Starting phenix.real_space_refine on Thu Mar 5 00:22:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dd3_27333/03_2026/8dd3_27333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd3_27333/03_2026/8dd3_27333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dd3_27333/03_2026/8dd3_27333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd3_27333/03_2026/8dd3_27333.map" model { file = "/net/cci-nas-00/data/ceres_data/8dd3_27333/03_2026/8dd3_27333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd3_27333/03_2026/8dd3_27333.cif" } resolution = 2.9 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= 0.003 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: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11276 2.51 5 N 2835 2.21 5 O 3251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17459 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'R63': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'R63': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'R63': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.81, per 1000 atoms: 0.22 Number of scatterers: 17459 At special positions: 0 Unit cell: (159.692, 134.875, 120.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3251 8.00 N 2835 7.00 C 11276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 401 " - " ASN A 80 " " NAG C 401 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 665.3 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 33.9% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 217 through 242 removed outlier: 4.459A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.141A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 270 Processing helix chain 'A' and resid 279 through 307 removed outlier: 4.123A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 339 removed outlier: 3.614A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.825A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.584A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.785A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 275 removed outlier: 3.611A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 347 Proline residue: B 330 - end of helix removed outlier: 3.759A pdb=" N ARG B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.520A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 272 removed outlier: 4.008A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 306 Processing helix chain 'C' and resid 309 through 340 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.635A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 87 through 93 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.608A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 275 removed outlier: 3.516A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 346 Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 85 through 88 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.585A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 257 removed outlier: 4.742A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.687A pdb=" N TRP E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 286 removed outlier: 3.669A pdb=" N LYS E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 324 removed outlier: 4.166A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 357 Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.078A pdb=" N LEU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.602A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 46 current: chain 'A' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 68 current: chain 'A' and resid 123 through 135 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 96 through 98 current: chain 'A' and resid 203 through 216 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 54 removed outlier: 6.487A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 71 current: chain 'B' and resid 126 through 138 Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.240A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 51 removed outlier: 8.282A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N MET C 40 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 50 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP C 56 " --> pdb=" O VAL C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.596A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 49 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.372A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 53 removed outlier: 6.157A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 56 through 66 removed outlier: 6.735A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU E 71 " --> pdb=" O PRO E 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 71 through 83 current: chain 'E' and resid 138 through 150 Processing sheet with id=AB2, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.683A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.624A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.992A pdb=" N GLU I 104 " --> pdb=" O MET I 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.516A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.594A pdb=" N THR J 115 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AC1, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.498A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.590A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 58 through 60 current: chain 'K' and resid 105 through 108 686 hydrogen bonds defined for protein. 1917 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: 2.91 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2671 1.31 - 1.43: 5285 1.43 - 1.56: 9774 1.56 - 1.69: 2 1.69 - 1.82: 167 Bond restraints: 17899 Sorted by residual: bond pdb=" C08 R63 C 403 " pdb=" O20 R63 C 403 " ideal model delta sigma weight residual 1.339 1.399 -0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" C08 R63 A 403 " pdb=" O20 R63 A 403 " ideal model delta sigma weight residual 1.339 1.398 -0.059 2.00e-02 2.50e+03 8.71e+00 bond pdb=" C08 R63 D 701 " pdb=" O20 R63 D 701 " ideal model delta sigma weight residual 1.339 1.396 -0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" C1 MAN G 7 " pdb=" C2 MAN G 7 " ideal model delta sigma weight residual 1.526 1.575 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C5 MAN G 8 " pdb=" O5 MAN G 8 " ideal model delta sigma weight residual 1.418 1.459 -0.041 2.00e-02 2.50e+03 4.30e+00 ... (remaining 17894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 23725 1.59 - 3.19: 458 3.19 - 4.78: 126 4.78 - 6.38: 34 6.38 - 7.97: 3 Bond angle restraints: 24346 Sorted by residual: angle pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta sigma weight residual 119.19 114.95 4.24 1.06e+00 8.90e-01 1.60e+01 angle pdb=" CA PHE B 329 " pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 121.01 117.89 3.12 9.50e-01 1.11e+00 1.08e+01 angle pdb=" C MET D 112 " pdb=" N THR D 113 " pdb=" CA THR D 113 " ideal model delta sigma weight residual 121.70 126.30 -4.60 1.80e+00 3.09e-01 6.53e+00 angle pdb=" C3 MAN G 7 " pdb=" C2 MAN G 7 " pdb=" O2 MAN G 7 " ideal model delta sigma weight residual 111.77 104.33 7.44 3.00e+00 1.11e-01 6.15e+00 angle pdb=" N GLY L 50 " pdb=" CA GLY L 50 " pdb=" C GLY L 50 " ideal model delta sigma weight residual 113.18 107.41 5.77 2.37e+00 1.78e-01 5.93e+00 ... (remaining 24341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 10177 21.47 - 42.94: 548 42.94 - 64.40: 44 64.40 - 85.87: 55 85.87 - 107.34: 20 Dihedral angle restraints: 10844 sinusoidal: 4588 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual 93.00 48.01 44.99 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 57.52 35.48 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 10841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 2795 0.190 - 0.380: 8 0.380 - 0.570: 1 0.570 - 0.760: 2 0.760 - 0.950: 1 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.45 0.95 2.00e-02 2.50e+03 2.25e+03 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 111 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.07 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 208 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.21e+00 ... (remaining 2804 not shown) Planarity restraints: 2995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 80 " -0.184 2.00e-02 2.50e+03 3.86e-01 1.86e+03 pdb=" CG ASN C 80 " 0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN C 80 " -0.138 2.00e-02 2.50e+03 pdb=" ND2 ASN C 80 " 0.677 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.469 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " -0.070 2.00e-02 2.50e+03 7.54e-02 7.11e+01 pdb=" CG ASN A 149 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " 0.116 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 111 " 0.031 2.00e-02 2.50e+03 7.31e-02 6.68e+01 pdb=" CG ASN B 111 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 111 " -0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN B 111 " 0.111 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.086 2.00e-02 2.50e+03 ... (remaining 2992 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 186 2.60 - 3.17: 15260 3.17 - 3.75: 25745 3.75 - 4.32: 38166 4.32 - 4.90: 63481 Nonbonded interactions: 142838 Sorted by model distance: nonbonded pdb=" O GLY I 30 " pdb=" OG1 THR I 31 " model vdw 2.021 3.040 nonbonded pdb=" OD1 ASP D 63 " pdb=" OG1 THR D 134 " model vdw 2.026 3.040 nonbonded pdb=" OG SER C 308 " pdb=" OE1 GLN C 309 " model vdw 2.052 3.040 nonbonded pdb=" OG SER E 217 " pdb=" OH TYR E 220 " model vdw 2.099 3.040 nonbonded pdb=" OG SER C 247 " pdb=" OH TYR C 299 " model vdw 2.099 3.040 ... (remaining 142833 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.280 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.010 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:8.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.006 0.202 17932 Z= 0.272 Angle : 0.720 30.077 24433 Z= 0.338 Chirality : 0.052 0.950 2807 Planarity : 0.004 0.071 2988 Dihedral : 14.766 107.341 6797 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.77 (0.19), residues: 2103 helix: 2.72 (0.20), residues: 572 sheet: -0.30 (0.20), residues: 679 loop : -0.24 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 249 TYR 0.015 0.001 TYR E 350 PHE 0.022 0.002 PHE D 226 TRP 0.016 0.001 TRP E 256 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00525 (17899) covalent geometry : angle 0.62003 (24346) SS BOND : bond 0.00337 ( 9) SS BOND : angle 0.89198 ( 18) hydrogen bonds : bond 0.16570 ( 686) hydrogen bonds : angle 6.53313 ( 1917) Misc. bond : bond 0.00039 ( 1) link_ALPHA1-2 : bond 0.08034 ( 3) link_ALPHA1-2 : angle 6.50560 ( 9) link_ALPHA1-3 : bond 0.00459 ( 2) link_ALPHA1-3 : angle 3.29732 ( 6) link_ALPHA1-6 : bond 0.01676 ( 2) link_ALPHA1-6 : angle 3.80709 ( 6) link_BETA1-4 : bond 0.00196 ( 9) link_BETA1-4 : angle 2.43109 ( 27) link_NAG-ASN : bond 0.12293 ( 7) link_NAG-ASN : angle 11.15398 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PRO cc_start: 0.6476 (Cg_exo) cc_final: 0.6046 (Cg_endo) REVERT: C 48 ASP cc_start: 0.7634 (m-30) cc_final: 0.7416 (m-30) REVERT: C 185 GLN cc_start: 0.7830 (pt0) cc_final: 0.7306 (pt0) REVERT: D 190 GLN cc_start: 0.8205 (pt0) cc_final: 0.7829 (pt0) REVERT: E 336 ARG cc_start: 0.7113 (mtm110) cc_final: 0.6889 (mtt180) REVERT: E 340 PRO cc_start: 0.7496 (Cg_exo) cc_final: 0.7180 (Cg_endo) REVERT: E 351 TRP cc_start: 0.7180 (m100) cc_final: 0.6926 (m100) REVERT: I 13 MET cc_start: 0.6153 (pmm) cc_final: 0.5881 (pmm) REVERT: I 17 GLU cc_start: 0.7073 (tt0) cc_final: 0.6838 (tt0) REVERT: J 34 MET cc_start: 0.8828 (mmp) cc_final: 0.8401 (mpp) REVERT: J 73 ASP cc_start: 0.7828 (t0) cc_final: 0.7475 (t0) REVERT: L 24 LYS cc_start: 0.8264 (tttp) cc_final: 0.7980 (mtpp) REVERT: K 63 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8650 (mmtm) REVERT: K 73 ASP cc_start: 0.8032 (t0) cc_final: 0.7761 (t0) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.6234 time to fit residues: 230.9448 Evaluate side-chains 268 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN C 113 ASN C 119 HIS D 229 GLN E 163 HIS E 318 HIS E 347 ASN K 55 ASN K 65 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.107770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.073353 restraints weight = 29779.964| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.41 r_work: 0.2816 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17932 Z= 0.144 Angle : 0.632 15.703 24433 Z= 0.312 Chirality : 0.046 0.825 2807 Planarity : 0.004 0.052 2988 Dihedral : 10.251 82.879 2857 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.07 % Allowed : 9.08 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.17 (0.19), residues: 2103 helix: 3.02 (0.20), residues: 587 sheet: -0.08 (0.20), residues: 674 loop : -0.02 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 28 TYR 0.022 0.001 TYR I 49 PHE 0.015 0.002 PHE B 304 TRP 0.022 0.001 TRP A 319 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00324 (17899) covalent geometry : angle 0.60501 (24346) SS BOND : bond 0.00380 ( 9) SS BOND : angle 0.71225 ( 18) hydrogen bonds : bond 0.04713 ( 686) hydrogen bonds : angle 4.82191 ( 1917) Misc. bond : bond 0.00014 ( 1) link_ALPHA1-2 : bond 0.00542 ( 3) link_ALPHA1-2 : angle 1.82205 ( 9) link_ALPHA1-3 : bond 0.00896 ( 2) link_ALPHA1-3 : angle 1.24105 ( 6) link_ALPHA1-6 : bond 0.00568 ( 2) link_ALPHA1-6 : angle 1.44255 ( 6) link_BETA1-4 : bond 0.00399 ( 9) link_BETA1-4 : angle 2.34103 ( 27) link_NAG-ASN : bond 0.00691 ( 7) link_NAG-ASN : angle 5.55077 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 290 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8496 (pt) cc_final: 0.8174 (mt) REVERT: B 90 MET cc_start: 0.8975 (tpt) cc_final: 0.8674 (tpt) REVERT: B 266 MET cc_start: 0.7903 (tpt) cc_final: 0.7620 (tpt) REVERT: B 277 LEU cc_start: 0.7509 (pt) cc_final: 0.7307 (pp) REVERT: C 48 ASP cc_start: 0.8488 (m-30) cc_final: 0.8252 (m-30) REVERT: C 64 GLN cc_start: 0.8738 (mt0) cc_final: 0.8519 (mp10) REVERT: C 185 GLN cc_start: 0.8200 (pt0) cc_final: 0.7444 (pt0) REVERT: D 190 GLN cc_start: 0.8723 (pt0) cc_final: 0.8318 (pt0) REVERT: D 242 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6831 (mp-120) REVERT: E 150 GLU cc_start: 0.8361 (pp20) cc_final: 0.8139 (pp20) REVERT: E 336 ARG cc_start: 0.7258 (mtm110) cc_final: 0.6768 (mtt180) REVERT: I 39 LYS cc_start: 0.8290 (mmmm) cc_final: 0.7920 (mmpt) REVERT: J 34 MET cc_start: 0.9259 (mmp) cc_final: 0.8879 (mpp) REVERT: L 24 LYS cc_start: 0.8595 (tttp) cc_final: 0.7895 (mtpp) REVERT: L 83 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8479 (pp) REVERT: K 63 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8650 (mmtm) REVERT: K 73 ASP cc_start: 0.8176 (t0) cc_final: 0.7693 (t0) outliers start: 39 outliers final: 23 residues processed: 307 average time/residue: 0.6195 time to fit residues: 211.3908 Evaluate side-chains 289 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 170 optimal weight: 4.9990 chunk 52 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN D 56 HIS D 229 GLN D 346 ASN E 318 HIS K 55 ASN K 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.071373 restraints weight = 30175.653| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.35 r_work: 0.2779 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17932 Z= 0.210 Angle : 0.637 13.830 24433 Z= 0.316 Chirality : 0.045 0.531 2807 Planarity : 0.004 0.053 2988 Dihedral : 8.974 80.772 2857 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.76 % Allowed : 11.90 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2103 helix: 2.90 (0.20), residues: 590 sheet: -0.09 (0.20), residues: 675 loop : -0.07 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 312 TYR 0.024 0.002 TYR L 49 PHE 0.016 0.002 PHE D 157 TRP 0.023 0.001 TRP A 319 HIS 0.008 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00502 (17899) covalent geometry : angle 0.61261 (24346) SS BOND : bond 0.00439 ( 9) SS BOND : angle 0.90220 ( 18) hydrogen bonds : bond 0.04672 ( 686) hydrogen bonds : angle 4.62779 ( 1917) Misc. bond : bond 0.00058 ( 1) link_ALPHA1-2 : bond 0.00494 ( 3) link_ALPHA1-2 : angle 1.84709 ( 9) link_ALPHA1-3 : bond 0.00854 ( 2) link_ALPHA1-3 : angle 1.26978 ( 6) link_ALPHA1-6 : bond 0.00260 ( 2) link_ALPHA1-6 : angle 1.74458 ( 6) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 2.31220 ( 27) link_NAG-ASN : bond 0.00432 ( 7) link_NAG-ASN : angle 5.19452 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8558 (pt) cc_final: 0.8227 (mt) REVERT: B 277 LEU cc_start: 0.7568 (pt) cc_final: 0.7364 (pp) REVERT: C 48 ASP cc_start: 0.8457 (m-30) cc_final: 0.8198 (m-30) REVERT: C 64 GLN cc_start: 0.8861 (mt0) cc_final: 0.8643 (mp10) REVERT: C 185 GLN cc_start: 0.8143 (pt0) cc_final: 0.7439 (pt0) REVERT: D 190 GLN cc_start: 0.8749 (pt0) cc_final: 0.8325 (pt0) REVERT: D 242 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.6470 (mp-120) REVERT: E 150 GLU cc_start: 0.8335 (pp20) cc_final: 0.8127 (pp20) REVERT: E 211 GLU cc_start: 0.8124 (pt0) cc_final: 0.7855 (tt0) REVERT: E 304 PHE cc_start: 0.8713 (t80) cc_final: 0.8482 (t80) REVERT: E 332 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: E 336 ARG cc_start: 0.7074 (mtm110) cc_final: 0.6621 (mtt180) REVERT: I 39 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7891 (mmpt) REVERT: J 43 GLN cc_start: 0.8402 (mp10) cc_final: 0.7743 (mp10) REVERT: J 52 ASP cc_start: 0.8343 (t0) cc_final: 0.7967 (t0) REVERT: L 24 LYS cc_start: 0.8601 (tttp) cc_final: 0.7992 (mtpp) REVERT: L 61 ARG cc_start: 0.7924 (ptt-90) cc_final: 0.7594 (ptt-90) REVERT: L 79 GLN cc_start: 0.7744 (mp10) cc_final: 0.7517 (mm-40) REVERT: L 83 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8477 (pp) REVERT: K 63 LYS cc_start: 0.9091 (mtpp) cc_final: 0.8660 (mmtm) REVERT: K 73 ASP cc_start: 0.8155 (t0) cc_final: 0.7671 (t0) outliers start: 52 outliers final: 33 residues processed: 301 average time/residue: 0.6380 time to fit residues: 212.8480 Evaluate side-chains 301 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 100 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 116 ASN D 56 HIS D 229 GLN D 346 ASN E 318 HIS K 55 ASN K 65 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.073470 restraints weight = 30081.348| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.54 r_work: 0.2789 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17932 Z= 0.142 Angle : 0.587 13.088 24433 Z= 0.290 Chirality : 0.043 0.442 2807 Planarity : 0.004 0.048 2988 Dihedral : 8.175 78.396 2857 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.03 % Allowed : 12.90 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.15 (0.19), residues: 2103 helix: 2.97 (0.20), residues: 590 sheet: -0.03 (0.20), residues: 653 loop : -0.08 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 312 TYR 0.028 0.001 TYR L 49 PHE 0.018 0.001 PHE E 308 TRP 0.025 0.001 TRP A 319 HIS 0.004 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00327 (17899) covalent geometry : angle 0.56541 (24346) SS BOND : bond 0.00329 ( 9) SS BOND : angle 0.67078 ( 18) hydrogen bonds : bond 0.04084 ( 686) hydrogen bonds : angle 4.38346 ( 1917) Misc. bond : bond 0.00062 ( 1) link_ALPHA1-2 : bond 0.00488 ( 3) link_ALPHA1-2 : angle 1.60959 ( 9) link_ALPHA1-3 : bond 0.00922 ( 2) link_ALPHA1-3 : angle 1.17272 ( 6) link_ALPHA1-6 : bond 0.00315 ( 2) link_ALPHA1-6 : angle 1.65695 ( 6) link_BETA1-4 : bond 0.00457 ( 9) link_BETA1-4 : angle 2.06112 ( 27) link_NAG-ASN : bond 0.00420 ( 7) link_NAG-ASN : angle 4.66894 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8211 (tp30) cc_final: 0.8001 (tm-30) REVERT: B 90 MET cc_start: 0.9041 (tpt) cc_final: 0.8682 (tpt) REVERT: B 277 LEU cc_start: 0.7578 (pt) cc_final: 0.7376 (pp) REVERT: C 48 ASP cc_start: 0.8436 (m-30) cc_final: 0.8227 (m-30) REVERT: C 185 GLN cc_start: 0.8195 (pt0) cc_final: 0.7466 (pt0) REVERT: D 190 GLN cc_start: 0.8715 (pt0) cc_final: 0.8301 (pt0) REVERT: D 242 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.6366 (mp-120) REVERT: E 211 GLU cc_start: 0.8177 (pt0) cc_final: 0.7923 (tt0) REVERT: E 304 PHE cc_start: 0.8729 (t80) cc_final: 0.8515 (t80) REVERT: E 332 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: J 34 MET cc_start: 0.9188 (tpp) cc_final: 0.8620 (mpp) REVERT: J 52 ASP cc_start: 0.8332 (t0) cc_final: 0.7966 (t0) REVERT: L 13 MET cc_start: 0.7771 (pp-130) cc_final: 0.7527 (ppp) REVERT: L 24 LYS cc_start: 0.8601 (tttp) cc_final: 0.8020 (mtpp) REVERT: L 61 ARG cc_start: 0.7914 (ptt-90) cc_final: 0.7668 (ptp-170) REVERT: L 79 GLN cc_start: 0.7802 (mp10) cc_final: 0.7534 (mm-40) REVERT: L 83 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8774 (pt) REVERT: K 63 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8678 (mmtm) REVERT: K 73 ASP cc_start: 0.8216 (t0) cc_final: 0.7709 (t0) outliers start: 57 outliers final: 32 residues processed: 303 average time/residue: 0.6237 time to fit residues: 209.7233 Evaluate side-chains 296 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 241 TRP Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 52 optimal weight: 0.0370 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN D 56 HIS D 229 GLN D 346 ASN E 318 HIS K 55 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.107491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.074620 restraints weight = 29874.321| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.54 r_work: 0.2809 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17932 Z= 0.118 Angle : 0.570 12.349 24433 Z= 0.281 Chirality : 0.042 0.387 2807 Planarity : 0.004 0.046 2988 Dihedral : 7.624 79.102 2857 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.08 % Allowed : 14.18 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 2103 helix: 3.04 (0.21), residues: 588 sheet: 0.08 (0.20), residues: 656 loop : -0.02 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 312 TYR 0.032 0.001 TYR L 49 PHE 0.021 0.001 PHE E 308 TRP 0.026 0.001 TRP A 319 HIS 0.004 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00265 (17899) covalent geometry : angle 0.55112 (24346) SS BOND : bond 0.00264 ( 9) SS BOND : angle 0.56063 ( 18) hydrogen bonds : bond 0.03677 ( 686) hydrogen bonds : angle 4.20262 ( 1917) Misc. bond : bond 0.00010 ( 1) link_ALPHA1-2 : bond 0.00472 ( 3) link_ALPHA1-2 : angle 1.54574 ( 9) link_ALPHA1-3 : bond 0.01063 ( 2) link_ALPHA1-3 : angle 1.18937 ( 6) link_ALPHA1-6 : bond 0.00328 ( 2) link_ALPHA1-6 : angle 1.67637 ( 6) link_BETA1-4 : bond 0.00449 ( 9) link_BETA1-4 : angle 1.81755 ( 27) link_NAG-ASN : bond 0.00450 ( 7) link_NAG-ASN : angle 4.29997 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8226 (tp30) cc_final: 0.8009 (tm-30) REVERT: B 90 MET cc_start: 0.9034 (tpt) cc_final: 0.8667 (tpt) REVERT: C 48 ASP cc_start: 0.8517 (m-30) cc_final: 0.8228 (m-30) REVERT: C 185 GLN cc_start: 0.8185 (pt0) cc_final: 0.7426 (pt0) REVERT: D 190 GLN cc_start: 0.8713 (pt0) cc_final: 0.8285 (pt0) REVERT: D 242 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: D 294 TYR cc_start: 0.8616 (t80) cc_final: 0.8270 (t80) REVERT: E 211 GLU cc_start: 0.8150 (pt0) cc_final: 0.7870 (tt0) REVERT: E 296 MET cc_start: 0.6943 (ppp) cc_final: 0.6573 (pp-130) REVERT: E 332 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: I 11 MET cc_start: 0.8593 (ppp) cc_final: 0.8234 (ppp) REVERT: J 52 ASP cc_start: 0.8333 (t0) cc_final: 0.7979 (t0) REVERT: L 13 MET cc_start: 0.7775 (pp-130) cc_final: 0.7538 (ppp) REVERT: L 24 LYS cc_start: 0.8613 (tttp) cc_final: 0.8015 (mtpp) REVERT: L 61 ARG cc_start: 0.7937 (ptt-90) cc_final: 0.7688 (ptp-170) REVERT: L 79 GLN cc_start: 0.7673 (mp10) cc_final: 0.7429 (mm-40) REVERT: L 83 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8765 (pt) REVERT: K 63 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8681 (mmtm) REVERT: K 73 ASP cc_start: 0.8295 (t0) cc_final: 0.7839 (t0) outliers start: 58 outliers final: 36 residues processed: 301 average time/residue: 0.6031 time to fit residues: 202.2123 Evaluate side-chains 299 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 241 TRP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 142 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 185 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 206 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 229 GLN D 346 ASN ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN E 347 ASN K 55 ASN K 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.075068 restraints weight = 29876.193| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.57 r_work: 0.2821 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17932 Z= 0.111 Angle : 0.561 11.986 24433 Z= 0.276 Chirality : 0.041 0.364 2807 Planarity : 0.003 0.044 2988 Dihedral : 7.328 80.081 2857 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.13 % Allowed : 15.03 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.29 (0.19), residues: 2103 helix: 3.01 (0.21), residues: 588 sheet: 0.19 (0.20), residues: 652 loop : -0.06 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 312 TYR 0.032 0.001 TYR L 49 PHE 0.017 0.001 PHE C 330 TRP 0.027 0.001 TRP A 319 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00247 (17899) covalent geometry : angle 0.54377 (24346) SS BOND : bond 0.00266 ( 9) SS BOND : angle 0.51306 ( 18) hydrogen bonds : bond 0.03487 ( 686) hydrogen bonds : angle 4.09333 ( 1917) Misc. bond : bond 0.00002 ( 1) link_ALPHA1-2 : bond 0.00462 ( 3) link_ALPHA1-2 : angle 1.52574 ( 9) link_ALPHA1-3 : bond 0.01073 ( 2) link_ALPHA1-3 : angle 1.17306 ( 6) link_ALPHA1-6 : bond 0.00308 ( 2) link_ALPHA1-6 : angle 1.69195 ( 6) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 1.71994 ( 27) link_NAG-ASN : bond 0.00486 ( 7) link_NAG-ASN : angle 4.11149 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 269 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8196 (tp30) cc_final: 0.7993 (tm-30) REVERT: B 90 MET cc_start: 0.9025 (tpt) cc_final: 0.8670 (tpt) REVERT: B 277 LEU cc_start: 0.7505 (pt) cc_final: 0.7292 (pp) REVERT: C 48 ASP cc_start: 0.8517 (m-30) cc_final: 0.8173 (m-30) REVERT: C 185 GLN cc_start: 0.8182 (pt0) cc_final: 0.7432 (pt0) REVERT: D 133 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8376 (pp) REVERT: D 190 GLN cc_start: 0.8707 (pt0) cc_final: 0.8269 (pt0) REVERT: D 242 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: D 294 TYR cc_start: 0.8588 (t80) cc_final: 0.8256 (t80) REVERT: E 211 GLU cc_start: 0.8152 (pt0) cc_final: 0.7877 (tt0) REVERT: E 296 MET cc_start: 0.6867 (ppp) cc_final: 0.6468 (pp-130) REVERT: E 318 HIS cc_start: 0.8155 (t70) cc_final: 0.7922 (t70) REVERT: E 332 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: I 11 MET cc_start: 0.8576 (ppp) cc_final: 0.8202 (ppp) REVERT: J 52 ASP cc_start: 0.8290 (t0) cc_final: 0.7958 (t0) REVERT: L 13 MET cc_start: 0.7745 (pp-130) cc_final: 0.7523 (ppp) REVERT: L 24 LYS cc_start: 0.8619 (tttp) cc_final: 0.8016 (mtpp) REVERT: L 61 ARG cc_start: 0.7933 (ptt-90) cc_final: 0.7719 (ptp-170) REVERT: L 83 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8568 (pt) REVERT: K 63 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8656 (mmtm) REVERT: K 73 ASP cc_start: 0.8338 (t0) cc_final: 0.7825 (t0) outliers start: 59 outliers final: 30 residues processed: 293 average time/residue: 0.5991 time to fit residues: 195.9950 Evaluate side-chains 286 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 241 TRP Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 141 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN C 85 ASN D 229 GLN D 346 ASN ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN K 55 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.073407 restraints weight = 29953.781| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.38 r_work: 0.2815 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17932 Z= 0.133 Angle : 0.575 11.736 24433 Z= 0.283 Chirality : 0.042 0.348 2807 Planarity : 0.004 0.044 2988 Dihedral : 7.182 80.004 2857 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.76 % Allowed : 16.46 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2103 helix: 3.01 (0.21), residues: 586 sheet: 0.16 (0.20), residues: 678 loop : 0.04 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 207 TYR 0.033 0.001 TYR L 49 PHE 0.021 0.001 PHE C 330 TRP 0.029 0.001 TRP A 319 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00309 (17899) covalent geometry : angle 0.55828 (24346) SS BOND : bond 0.00297 ( 9) SS BOND : angle 0.61176 ( 18) hydrogen bonds : bond 0.03561 ( 686) hydrogen bonds : angle 4.08528 ( 1917) Misc. bond : bond 0.00016 ( 1) link_ALPHA1-2 : bond 0.00430 ( 3) link_ALPHA1-2 : angle 1.63845 ( 9) link_ALPHA1-3 : bond 0.01113 ( 2) link_ALPHA1-3 : angle 1.21293 ( 6) link_ALPHA1-6 : bond 0.00183 ( 2) link_ALPHA1-6 : angle 1.82587 ( 6) link_BETA1-4 : bond 0.00478 ( 9) link_BETA1-4 : angle 1.77180 ( 27) link_NAG-ASN : bond 0.00459 ( 7) link_NAG-ASN : angle 4.12901 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8187 (tp30) cc_final: 0.7984 (tm-30) REVERT: B 90 MET cc_start: 0.9050 (tpt) cc_final: 0.8695 (tpt) REVERT: B 213 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8807 (mmp) REVERT: B 277 LEU cc_start: 0.7546 (pt) cc_final: 0.7329 (pp) REVERT: C 48 ASP cc_start: 0.8493 (m-30) cc_final: 0.8159 (m-30) REVERT: C 185 GLN cc_start: 0.8179 (pt0) cc_final: 0.7423 (pt0) REVERT: D 133 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8373 (pp) REVERT: D 190 GLN cc_start: 0.8690 (pt0) cc_final: 0.8290 (pt0) REVERT: D 242 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: E 211 GLU cc_start: 0.8129 (pt0) cc_final: 0.7847 (tt0) REVERT: E 318 HIS cc_start: 0.8059 (t70) cc_final: 0.7821 (t70) REVERT: E 332 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7270 (m-30) REVERT: E 351 TRP cc_start: 0.6823 (m100) cc_final: 0.6541 (m100) REVERT: I 11 MET cc_start: 0.8516 (ppp) cc_final: 0.8298 (ppp) REVERT: J 52 ASP cc_start: 0.8333 (t0) cc_final: 0.8036 (t0) REVERT: L 13 MET cc_start: 0.7790 (pp-130) cc_final: 0.7588 (ppp) REVERT: L 24 LYS cc_start: 0.8608 (tttp) cc_final: 0.8016 (mtpp) REVERT: L 61 ARG cc_start: 0.7974 (ptt-90) cc_final: 0.7763 (ptp-170) REVERT: L 83 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8563 (pt) REVERT: K 3 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7867 (mm-40) REVERT: K 73 ASP cc_start: 0.8351 (t0) cc_final: 0.7844 (t0) REVERT: K 89 GLU cc_start: 0.7944 (mp0) cc_final: 0.7650 (mp0) outliers start: 52 outliers final: 31 residues processed: 288 average time/residue: 0.6095 time to fit residues: 195.6215 Evaluate side-chains 291 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 241 TRP Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 116 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN D 229 GLN E 318 HIS ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.074900 restraints weight = 29953.467| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.53 r_work: 0.2815 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17932 Z= 0.121 Angle : 0.577 11.720 24433 Z= 0.284 Chirality : 0.042 0.339 2807 Planarity : 0.003 0.043 2988 Dihedral : 7.076 80.576 2857 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.03 % Allowed : 16.52 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.35 (0.19), residues: 2103 helix: 3.01 (0.21), residues: 586 sheet: 0.18 (0.20), residues: 679 loop : 0.06 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.034 0.001 TYR L 49 PHE 0.022 0.001 PHE C 330 TRP 0.031 0.001 TRP A 319 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00277 (17899) covalent geometry : angle 0.56136 (24346) SS BOND : bond 0.00276 ( 9) SS BOND : angle 0.53766 ( 18) hydrogen bonds : bond 0.03423 ( 686) hydrogen bonds : angle 4.05642 ( 1917) Misc. bond : bond 0.00008 ( 1) link_ALPHA1-2 : bond 0.00443 ( 3) link_ALPHA1-2 : angle 1.55763 ( 9) link_ALPHA1-3 : bond 0.01204 ( 2) link_ALPHA1-3 : angle 1.19747 ( 6) link_ALPHA1-6 : bond 0.00231 ( 2) link_ALPHA1-6 : angle 1.78562 ( 6) link_BETA1-4 : bond 0.00504 ( 9) link_BETA1-4 : angle 1.69278 ( 27) link_NAG-ASN : bond 0.00490 ( 7) link_NAG-ASN : angle 4.00659 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8201 (tp30) cc_final: 0.7996 (tm-30) REVERT: B 90 MET cc_start: 0.9055 (tpt) cc_final: 0.8703 (tpt) REVERT: B 277 LEU cc_start: 0.7548 (pt) cc_final: 0.7340 (pp) REVERT: C 48 ASP cc_start: 0.8512 (m-30) cc_final: 0.8224 (m-30) REVERT: C 185 GLN cc_start: 0.8187 (pt0) cc_final: 0.7439 (pt0) REVERT: C 259 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7196 (mm) REVERT: D 133 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8349 (pp) REVERT: D 190 GLN cc_start: 0.8702 (pt0) cc_final: 0.8307 (pt0) REVERT: D 242 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: D 294 TYR cc_start: 0.8650 (t80) cc_final: 0.8380 (t80) REVERT: E 211 GLU cc_start: 0.8149 (pt0) cc_final: 0.7883 (tt0) REVERT: E 334 TYR cc_start: 0.7889 (m-80) cc_final: 0.7513 (m-80) REVERT: E 351 TRP cc_start: 0.6886 (m100) cc_final: 0.6645 (m100) REVERT: I 11 MET cc_start: 0.8561 (ppp) cc_final: 0.8266 (ppp) REVERT: J 52 ASP cc_start: 0.8326 (t0) cc_final: 0.8027 (t0) REVERT: L 19 VAL cc_start: 0.8171 (t) cc_final: 0.7626 (m) REVERT: L 24 LYS cc_start: 0.8653 (tttp) cc_final: 0.8056 (mtpp) REVERT: L 61 ARG cc_start: 0.7982 (ptt-90) cc_final: 0.7773 (ptp-170) REVERT: L 83 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8737 (pt) REVERT: K 73 ASP cc_start: 0.8356 (t0) cc_final: 0.7800 (t0) REVERT: K 89 GLU cc_start: 0.7916 (mp0) cc_final: 0.7628 (mp0) outliers start: 57 outliers final: 33 residues processed: 295 average time/residue: 0.5899 time to fit residues: 193.9347 Evaluate side-chains 294 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 241 TRP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 105 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 141 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN D 229 GLN E 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.075037 restraints weight = 29956.238| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.54 r_work: 0.2820 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17932 Z= 0.119 Angle : 0.581 11.945 24433 Z= 0.287 Chirality : 0.042 0.336 2807 Planarity : 0.003 0.043 2988 Dihedral : 7.020 81.687 2857 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.60 % Allowed : 17.15 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.31 (0.19), residues: 2103 helix: 2.95 (0.21), residues: 587 sheet: 0.26 (0.20), residues: 652 loop : -0.04 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 312 TYR 0.034 0.001 TYR L 49 PHE 0.022 0.001 PHE C 330 TRP 0.033 0.001 TRP A 319 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00273 (17899) covalent geometry : angle 0.56596 (24346) SS BOND : bond 0.00273 ( 9) SS BOND : angle 0.52208 ( 18) hydrogen bonds : bond 0.03387 ( 686) hydrogen bonds : angle 4.07104 ( 1917) Misc. bond : bond 0.00006 ( 1) link_ALPHA1-2 : bond 0.00428 ( 3) link_ALPHA1-2 : angle 1.56849 ( 9) link_ALPHA1-3 : bond 0.01158 ( 2) link_ALPHA1-3 : angle 1.20885 ( 6) link_ALPHA1-6 : bond 0.00221 ( 2) link_ALPHA1-6 : angle 1.80033 ( 6) link_BETA1-4 : bond 0.00500 ( 9) link_BETA1-4 : angle 1.66094 ( 27) link_NAG-ASN : bond 0.00503 ( 7) link_NAG-ASN : angle 3.93137 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8238 (tp30) cc_final: 0.8034 (tm-30) REVERT: B 90 MET cc_start: 0.9047 (tpt) cc_final: 0.8694 (tpt) REVERT: C 48 ASP cc_start: 0.8514 (m-30) cc_final: 0.8235 (m-30) REVERT: C 185 GLN cc_start: 0.8186 (pt0) cc_final: 0.7440 (pt0) REVERT: C 259 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7183 (mm) REVERT: D 133 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8339 (pp) REVERT: D 190 GLN cc_start: 0.8698 (pt0) cc_final: 0.8301 (pt0) REVERT: D 242 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: D 294 TYR cc_start: 0.8649 (t80) cc_final: 0.8383 (t80) REVERT: E 211 GLU cc_start: 0.8152 (pt0) cc_final: 0.7891 (tt0) REVERT: E 296 MET cc_start: 0.6910 (ppp) cc_final: 0.6533 (pp-130) REVERT: E 334 TYR cc_start: 0.7892 (m-80) cc_final: 0.7591 (m-80) REVERT: E 351 TRP cc_start: 0.6850 (m100) cc_final: 0.6599 (m100) REVERT: I 11 MET cc_start: 0.8585 (ppp) cc_final: 0.8320 (ppp) REVERT: I 24 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8357 (mtpt) REVERT: J 52 ASP cc_start: 0.8324 (t0) cc_final: 0.8027 (t0) REVERT: L 24 LYS cc_start: 0.8697 (tttp) cc_final: 0.8077 (mtpp) REVERT: L 61 ARG cc_start: 0.7966 (ptt-90) cc_final: 0.7713 (ptp-170) REVERT: L 79 GLN cc_start: 0.7582 (mp10) cc_final: 0.7359 (mm-40) REVERT: L 83 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8720 (pt) REVERT: K 73 ASP cc_start: 0.8374 (t0) cc_final: 0.7852 (t0) REVERT: K 89 GLU cc_start: 0.7907 (mp0) cc_final: 0.7618 (mp0) REVERT: K 106 ASP cc_start: 0.8954 (p0) cc_final: 0.8718 (p0) outliers start: 49 outliers final: 33 residues processed: 291 average time/residue: 0.6268 time to fit residues: 202.8132 Evaluate side-chains 296 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 15 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 175 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 202 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN D 229 GLN E 239 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.074820 restraints weight = 29761.203| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.53 r_work: 0.2816 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17932 Z= 0.129 Angle : 0.599 12.520 24433 Z= 0.293 Chirality : 0.043 0.333 2807 Planarity : 0.004 0.044 2988 Dihedral : 7.047 84.649 2857 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.34 % Allowed : 17.47 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.32 (0.19), residues: 2103 helix: 2.95 (0.21), residues: 587 sheet: 0.19 (0.20), residues: 678 loop : 0.05 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 136 TYR 0.046 0.001 TYR E 235 PHE 0.039 0.001 PHE C 323 TRP 0.035 0.001 TRP A 319 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00300 (17899) covalent geometry : angle 0.58428 (24346) SS BOND : bond 0.00290 ( 9) SS BOND : angle 0.56722 ( 18) hydrogen bonds : bond 0.03431 ( 686) hydrogen bonds : angle 4.07379 ( 1917) Misc. bond : bond 0.00009 ( 1) link_ALPHA1-2 : bond 0.00410 ( 3) link_ALPHA1-2 : angle 1.61256 ( 9) link_ALPHA1-3 : bond 0.01254 ( 2) link_ALPHA1-3 : angle 1.23482 ( 6) link_ALPHA1-6 : bond 0.00152 ( 2) link_ALPHA1-6 : angle 1.85973 ( 6) link_BETA1-4 : bond 0.00513 ( 9) link_BETA1-4 : angle 1.68678 ( 27) link_NAG-ASN : bond 0.00508 ( 7) link_NAG-ASN : angle 3.94026 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9047 (tpt) cc_final: 0.8699 (tpt) REVERT: B 277 LEU cc_start: 0.7422 (pt) cc_final: 0.7194 (pp) REVERT: C 48 ASP cc_start: 0.8518 (m-30) cc_final: 0.8241 (m-30) REVERT: C 185 GLN cc_start: 0.8183 (pt0) cc_final: 0.7436 (pt0) REVERT: C 259 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7191 (mm) REVERT: D 133 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8358 (pp) REVERT: D 190 GLN cc_start: 0.8706 (pt0) cc_final: 0.8312 (pt0) REVERT: D 242 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: D 294 TYR cc_start: 0.8623 (t80) cc_final: 0.8353 (t80) REVERT: E 211 GLU cc_start: 0.8167 (pt0) cc_final: 0.7912 (tt0) REVERT: E 296 MET cc_start: 0.6918 (ppp) cc_final: 0.6543 (pp-130) REVERT: E 332 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: E 351 TRP cc_start: 0.6873 (m100) cc_final: 0.6600 (m100) REVERT: I 11 MET cc_start: 0.8582 (ppp) cc_final: 0.8308 (ppp) REVERT: I 24 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8323 (mtpt) REVERT: J 34 MET cc_start: 0.9171 (tpp) cc_final: 0.8659 (mpp) REVERT: J 52 ASP cc_start: 0.8329 (t0) cc_final: 0.8032 (t0) REVERT: L 24 LYS cc_start: 0.8756 (tttp) cc_final: 0.8125 (mtpp) REVERT: L 61 ARG cc_start: 0.7960 (ptt-90) cc_final: 0.7700 (ptp-170) REVERT: L 79 GLN cc_start: 0.7617 (mp10) cc_final: 0.7396 (mm-40) REVERT: L 83 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8729 (pt) REVERT: K 73 ASP cc_start: 0.8369 (t0) cc_final: 0.7874 (t0) REVERT: K 89 GLU cc_start: 0.7907 (mp0) cc_final: 0.7622 (mp0) REVERT: K 106 ASP cc_start: 0.8984 (p0) cc_final: 0.8740 (p0) outliers start: 44 outliers final: 31 residues processed: 289 average time/residue: 0.6148 time to fit residues: 197.6592 Evaluate side-chains 301 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 319 TRP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 167 optimal weight: 0.9980 chunk 158 optimal weight: 0.0970 chunk 139 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN D 229 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.074185 restraints weight = 29964.949| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.39 r_work: 0.2831 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17932 Z= 0.117 Angle : 0.595 12.079 24433 Z= 0.294 Chirality : 0.042 0.330 2807 Planarity : 0.003 0.044 2988 Dihedral : 7.030 84.871 2857 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.23 % Allowed : 17.42 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2103 helix: 2.95 (0.21), residues: 587 sheet: 0.19 (0.20), residues: 678 loop : 0.06 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 136 TYR 0.033 0.001 TYR L 49 PHE 0.025 0.001 PHE C 330 TRP 0.035 0.001 TRP A 319 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00265 (17899) covalent geometry : angle 0.58097 (24346) SS BOND : bond 0.00264 ( 9) SS BOND : angle 0.51069 ( 18) hydrogen bonds : bond 0.03370 ( 686) hydrogen bonds : angle 4.06940 ( 1917) Misc. bond : bond 0.00005 ( 1) link_ALPHA1-2 : bond 0.00428 ( 3) link_ALPHA1-2 : angle 1.56826 ( 9) link_ALPHA1-3 : bond 0.01328 ( 2) link_ALPHA1-3 : angle 1.22942 ( 6) link_ALPHA1-6 : bond 0.00207 ( 2) link_ALPHA1-6 : angle 1.81200 ( 6) link_BETA1-4 : bond 0.00512 ( 9) link_BETA1-4 : angle 1.64491 ( 27) link_NAG-ASN : bond 0.00516 ( 7) link_NAG-ASN : angle 3.86935 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6693.85 seconds wall clock time: 114 minutes 25.32 seconds (6865.32 seconds total)