Starting phenix.real_space_refine on Sat Sep 12 02:43:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ux4_20929/09_2026/6ux4_20929.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ux4_20929/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6ux4_20929/09_2026/6ux4_20929.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ux4_20929/09_2026/6ux4_20929.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ux4_20929/09_2026/6ux4_20929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ux4_20929/09_2026/6ux4_20929.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ux4_20929/09_2026/6ux4_20929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ux4_20929/09_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-2.2.1-6174/lib/python3.11/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: 3.97, per 1000 atoms: 0.30 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: 1.07 Conformation dependent library (CDL) restraints added in 737.4 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: 0.45 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: 2.07 Time building geometry restraints manager: 1.45 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.070 Set scattering table: 0.020 Process input model: 14.090 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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/Z covalent geometry : bond 0.01072 / 0.44 (13400) covalent geometry : angle 0.83176 / 0.48 (18152) hydrogen bonds : bond 0.28530 / 19.29 ( 503) hydrogen bonds : angle 9.11414 / 6.58 ( 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 : 0.540 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: 0.7367 (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: 0.6718 (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: 0.1601 time to fit residues: 56.8392 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 : 0.525 ------------------------------------------------------------------------------- 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: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3426 r_free = 0.3426 target = 0.140188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.109674 restraints weight = 29832.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.111466 restraints weight = 15477.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.112878 restraints weight = 11756.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.113776 restraints weight = 7694.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.116460 restraints weight = 6784.599| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 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 = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13400 Z= 0.122 Angle : 0.452 4.823 18152 Z= 0.245 Chirality : 0.046 0.157 2174 Planarity : 0.004 0.043 2360 Dihedral : 3.936 15.447 1944 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.67 % Allowed : 10.96 % Favored : 87.37 % 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: -2.73 (0.17), residues: 1766 helix: -2.63 (0.14), residues: 798 sheet: 0.79 (0.26), residues: 336 loop : -1.92 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 262 TYR 0.009 0.001 TYR B 247 PHE 0.008 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/Z covalent geometry : bond 0.00285 / 0.12 (13400) covalent geometry : angle 0.45201 / 0.24 (18152) hydrogen bonds : bond 0.04218 / 2.83 ( 503) hydrogen bonds : angle 4.99698 / 3.58 ( 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 237 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.501 Fit side-chains REVERT: A 184 ASP cc_start: 0.8637 (t0) cc_final: 0.7816 (t70) REVERT: A 210 GLU cc_start: 0.7447 (tt0) cc_final: 0.6821 (tt0) REVERT: A 298 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7199 (ptp-110) REVERT: E 153 LEU cc_start: 0.8191 (mt) cc_final: 0.7934 (mm) REVERT: E 266 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8259 (mt-10) REVERT: E 309 ASP cc_start: 0.7031 (p0) cc_final: 0.6571 (p0) REVERT: B 174 ASN cc_start: 0.8803 (m-40) cc_final: 0.8478 (m-40) REVERT: B 254 ASP cc_start: 0.8128 (t0) cc_final: 0.7823 (t0) REVERT: F 262 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7502 (mmt90) REVERT: C 132 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7588 (mtp-110) REVERT: C 210 GLU cc_start: 0.7489 (tt0) cc_final: 0.7019 (tt0) REVERT: C 298 ARG cc_start: 0.7462 (ttm110) cc_final: 0.7183 (ptp-110) REVERT: G 309 ASP cc_start: 0.7035 (p0) cc_final: 0.6573 (p0) REVERT: D 174 ASN cc_start: 0.8787 (m-40) cc_final: 0.8485 (m-40) REVERT: D 250 MET cc_start: 0.8293 (ttm) cc_final: 0.8057 (mtp) REVERT: D 254 ASP cc_start: 0.8145 (t0) cc_final: 0.7853 (t0) outliers start: 21 outliers final: 17 residues processed: 228 average time/residue: 0.1453 time to fit residues: 45.4458 Evaluate side-chains 212 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 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 248 GLU 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: 3.9990 chunk 102 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN E 332 ASN B 253 GLN F 286 HIS D 253 GLN H 286 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.139409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.107774 restraints weight = 26751.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.109861 restraints weight = 14456.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.111863 restraints weight = 10641.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.112800 restraints weight = 7870.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.115053 restraints weight = 6813.997| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13400 Z= 0.146 Angle : 0.441 4.887 18152 Z= 0.234 Chirality : 0.047 0.138 2174 Planarity : 0.004 0.035 2360 Dihedral : 3.612 18.071 1944 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.96 % Allowed : 12.99 % Favored : 85.05 % 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: -1.63 (0.19), residues: 1766 helix: -1.44 (0.17), residues: 798 sheet: 0.85 (0.26), residues: 336 loop : -1.49 (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 0.005 0.001 PHE E 251 TRP 0.002 0.001 TRP C 123 HIS 0.005 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (13400) covalent geometry : angle 0.44111 / 0.23 (18152) hydrogen bonds : bond 0.03664 / 2.47 ( 503) hydrogen bonds : angle 4.39907 / 3.14 ( 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 230 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7989 (t0) cc_final: 0.7672 (t0) REVERT: A 298 ARG cc_start: 0.7442 (ttm110) cc_final: 0.7187 (ptp-110) REVERT: E 309 ASP cc_start: 0.7089 (p0) cc_final: 0.6672 (p0) REVERT: B 174 ASN cc_start: 0.8822 (m-40) cc_final: 0.8514 (m-40) REVERT: B 218 GLU cc_start: 0.8171 (tp30) cc_final: 0.7859 (mm-30) REVERT: B 254 ASP cc_start: 0.8128 (t0) cc_final: 0.7747 (t0) REVERT: B 262 ARG cc_start: 0.8435 (mmt-90) cc_final: 0.8198 (mmt-90) REVERT: B 285 ILE cc_start: 0.7863 (mm) cc_final: 0.7650 (mm) REVERT: F 262 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.7350 (mmt180) REVERT: F 267 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8430 (m) REVERT: C 151 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8034 (mmmm) REVERT: C 200 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8014 (mtpp) REVERT: C 210 GLU cc_start: 0.7520 (tt0) cc_final: 0.6980 (tt0) REVERT: C 298 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7199 (ptp-110) REVERT: G 309 ASP cc_start: 0.7086 (p0) cc_final: 0.6666 (p0) REVERT: D 174 ASN cc_start: 0.8823 (m-40) cc_final: 0.8526 (m-40) REVERT: D 218 GLU cc_start: 0.8164 (tp30) cc_final: 0.7832 (mm-30) REVERT: D 254 ASP cc_start: 0.8169 (t0) cc_final: 0.7838 (t0) REVERT: H 144 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6967 (tm-30) REVERT: H 267 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8414 (m) outliers start: 25 outliers final: 15 residues processed: 218 average time/residue: 0.1347 time to fit residues: 41.2436 Evaluate side-chains 209 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 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 265 VAL Chi-restraints excluded: chain G residue 288 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: 4.9990 chunk 75 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 135 optimal weight: 0.0040 chunk 172 optimal weight: 4.9990 chunk 134 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 332 ASN B 253 GLN C 332 ASN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.141071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.108836 restraints weight = 25841.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.111811 restraints weight = 14487.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.114085 restraints weight = 9722.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.115583 restraints weight = 7302.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.116234 restraints weight = 5788.792| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2204 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= 0.115 Angle : 0.402 4.300 18152 Z= 0.214 Chirality : 0.046 0.136 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.349 16.128 1944 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.81 % Allowed : 14.30 % Favored : 83.89 % 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: -0.90 (0.19), residues: 1766 helix: -0.69 (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 0.005 0.000 ARG E 213 TYR 0.020 0.001 TYR F 333 PHE 0.004 0.001 PHE G 251 TRP 0.003 0.000 TRP E 123 HIS 0.003 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13400) covalent geometry : angle 0.40194 / 0.21 (18152) hydrogen bonds : bond 0.03050 / 2.05 ( 503) hydrogen bonds : angle 4.10835 / 2.93 ( 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 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7871 (t0) cc_final: 0.7449 (t0) REVERT: A 298 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7259 (ptp-110) REVERT: E 309 ASP cc_start: 0.6994 (p0) cc_final: 0.6626 (p0) REVERT: B 174 ASN cc_start: 0.8773 (m-40) cc_final: 0.8469 (m-40) REVERT: B 218 GLU cc_start: 0.8123 (tp30) cc_final: 0.7813 (mm-30) REVERT: B 254 ASP cc_start: 0.8050 (t0) cc_final: 0.7736 (t0) REVERT: F 144 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6969 (tm-30) REVERT: F 222 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7571 (mmt) REVERT: F 262 ARG cc_start: 0.7774 (mmt-90) cc_final: 0.7408 (mmt180) REVERT: F 267 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (m) REVERT: C 132 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7569 (mtp-110) REVERT: C 151 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8024 (mmmm) REVERT: C 200 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8099 (mtpp) REVERT: C 210 GLU cc_start: 0.7517 (tt0) cc_final: 0.7065 (tt0) REVERT: C 247 TYR cc_start: 0.8965 (m-80) cc_final: 0.8737 (m-80) REVERT: C 298 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7262 (ptp-110) REVERT: G 266 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8392 (mt-10) REVERT: G 309 ASP cc_start: 0.6995 (p0) cc_final: 0.6626 (p0) REVERT: D 174 ASN cc_start: 0.8770 (m-40) cc_final: 0.8474 (m-40) REVERT: D 218 GLU cc_start: 0.8162 (tp30) cc_final: 0.7839 (mm-30) REVERT: D 254 ASP cc_start: 0.8093 (t0) cc_final: 0.7836 (t0) REVERT: H 144 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6979 (tm-30) REVERT: H 262 ARG cc_start: 0.7730 (mmt-90) cc_final: 0.7401 (mmt180) REVERT: H 267 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8428 (m) outliers start: 23 outliers final: 18 residues processed: 209 average time/residue: 0.1360 time to fit residues: 39.8591 Evaluate side-chains 212 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 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 265 VAL 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 222 MET Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 267 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 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 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 157 optimal weight: 0.6980 chunk 91 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 0.0870 chunk 163 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 332 ASN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.143638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.111719 restraints weight = 34644.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.113848 restraints weight = 15883.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.116614 restraints weight = 11097.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.117269 restraints weight = 7175.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.118722 restraints weight = 5718.305| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13400 Z= 0.083 Angle : 0.379 4.372 18152 Z= 0.201 Chirality : 0.045 0.142 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.115 15.229 1944 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.74 % Allowed : 15.31 % Favored : 82.95 % 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: -0.34 (0.20), residues: 1766 helix: -0.18 (0.19), residues: 798 sheet: 1.14 (0.27), residues: 336 loop : -0.88 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 213 TYR 0.013 0.001 TYR F 333 PHE 0.005 0.001 PHE G 251 TRP 0.003 0.000 TRP A 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.08 (13400) covalent geometry : angle 0.37887 / 0.20 (18152) hydrogen bonds : bond 0.02615 / 1.75 ( 503) hydrogen bonds : angle 3.89571 / 2.78 ( 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 231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 0.466 Fit side-chains REVERT: A 210 GLU cc_start: 0.7619 (tt0) cc_final: 0.6955 (tt0) REVERT: A 284 ASP cc_start: 0.7792 (t0) cc_final: 0.7297 (t0) REVERT: A 298 ARG cc_start: 0.7401 (ttm110) cc_final: 0.7138 (ptp-110) REVERT: E 153 LEU cc_start: 0.8139 (mt) cc_final: 0.7867 (mm) REVERT: E 309 ASP cc_start: 0.7208 (p0) cc_final: 0.6867 (p0) REVERT: B 150 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8100 (pttm) REVERT: B 174 ASN cc_start: 0.8853 (m-40) cc_final: 0.8543 (m-40) REVERT: B 218 GLU cc_start: 0.8225 (tp30) cc_final: 0.7890 (mm-30) REVERT: B 254 ASP cc_start: 0.7974 (t0) cc_final: 0.7653 (t0) REVERT: B 285 ILE cc_start: 0.7865 (mm) cc_final: 0.7614 (mm) REVERT: B 316 ASP cc_start: 0.7192 (m-30) cc_final: 0.6814 (m-30) REVERT: F 144 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6958 (tm-30) REVERT: F 262 ARG cc_start: 0.7645 (mmt-90) cc_final: 0.7352 (mmt180) REVERT: F 267 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8188 (m) REVERT: C 200 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8070 (mtpp) REVERT: C 210 GLU cc_start: 0.7506 (tt0) cc_final: 0.6977 (tt0) REVERT: C 298 ARG cc_start: 0.7419 (ttm110) cc_final: 0.7178 (ptp-110) REVERT: D 174 ASN cc_start: 0.8808 (m-40) cc_final: 0.8504 (m-40) REVERT: D 218 GLU cc_start: 0.8213 (tp30) cc_final: 0.7878 (mm-30) REVERT: D 254 ASP cc_start: 0.8084 (t0) cc_final: 0.7867 (t0) REVERT: D 266 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: D 285 ILE cc_start: 0.7831 (mm) cc_final: 0.7582 (mm) REVERT: H 144 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6966 (tm-30) REVERT: H 262 ARG cc_start: 0.7627 (mmt-90) cc_final: 0.7315 (mmt180) REVERT: H 267 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8210 (m) outliers start: 22 outliers final: 12 residues processed: 222 average time/residue: 0.1292 time to fit residues: 40.7387 Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.142036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.110756 restraints weight = 29849.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.112026 restraints weight = 16485.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.114640 restraints weight = 12036.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.115291 restraints weight = 7667.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.116416 restraints weight = 6680.718| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13400 Z= 0.109 Angle : 0.398 4.782 18152 Z= 0.209 Chirality : 0.046 0.147 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.103 16.182 1943 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 16.33 % Favored : 81.93 % 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: -0.07 (0.20), residues: 1766 helix: 0.06 (0.19), residues: 798 sheet: 1.22 (0.27), residues: 336 loop : -0.75 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 213 TYR 0.009 0.001 TYR F 333 PHE 0.005 0.001 PHE G 251 TRP 0.002 0.000 TRP G 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (13400) covalent geometry : angle 0.39763 / 0.21 (18152) hydrogen bonds : bond 0.02793 / 1.86 ( 503) hydrogen bonds : angle 3.91171 / 2.79 ( 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 222 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.509 Fit side-chains REVERT: A 169 ASP cc_start: 0.8097 (m-30) cc_final: 0.7807 (t70) REVERT: A 210 GLU cc_start: 0.7632 (tt0) cc_final: 0.7029 (tt0) REVERT: A 284 ASP cc_start: 0.7876 (t0) cc_final: 0.7457 (t0) REVERT: A 298 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7259 (ptp-110) REVERT: E 153 LEU cc_start: 0.8215 (mt) cc_final: 0.7944 (mm) REVERT: E 309 ASP cc_start: 0.7039 (p0) cc_final: 0.6698 (p0) REVERT: B 174 ASN cc_start: 0.8760 (m-40) cc_final: 0.8449 (m-40) REVERT: B 218 GLU cc_start: 0.8216 (tp30) cc_final: 0.7901 (mm-30) REVERT: B 254 ASP cc_start: 0.7975 (t0) cc_final: 0.7674 (t0) REVERT: B 316 ASP cc_start: 0.7340 (m-30) cc_final: 0.7011 (m-30) REVERT: F 144 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6971 (tm-30) REVERT: F 262 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7416 (mmt180) REVERT: F 267 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8379 (m) REVERT: C 144 GLU cc_start: 0.6744 (mp0) cc_final: 0.6538 (mp0) REVERT: C 151 LYS cc_start: 0.8281 (mmmm) cc_final: 0.8049 (tptm) REVERT: C 200 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8067 (mtpp) REVERT: C 210 GLU cc_start: 0.7517 (tt0) cc_final: 0.7015 (tt0) REVERT: G 309 ASP cc_start: 0.7269 (p0) cc_final: 0.6515 (p0) REVERT: D 174 ASN cc_start: 0.8757 (m-40) cc_final: 0.8459 (m-40) REVERT: D 218 GLU cc_start: 0.8223 (tp30) cc_final: 0.7904 (mm-30) REVERT: D 254 ASP cc_start: 0.8045 (t0) cc_final: 0.7803 (t0) REVERT: H 144 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6983 (tm-30) REVERT: H 262 ARG cc_start: 0.7742 (mmt-90) cc_final: 0.7456 (mmt180) REVERT: H 267 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8359 (m) outliers start: 22 outliers final: 16 residues processed: 214 average time/residue: 0.1419 time to fit residues: 42.0483 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 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 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 83 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3439 r_free = 0.3439 target = 0.140871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.109412 restraints weight = 29588.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.111492 restraints weight = 16260.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.112197 restraints weight = 13472.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.113409 restraints weight = 8881.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.114207 restraints weight = 7609.652| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13400 Z= 0.168 Angle : 0.444 4.676 18152 Z= 0.231 Chirality : 0.047 0.135 2174 Planarity : 0.003 0.039 2360 Dihedral : 3.321 17.740 1943 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.18 % Allowed : 16.62 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1766 helix: 0.01 (0.19), residues: 798 sheet: 1.15 (0.27), residues: 336 loop : -0.71 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 213 TYR 0.007 0.001 TYR F 333 PHE 0.006 0.001 PHE A 232 TRP 0.002 0.001 TRP G 123 HIS 0.004 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (13400) covalent geometry : angle 0.44373 / 0.23 (18152) hydrogen bonds : bond 0.03253 / 2.16 ( 503) hydrogen bonds : angle 4.08663 / 2.91 ( 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 224 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.490 Fit side-chains REVERT: A 184 ASP cc_start: 0.8436 (t70) cc_final: 0.7404 (t70) REVERT: A 210 GLU cc_start: 0.7652 (tt0) cc_final: 0.6924 (tt0) REVERT: A 284 ASP cc_start: 0.7969 (t0) cc_final: 0.7529 (t0) REVERT: A 298 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7330 (ptp-110) REVERT: E 309 ASP cc_start: 0.7170 (p0) cc_final: 0.6845 (p0) REVERT: B 174 ASN cc_start: 0.8782 (m-40) cc_final: 0.8451 (m-40) REVERT: B 218 GLU cc_start: 0.8272 (tp30) cc_final: 0.7950 (mm-30) REVERT: B 254 ASP cc_start: 0.8022 (t0) cc_final: 0.7625 (t0) REVERT: F 144 GLU cc_start: 0.7247 (tm-30) cc_final: 0.7011 (tm-30) REVERT: F 262 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7443 (mmt180) REVERT: F 303 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7829 (mt) REVERT: C 200 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8207 (mtpp) REVERT: C 210 GLU cc_start: 0.7610 (tt0) cc_final: 0.7087 (tt0) REVERT: G 309 ASP cc_start: 0.7364 (p0) cc_final: 0.6666 (p0) REVERT: D 174 ASN cc_start: 0.8753 (m-40) cc_final: 0.8424 (m-40) REVERT: D 218 GLU cc_start: 0.8296 (tp30) cc_final: 0.7956 (mm-30) REVERT: D 254 ASP cc_start: 0.8077 (t0) cc_final: 0.7755 (t0) REVERT: D 285 ILE cc_start: 0.7977 (mm) cc_final: 0.7670 (mm) REVERT: H 144 GLU cc_start: 0.7249 (tm-30) cc_final: 0.7012 (tm-30) REVERT: H 262 ARG cc_start: 0.7795 (mmt-90) cc_final: 0.7468 (mmt180) REVERT: H 267 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8376 (m) outliers start: 28 outliers final: 25 residues processed: 213 average time/residue: 0.1396 time to fit residues: 41.1699 Evaluate side-chains 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 F residue 304 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 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 296 VAL Chi-restraints excluded: chain H residue 190 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: 0.8980 chunk 146 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 3 optimal weight: 0.0670 chunk 158 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3476 r_free = 0.3476 target = 0.144278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.111224 restraints weight = 22220.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114938 restraints weight = 14290.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.118149 restraints weight = 8311.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.118040 restraints weight = 5884.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.118552 restraints weight = 5503.022| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13400 Z= 0.079 Angle : 0.386 5.091 18152 Z= 0.203 Chirality : 0.045 0.140 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.018 13.988 1943 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.74 % Allowed : 17.20 % Favored : 81.06 % 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: 0.21 (0.21), residues: 1766 helix: 0.30 (0.19), residues: 798 sheet: 1.27 (0.28), residues: 336 loop : -0.56 (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 F 333 PHE 0.003 0.001 PHE G 251 TRP 0.004 0.000 TRP G 123 HIS 0.001 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 (13400) covalent geometry : angle 0.38561 / 0.20 (18152) hydrogen bonds : bond 0.02479 / 1.67 ( 503) hydrogen bonds : angle 3.87630 / 2.76 ( 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 236 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.504 Fit side-chains REVERT: A 169 ASP cc_start: 0.8024 (m-30) cc_final: 0.7809 (t70) REVERT: A 184 ASP cc_start: 0.8347 (t70) cc_final: 0.7194 (t70) REVERT: A 210 GLU cc_start: 0.7639 (tt0) cc_final: 0.6969 (tt0) REVERT: A 284 ASP cc_start: 0.7886 (t0) cc_final: 0.7445 (t0) REVERT: A 298 ARG cc_start: 0.7441 (ttm110) cc_final: 0.7206 (ptp-110) REVERT: E 153 LEU cc_start: 0.8179 (mt) cc_final: 0.7914 (mm) REVERT: E 309 ASP cc_start: 0.6977 (p0) cc_final: 0.6662 (p0) REVERT: B 174 ASN cc_start: 0.8821 (m-40) cc_final: 0.8514 (m-40) REVERT: B 218 GLU cc_start: 0.8210 (tp30) cc_final: 0.7896 (mm-30) REVERT: B 254 ASP cc_start: 0.7885 (t0) cc_final: 0.7609 (t0) REVERT: F 144 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6971 (tm-30) REVERT: F 262 ARG cc_start: 0.7711 (mmt-90) cc_final: 0.7443 (mmt180) REVERT: F 267 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8296 (m) REVERT: C 184 ASP cc_start: 0.8590 (t0) cc_final: 0.8015 (t70) REVERT: C 200 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8139 (mtpp) REVERT: C 210 GLU cc_start: 0.7637 (tt0) cc_final: 0.7141 (tt0) REVERT: C 284 ASP cc_start: 0.7868 (t0) cc_final: 0.7584 (t0) REVERT: G 309 ASP cc_start: 0.7125 (p0) cc_final: 0.6491 (p0) REVERT: D 174 ASN cc_start: 0.8807 (m-40) cc_final: 0.8484 (m-40) REVERT: D 218 GLU cc_start: 0.8231 (tp30) cc_final: 0.7910 (mm-30) REVERT: D 254 ASP cc_start: 0.8010 (t0) cc_final: 0.7790 (t0) REVERT: H 144 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6978 (tm-30) REVERT: H 262 ARG cc_start: 0.7747 (mmt-90) cc_final: 0.7511 (mmt180) REVERT: H 267 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8263 (m) outliers start: 22 outliers final: 20 residues processed: 228 average time/residue: 0.1428 time to fit residues: 44.8989 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 185 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 265 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 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 69 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 128 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3467 r_free = 0.3467 target = 0.143491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.112453 restraints weight = 28734.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.114078 restraints weight = 14424.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.115552 restraints weight = 10877.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.116623 restraints weight = 7106.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.120010 restraints weight = 6294.939| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13400 Z= 0.083 Angle : 0.384 5.380 18152 Z= 0.201 Chirality : 0.046 0.138 2174 Planarity : 0.003 0.036 2360 Dihedral : 2.955 15.293 1943 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.81 % Allowed : 17.27 % Favored : 80.91 % 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: 0.41 (0.21), residues: 1766 helix: 0.46 (0.19), residues: 798 sheet: 1.38 (0.28), residues: 336 loop : -0.46 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 213 TYR 0.007 0.000 TYR F 333 PHE 0.004 0.001 PHE A 232 TRP 0.002 0.000 TRP G 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.08 (13400) covalent geometry : angle 0.38350 / 0.20 (18152) hydrogen bonds : bond 0.02489 / 1.66 ( 503) hydrogen bonds : angle 3.79363 / 2.70 ( 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 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.580 Fit side-chains REVERT: A 169 ASP cc_start: 0.8035 (m-30) cc_final: 0.7818 (t70) REVERT: A 184 ASP cc_start: 0.8376 (t70) cc_final: 0.7397 (t70) REVERT: A 210 GLU cc_start: 0.7647 (tt0) cc_final: 0.6945 (tt0) REVERT: A 284 ASP cc_start: 0.7873 (t0) cc_final: 0.7409 (t0) REVERT: A 298 ARG cc_start: 0.7475 (ttm110) cc_final: 0.7228 (ptp-110) REVERT: E 153 LEU cc_start: 0.8206 (mt) cc_final: 0.7952 (mm) REVERT: E 309 ASP cc_start: 0.7019 (p0) cc_final: 0.6711 (p0) REVERT: B 218 GLU cc_start: 0.8219 (tp30) cc_final: 0.7904 (mm-30) REVERT: B 254 ASP cc_start: 0.7851 (t0) cc_final: 0.7562 (t0) REVERT: F 144 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6975 (tm-30) REVERT: F 262 ARG cc_start: 0.7706 (mmt-90) cc_final: 0.7460 (mmt180) REVERT: F 267 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8290 (m) REVERT: C 184 ASP cc_start: 0.8644 (t0) cc_final: 0.8106 (t70) REVERT: C 200 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8195 (mtpp) REVERT: C 210 GLU cc_start: 0.7681 (tt0) cc_final: 0.7136 (tt0) REVERT: G 309 ASP cc_start: 0.7193 (p0) cc_final: 0.6515 (p0) REVERT: D 218 GLU cc_start: 0.8232 (tp30) cc_final: 0.7899 (mm-30) REVERT: D 254 ASP cc_start: 0.8016 (t0) cc_final: 0.7782 (t0) REVERT: H 144 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6975 (tm-30) REVERT: H 262 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7558 (mmt180) REVERT: H 267 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8269 (m) outliers start: 23 outliers final: 19 residues processed: 208 average time/residue: 0.1447 time to fit residues: 41.6021 Evaluate side-chains 214 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 205 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 139 VAL Chi-restraints excluded: chain C residue 240 SER 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 H residue 267 VAL Chi-restraints excluded: chain H residue 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 122 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 0.0980 chunk 41 optimal weight: 5.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.143704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.112750 restraints weight = 40477.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.116357 restraints weight = 24034.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.116996 restraints weight = 12832.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.120703 restraints weight = 7102.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.121767 restraints weight = 4682.472| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13400 Z= 0.087 Angle : 0.389 7.283 18152 Z= 0.202 Chirality : 0.046 0.137 2174 Planarity : 0.003 0.037 2360 Dihedral : 2.940 15.018 1943 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.89 % Allowed : 17.27 % Favored : 80.84 % 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: 0.52 (0.21), residues: 1766 helix: 0.56 (0.19), residues: 798 sheet: 1.43 (0.28), residues: 336 loop : -0.40 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 213 TYR 0.006 0.000 TYR F 333 PHE 0.003 0.001 PHE A 232 TRP 0.003 0.000 TRP G 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (13400) covalent geometry : angle 0.38943 / 0.20 (18152) hydrogen bonds : bond 0.02465 / 1.64 ( 503) hydrogen bonds : angle 3.74799 / 2.66 ( 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 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.519 Fit side-chains REVERT: A 169 ASP cc_start: 0.8035 (m-30) cc_final: 0.7748 (t70) REVERT: A 184 ASP cc_start: 0.8341 (t70) cc_final: 0.7308 (t70) REVERT: A 210 GLU cc_start: 0.7673 (tt0) cc_final: 0.6922 (tt0) REVERT: A 284 ASP cc_start: 0.7860 (t0) cc_final: 0.7344 (t0) REVERT: A 298 ARG cc_start: 0.7461 (ttm110) cc_final: 0.7183 (ptp-110) REVERT: E 153 LEU cc_start: 0.8175 (mt) cc_final: 0.7919 (mm) REVERT: E 309 ASP cc_start: 0.7138 (p0) cc_final: 0.6825 (p0) REVERT: B 218 GLU cc_start: 0.8217 (tp30) cc_final: 0.7899 (mm-30) REVERT: B 254 ASP cc_start: 0.7883 (t0) cc_final: 0.7499 (t0) REVERT: F 144 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6960 (tm-30) REVERT: F 262 ARG cc_start: 0.7773 (mmt-90) cc_final: 0.7555 (mmt180) REVERT: F 267 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8232 (m) REVERT: F 303 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7700 (mt) REVERT: C 184 ASP cc_start: 0.8628 (t0) cc_final: 0.8086 (t70) REVERT: C 200 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8128 (mtpp) REVERT: C 210 GLU cc_start: 0.7667 (tt0) cc_final: 0.7104 (tt0) REVERT: G 309 ASP cc_start: 0.7328 (p0) cc_final: 0.6671 (p0) REVERT: D 218 GLU cc_start: 0.8232 (tp30) cc_final: 0.7908 (mm-30) REVERT: D 254 ASP cc_start: 0.8034 (t0) cc_final: 0.7763 (t0) REVERT: H 144 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6965 (tm-30) REVERT: H 267 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8227 (m) REVERT: H 303 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7760 (mt) outliers start: 24 outliers final: 18 residues processed: 209 average time/residue: 0.1291 time to fit residues: 37.7662 Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 205 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 F residue 303 ILE Chi-restraints excluded: chain C residue 139 VAL 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 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 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: 7.9990 chunk 5 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3459 r_free = 0.3459 target = 0.142769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.110790 restraints weight = 38332.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.115542 restraints weight = 19016.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.115536 restraints weight = 11700.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.119464 restraints weight = 6746.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.120831 restraints weight = 4498.586| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2776 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= 0.113 Angle : 0.400 7.086 18152 Z= 0.207 Chirality : 0.046 0.142 2174 Planarity : 0.003 0.038 2360 Dihedral : 3.022 15.770 1943 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.03 % Allowed : 17.05 % Favored : 80.91 % 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: 0.41 (0.21), residues: 1766 helix: 0.35 (0.19), residues: 822 sheet: 1.43 (0.28), residues: 336 loop : -0.35 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 213 TYR 0.005 0.000 TYR H 333 PHE 0.005 0.001 PHE A 232 TRP 0.003 0.000 TRP G 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 (13400) covalent geometry : angle 0.39968 / 0.21 (18152) hydrogen bonds : bond 0.02661 / 1.76 ( 503) hydrogen bonds : angle 3.81149 / 2.70 ( 1417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2270.67 seconds wall clock time: 39 minutes 52.03 seconds (2392.03 seconds total)