc_start: 0.8158 (mt) cc_final: 0.7910 (mm) REVERT: E 309 ASP cc_start: 0.7138 (p0) cc_final: 0.6785 (p0) REVERT: B 174 ASN cc_start: 0.8855 (m-40) cc_final: 0.8553 (m-40) REVERT: B 218 GLU cc_start: 0.8205 (tp30) cc_final: 0.7877 (mm-30) REVERT: B 254 ASP cc_start: 0.8032 (t0) cc_final: 0.7683 (t0) REVERT: B 285 ILE cc_start: 0.7878 (mm) cc_final: 0.7632 (mm) REVERT: B 316 ASP cc_start: 0.7219 (m-30) cc_final: 0.6869 (m-30) REVERT: F 144 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6945 (tm-30) REVERT: F 262 ARG cc_start: 0.7699 (mmt-90) cc_final: 0.7418 (mmt180) REVERT: F 267 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8215 (m) REVERT: C 200 LYS cc_start: 0.8435 (ttmm) cc_final: 0.7984 (mtpp) REVERT: C 210 GLU cc_start: 0.7475 (tt0) cc_final: 0.6956 (tt0) REVERT: C 298 ARG cc_start: 0.7425 (ttm110) cc_final: 0.7185 (ptp-110) REVERT: D 174 ASN cc_start: 0.8813 (m-40) cc_final: 0.8517 (m-40) REVERT: D 218 GLU cc_start: 0.8207 (tp30) cc_final: 0.7879 (mm-30) REVERT: D 254 ASP cc_start: 0.7973 (t0) cc_final: 0.7747 (t0) REVERT: D 285 ILE cc_start: 0.7869 (mm) cc_final: 0.7622 (mm) REVERT: D 316 ASP cc_start: 0.7144 (m-30) cc_final: 0.6763 (m-30) REVERT: H 144 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6941 (tm-30) REVERT: H 262 ARG cc_start: 0.7679 (mmt-90) cc_final: 0.7422 (mmt180) REVERT: H 267 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8183 (m) outliers start: 16 outliers final: 12 residues processed: 220 average time/residue: 0.1390 time to fit residues: 42.2604 Evaluate side-chains 217 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 47 optimal weight: 0.0050 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN C 253 GLN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.141666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.110248 restraints weight = 30688.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.112611 restraints weight = 16349.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.113797 restraints weight = 12270.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.114770 restraints weight = 8572.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.115695 restraints weight = 7455.271| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13400 Z= 0.106 Angle : 0.393 4.577 18152 Z= 0.207 Chirality : 0.046 0.135 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.086 16.024 1943 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.89 % Allowed : 15.75 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1766 helix: 0.05 (0.19), residues: 798 sheet: 1.25 (0.27), residues: 336 loop : -0.76 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 213 TYR 0.010 0.001 TYR H 333 PHE 0.004 0.001 PHE A 232 TRP 0.001 0.000 TRP A 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00259 (13400) covalent geometry : angle 0.39314 (18152) hydrogen bonds : bond 0.02735 ( 503) hydrogen bonds : angle 3.90903 ( 1417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.517 Fit side-chains REVERT: A 210 GLU cc_start: 0.7655 (tt0) cc_final: 0.7067 (tt0) REVERT: A 284 ASP cc_start: 0.7869 (t0) cc_final: 0.7428 (t0) REVERT: A 298 ARG cc_start: 0.7482 (ttm110) cc_final: 0.7244 (ptp-110) REVERT: E 153 LEU cc_start: 0.8180 (mt) cc_final: 0.7925 (mm) REVERT: E 309 ASP cc_start: 0.7075 (p0) cc_final: 0.6753 (p0) REVERT: B 174 ASN cc_start: 0.8782 (m-40) cc_final: 0.8477 (m-40) REVERT: B 218 GLU cc_start: 0.8236 (tp30) cc_final: 0.7918 (mm-30) REVERT: B 254 ASP cc_start: 0.7986 (t0) cc_final: 0.7577 (t0) REVERT: B 316 ASP cc_start: 0.7330 (m-30) cc_final: 0.6979 (m-30) REVERT: F 144 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6975 (tm-30) REVERT: F 262 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7414 (mmt180) REVERT: F 267 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8359 (m) REVERT: C 151 LYS cc_start: 0.8272 (mmmm) cc_final: 0.8048 (tptm) REVERT: C 200 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8129 (mtpp) REVERT: C 210 GLU cc_start: 0.7511 (tt0) cc_final: 0.7017 (tt0) REVERT: C 298 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7327 (ptp-110) REVERT: G 309 ASP cc_start: 0.7286 (p0) cc_final: 0.6515 (p0) REVERT: D 174 ASN cc_start: 0.8756 (m-40) cc_final: 0.8460 (m-40) REVERT: D 218 GLU cc_start: 0.8240 (tp30) cc_final: 0.7919 (mm-30) REVERT: D 316 ASP cc_start: 0.7301 (m-30) cc_final: 0.6962 (m-30) REVERT: H 144 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6977 (tm-30) REVERT: H 262 ARG cc_start: 0.7814 (mmt-90) cc_final: 0.7553 (mmt180) REVERT: H 267 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8359 (m) outliers start: 24 outliers final: 18 residues processed: 219 average time/residue: 0.1557 time to fit residues: 46.1541 Evaluate side-chains 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 83 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN D 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.138333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.107100 restraints weight = 28774.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.108499 restraints weight = 16191.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.109177 restraints weight = 14290.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.110414 restraints weight = 9357.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111307 restraints weight = 7981.383| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13400 Z= 0.243 Angle : 0.506 5.302 18152 Z= 0.263 Chirality : 0.049 0.140 2174 Planarity : 0.004 0.040 2360 Dihedral : 3.581 20.152 1943 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.32 % Allowed : 16.26 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1766 helix: -0.19 (0.19), residues: 798 sheet: 1.03 (0.27), residues: 336 loop : -0.77 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 213 TYR 0.007 0.001 TYR G 247 PHE 0.008 0.001 PHE A 232 TRP 0.003 0.001 TRP H 123 HIS 0.005 0.001 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00607 (13400) covalent geometry : angle 0.50553 (18152) hydrogen bonds : bond 0.03761 ( 503) hydrogen bonds : angle 4.30452 ( 1417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.520 Fit side-chains REVERT: A 210 GLU cc_start: 0.7743 (tt0) cc_final: 0.7062 (tt0) REVERT: A 284 ASP cc_start: 0.8011 (t0) cc_final: 0.7582 (t0) REVERT: A 298 ARG cc_start: 0.7543 (ttm110) cc_final: 0.7300 (ptp-110) REVERT: E 309 ASP cc_start: 0.7264 (p0) cc_final: 0.6937 (p0) REVERT: B 174 ASN cc_start: 0.8784 (m-40) cc_final: 0.8434 (m-40) REVERT: B 218 GLU cc_start: 0.8299 (tp30) cc_final: 0.7964 (mm-30) REVERT: B 254 ASP cc_start: 0.8051 (t0) cc_final: 0.7617 (t0) REVERT: F 144 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6993 (tm-30) REVERT: F 262 ARG cc_start: 0.7869 (mmt-90) cc_final: 0.7428 (mmt180) REVERT: F 303 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7752 (mt) REVERT: C 200 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8125 (mtpp) REVERT: C 210 GLU cc_start: 0.7552 (tt0) cc_final: 0.7053 (tt0) REVERT: C 247 TYR cc_start: 0.9128 (m-80) cc_final: 0.7815 (m-80) REVERT: C 298 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7321 (ptp-110) REVERT: G 309 ASP cc_start: 0.7441 (p0) cc_final: 0.6737 (p0) REVERT: D 174 ASN cc_start: 0.8731 (m-40) cc_final: 0.8396 (m-40) REVERT: D 218 GLU cc_start: 0.8314 (tp30) cc_final: 0.7974 (mm-30) REVERT: D 254 ASP cc_start: 0.8144 (t0) cc_final: 0.7735 (t0) REVERT: H 144 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6997 (tm-30) REVERT: H 262 ARG cc_start: 0.7885 (mmt-90) cc_final: 0.7489 (mmt180) outliers start: 30 outliers final: 29 residues processed: 231 average time/residue: 0.1438 time to fit residues: 45.4062 Evaluate side-chains 231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 0.0570 chunk 146 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN C 253 GLN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.141450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.108099 restraints weight = 22312.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.110718 restraints weight = 16630.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.113649 restraints weight = 9498.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.114105 restraints weight = 6663.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.114732 restraints weight = 6286.039| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13400 Z= 0.091 Angle : 0.399 4.519 18152 Z= 0.211 Chirality : 0.046 0.226 2174 Planarity : 0.003 0.039 2360 Dihedral : 3.177 14.991 1943 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.96 % Allowed : 17.42 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.20), residues: 1766 helix: 0.13 (0.19), residues: 798 sheet: 1.12 (0.27), residues: 336 loop : -0.64 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 213 TYR 0.008 0.001 TYR H 333 PHE 0.004 0.001 PHE H 251 TRP 0.002 0.000 TRP A 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00214 (13400) covalent geometry : angle 0.39864 (18152) hydrogen bonds : bond 0.02743 ( 503) hydrogen bonds : angle 4.02587 ( 1417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.499 Fit side-chains REVERT: A 210 GLU cc_start: 0.7674 (tt0) cc_final: 0.7085 (tt0) REVERT: A 284 ASP cc_start: 0.7944 (t0) cc_final: 0.7489 (t0) REVERT: A 298 ARG cc_start: 0.7439 (ttm110) cc_final: 0.7221 (ptp-110) REVERT: E 309 ASP cc_start: 0.7041 (p0) cc_final: 0.6711 (p0) REVERT: B 174 ASN cc_start: 0.8824 (m-40) cc_final: 0.8499 (m-40) REVERT: B 218 GLU cc_start: 0.8218 (tp30) cc_final: 0.7898 (mm-30) REVERT: B 254 ASP cc_start: 0.7926 (t0) cc_final: 0.7641 (t0) REVERT: F 144 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6983 (tm-30) REVERT: F 262 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7436 (mmt180) REVERT: F 267 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8324 (m) REVERT: C 200 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8158 (mtpp) REVERT: C 210 GLU cc_start: 0.7504 (tt0) cc_final: 0.7060 (tt0) REVERT: G 309 ASP cc_start: 0.7177 (p0) cc_final: 0.6506 (p0) REVERT: D 174 ASN cc_start: 0.8802 (m-40) cc_final: 0.8485 (m-40) REVERT: D 218 GLU cc_start: 0.8239 (tp30) cc_final: 0.7913 (mm-30) REVERT: D 254 ASP cc_start: 0.8095 (t0) cc_final: 0.7651 (t0) REVERT: D 316 ASP cc_start: 0.7252 (m-30) cc_final: 0.6976 (m-30) REVERT: H 144 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6997 (tm-30) REVERT: H 262 ARG cc_start: 0.7717 (mmt-90) cc_final: 0.7409 (mmt180) REVERT: H 267 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8347 (m) outliers start: 25 outliers final: 23 residues processed: 219 average time/residue: 0.1486 time to fit residues: 44.2023 Evaluate side-chains 221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 155 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN D 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.142188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.111148 restraints weight = 30720.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.112579 restraints weight = 15475.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.114230 restraints weight = 11464.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.115212 restraints weight = 7476.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.118180 restraints weight = 6583.389| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13400 Z= 0.094 Angle : 0.400 5.034 18152 Z= 0.210 Chirality : 0.046 0.213 2174 Planarity : 0.003 0.040 2360 Dihedral : 3.061 15.542 1943 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.25 % Allowed : 17.34 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1766 helix: 0.27 (0.19), residues: 806 sheet: 1.17 (0.28), residues: 336 loop : -0.47 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 213 TYR 0.007 0.001 TYR H 333 PHE 0.003 0.001 PHE B 232 TRP 0.002 0.000 TRP G 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00229 (13400) covalent geometry : angle 0.40038 (18152) hydrogen bonds : bond 0.02684 ( 503) hydrogen bonds : angle 3.95341 ( 1417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.508 Fit side-chains REVERT: A 169 ASP cc_start: 0.8071 (m-30) cc_final: 0.7861 (t70) REVERT: A 184 ASP cc_start: 0.8348 (t70) cc_final: 0.7187 (t70) REVERT: A 210 GLU cc_start: 0.7665 (tt0) cc_final: 0.6961 (tt0) REVERT: A 284 ASP cc_start: 0.7924 (t0) cc_final: 0.7460 (t0) REVERT: A 298 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7219 (ptp-110) REVERT: E 153 LEU cc_start: 0.8212 (mt) cc_final: 0.7946 (mm) REVERT: E 309 ASP cc_start: 0.7075 (p0) cc_final: 0.6746 (p0) REVERT: B 218 GLU cc_start: 0.8220 (tp30) cc_final: 0.7888 (mm-30) REVERT: B 254 ASP cc_start: 0.7871 (t0) cc_final: 0.7587 (t0) REVERT: F 144 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6979 (tm-30) REVERT: F 262 ARG cc_start: 0.7648 (mmt-90) cc_final: 0.7363 (mmt180) REVERT: F 267 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8279 (m) REVERT: C 200 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8159 (mtpp) REVERT: C 210 GLU cc_start: 0.7581 (tt0) cc_final: 0.7126 (tt0) REVERT: G 309 ASP cc_start: 0.7251 (p0) cc_final: 0.6574 (p0) REVERT: D 218 GLU cc_start: 0.8237 (tp30) cc_final: 0.7895 (mm-30) REVERT: D 254 ASP cc_start: 0.8103 (t0) cc_final: 0.7659 (t0) REVERT: D 285 ILE cc_start: 0.7948 (mm) cc_final: 0.7677 (mm) REVERT: D 316 ASP cc_start: 0.7213 (m-30) cc_final: 0.6925 (m-30) REVERT: H 144 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6975 (tm-30) REVERT: H 262 ARG cc_start: 0.7670 (mmt-90) cc_final: 0.7433 (mmt180) REVERT: H 267 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8264 (m) REVERT: H 303 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7815 (mt) outliers start: 29 outliers final: 24 residues processed: 223 average time/residue: 0.1494 time to fit residues: 45.5271 Evaluate side-chains 221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 122 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 138 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 41 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: E 332 ASN B 253 GLN D 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.142669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.112689 restraints weight = 41403.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.115111 restraints weight = 28443.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.116338 restraints weight = 13677.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.120358 restraints weight = 7464.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.120932 restraints weight = 4649.790| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13400 Z= 0.096 Angle : 0.390 5.297 18152 Z= 0.205 Chirality : 0.046 0.188 2174 Planarity : 0.003 0.040 2360 Dihedral : 2.996 11.014 1942 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.10 % Allowed : 17.63 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1766 helix: 0.37 (0.19), residues: 806 sheet: 1.20 (0.28), residues: 336 loop : -0.43 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 213 TYR 0.006 0.000 TYR H 333 PHE 0.003 0.001 PHE C 232 TRP 0.002 0.000 TRP G 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00233 (13400) covalent geometry : angle 0.39040 (18152) hydrogen bonds : bond 0.02639 ( 503) hydrogen bonds : angle 3.88641 ( 1417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.382 Fit side-chains REVERT: A 184 ASP cc_start: 0.8410 (t70) cc_final: 0.7315 (t70) REVERT: A 210 GLU cc_start: 0.7683 (tt0) cc_final: 0.6891 (tt0) REVERT: A 284 ASP cc_start: 0.7907 (t0) cc_final: 0.7424 (t0) REVERT: A 298 ARG cc_start: 0.7383 (ttm110) cc_final: 0.7140 (ptp-110) REVERT: E 153 LEU cc_start: 0.8197 (mt) cc_final: 0.7925 (mm) REVERT: E 309 ASP cc_start: 0.7144 (p0) cc_final: 0.6816 (p0) REVERT: B 218 GLU cc_start: 0.8205 (tp30) cc_final: 0.7880 (mm-30) REVERT: B 254 ASP cc_start: 0.7897 (t0) cc_final: 0.7620 (t0) REVERT: F 144 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6969 (tm-30) REVERT: F 262 ARG cc_start: 0.7636 (mmt-90) cc_final: 0.7369 (mmt180) REVERT: F 267 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8211 (m) REVERT: C 200 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8144 (mtpp) REVERT: C 210 GLU cc_start: 0.7607 (tt0) cc_final: 0.7120 (tt0) REVERT: G 309 ASP cc_start: 0.7415 (p0) cc_final: 0.6731 (p0) REVERT: D 218 GLU cc_start: 0.8220 (tp30) cc_final: 0.7896 (mm-30) REVERT: D 254 ASP cc_start: 0.8137 (t0) cc_final: 0.7662 (t0) REVERT: D 316 ASP cc_start: 0.7166 (m-30) cc_final: 0.6854 (m-30) REVERT: H 144 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6959 (tm-30) REVERT: H 262 ARG cc_start: 0.7647 (mmt-90) cc_final: 0.7399 (mmt180) REVERT: H 267 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8226 (m) REVERT: H 303 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7769 (mt) outliers start: 27 outliers final: 23 residues processed: 212 average time/residue: 0.1468 time to fit residues: 42.5916 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 83 optimal weight: 0.0670 chunk 5 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 168 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN D 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.143846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.112661 restraints weight = 38429.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.115284 restraints weight = 23571.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.116466 restraints weight = 14828.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.119937 restraints weight = 8680.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.122196 restraints weight = 6106.532| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13400 Z= 0.079 Angle : 0.382 5.464 18152 Z= 0.200 Chirality : 0.046 0.163 2174 Planarity : 0.003 0.038 2360 Dihedral : 2.917 10.434 1942 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.18 % Allowed : 17.34 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1766 helix: 0.55 (0.19), residues: 814 sheet: 1.27 (0.27), residues: 336 loop : -0.32 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 176 TYR 0.006 0.000 TYR H 333 PHE 0.003 0.000 PHE F 232 TRP 0.003 0.000 TRP G 123 HIS 0.001 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00188 (13400) covalent geometry : angle 0.38225 (18152) hydrogen bonds : bond 0.02465 ( 503) hydrogen bonds : angle 3.80516 ( 1417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2226.47 seconds wall clock time: 39 minutes 1.01 seconds (2341.01 seconds total)