Starting phenix.real_space_refine on Sun May 18 22:18:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dd3_27333/05_2025/8dd3_27333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd3_27333/05_2025/8dd3_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_27333/05_2025/8dd3_27333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd3_27333/05_2025/8dd3_27333.map" model { file = "/net/cci-nas-00/data/ceres_data/8dd3_27333/05_2025/8dd3_27333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd3_27333/05_2025/8dd3_27333.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.34, per 1000 atoms: 0.65 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: 5.39 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.88 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: 5.12 Time building geometry restraints manager: 6.09 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: 3.840 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.010 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.970 ------------------------------------------------------------------------------- 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 : 6.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (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 TRP 0.016 0.001 TRP E 256 HIS 0.005 0.001 HIS C 267 PHE 0.022 0.002 PHE D 226 TYR 0.015 0.001 TYR E 350 ARG 0.008 0.000 ARG B 249 Details of bonding type rmsd link_NAG-ASN : bond 0.12293 ( 7) link_NAG-ASN : angle 11.15398 ( 21) 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_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) hydrogen bonds : bond 0.16570 ( 686) hydrogen bonds : angle 6.53313 ( 1917) SS BOND : bond 0.00337 ( 9) SS BOND : angle 0.89198 ( 18) covalent geometry : bond 0.00525 (17899) covalent geometry : angle 0.62003 (24346) Misc. bond : bond 0.00039 ( 1) *********************** 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 : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PRO cc_start: 0.6476 (Cg_exo) cc_final: 0.6047 (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: 0.6837 (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: 0.7465 (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: 1.2428 time to fit residues: 462.9560 Evaluate side-chains 269 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.3980 chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.108016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.073662 restraints weight = 29718.491| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.41 r_work: 0.2821 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17932 Z= 0.137 Angle : 0.620 15.499 24433 Z= 0.306 Chirality : 0.046 0.906 2807 Planarity : 0.004 0.053 2988 Dihedral : 10.222 82.515 2857 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.96 % Allowed : 9.08 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2103 helix: 3.07 (0.20), residues: 587 sheet: -0.08 (0.20), residues: 674 loop : -0.00 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 319 HIS 0.003 0.001 HIS D 56 PHE 0.015 0.002 PHE A 221 TYR 0.021 0.001 TYR I 49 ARG 0.005 0.000 ARG C 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 7) link_NAG-ASN : angle 5.49352 ( 21) link_ALPHA1-6 : bond 0.00668 ( 2) link_ALPHA1-6 : angle 1.38969 ( 6) link_BETA1-4 : bond 0.00389 ( 9) link_BETA1-4 : angle 2.30782 ( 27) link_ALPHA1-2 : bond 0.00671 ( 3) link_ALPHA1-2 : angle 1.74443 ( 9) link_ALPHA1-3 : bond 0.01092 ( 2) link_ALPHA1-3 : angle 1.25008 ( 6) hydrogen bonds : bond 0.04734 ( 686) hydrogen bonds : angle 4.82214 ( 1917) SS BOND : bond 0.00334 ( 9) SS BOND : angle 0.66127 ( 18) covalent geometry : bond 0.00301 (17899) covalent geometry : angle 0.59243 (24346) Misc. bond : bond 0.00009 ( 1) *********************** 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 327 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8487 (pt) cc_final: 0.8164 (mt) REVERT: B 90 MET cc_start: 0.8982 (tpt) cc_final: 0.8661 (tpt) REVERT: B 266 MET cc_start: 0.7898 (tpt) cc_final: 0.7625 (tpt) REVERT: B 277 LEU cc_start: 0.7443 (pt) cc_final: 0.7231 (pp) REVERT: C 48 ASP cc_start: 0.8476 (m-30) cc_final: 0.8265 (m-30) REVERT: C 64 GLN cc_start: 0.8730 (mt0) cc_final: 0.8472 (mp10) REVERT: C 185 GLN cc_start: 0.8179 (pt0) cc_final: 0.7469 (pt0) REVERT: D 190 GLN cc_start: 0.8704 (pt0) cc_final: 0.8297 (pt0) REVERT: D 242 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.6830 (mp-120) REVERT: E 150 GLU cc_start: 0.8375 (pp20) cc_final: 0.8153 (pp20) REVERT: E 336 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6769 (mtt180) REVERT: I 39 LYS cc_start: 0.8264 (mmmm) cc_final: 0.7885 (mmpt) REVERT: J 34 MET cc_start: 0.9257 (mmp) cc_final: 0.8874 (mpp) REVERT: L 24 LYS cc_start: 0.8589 (tttp) cc_final: 0.7904 (mtpp) REVERT: L 83 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8474 (pp) REVERT: K 63 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8650 (mmtm) REVERT: K 73 ASP cc_start: 0.8129 (t0) cc_final: 0.7649 (t0) outliers start: 37 outliers final: 21 residues processed: 305 average time/residue: 1.2694 time to fit residues: 432.7438 Evaluate side-chains 284 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 294 MET 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 19 optimal weight: 0.0870 chunk 151 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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** ** A 309 GLN ** 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 = 0.3464 r_free = 0.3464 target = 0.104203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.069758 restraints weight = 29910.766| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.38 r_work: 0.2747 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 17932 Z= 0.315 Angle : 0.720 14.236 24433 Z= 0.359 Chirality : 0.049 0.550 2807 Planarity : 0.005 0.059 2988 Dihedral : 9.203 85.729 2857 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.13 % Allowed : 12.32 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2103 helix: 2.63 (0.20), residues: 588 sheet: -0.19 (0.20), residues: 671 loop : -0.16 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 319 HIS 0.007 0.001 HIS E 163 PHE 0.021 0.002 PHE D 226 TYR 0.023 0.002 TYR L 49 ARG 0.005 0.001 ARG C 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 7) link_NAG-ASN : angle 5.60236 ( 21) link_ALPHA1-6 : bond 0.00168 ( 2) link_ALPHA1-6 : angle 2.00928 ( 6) link_BETA1-4 : bond 0.00487 ( 9) link_BETA1-4 : angle 2.56844 ( 27) link_ALPHA1-2 : bond 0.00481 ( 3) link_ALPHA1-2 : angle 2.29720 ( 9) link_ALPHA1-3 : bond 0.00628 ( 2) link_ALPHA1-3 : angle 1.29217 ( 6) hydrogen bonds : bond 0.05323 ( 686) hydrogen bonds : angle 4.82237 ( 1917) SS BOND : bond 0.00560 ( 9) SS BOND : angle 1.23725 ( 18) covalent geometry : bond 0.00763 (17899) covalent geometry : angle 0.69411 (24346) Misc. bond : bond 0.00793 ( 1) *********************** 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 329 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 185 GLN cc_start: 0.8188 (pt0) cc_final: 0.7502 (pt0) REVERT: D 242 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.6533 (mp-120) REVERT: E 296 MET cc_start: 0.7038 (ppp) cc_final: 0.6602 (pp-130) REVERT: E 304 PHE cc_start: 0.8760 (t80) cc_final: 0.8509 (t80) REVERT: E 332 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: E 336 ARG cc_start: 0.6982 (mtm110) cc_final: 0.6514 (mtt180) REVERT: I 11 MET cc_start: 0.8501 (ppp) cc_final: 0.8226 (ppp) REVERT: I 81 GLU cc_start: 0.7947 (pp20) cc_final: 0.7246 (pm20) REVERT: J 52 ASP cc_start: 0.8434 (t0) cc_final: 0.8103 (t0) REVERT: L 18 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6704 (ttm110) REVERT: L 24 LYS cc_start: 0.8636 (tttp) cc_final: 0.8025 (mtpp) REVERT: L 61 ARG cc_start: 0.8002 (ptt-90) cc_final: 0.7651 (ptt-90) REVERT: L 79 GLN cc_start: 0.7805 (mp10) cc_final: 0.7570 (mm-40) REVERT: L 83 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8551 (pp) REVERT: K 63 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8659 (mmtm) REVERT: K 73 ASP cc_start: 0.8185 (t0) cc_final: 0.7701 (t0) outliers start: 59 outliers final: 33 residues processed: 299 average time/residue: 1.2863 time to fit residues: 428.6240 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 : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 240 PHE 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 108 VAL 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 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 269 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 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 18 ARG 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 195 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN D 229 GLN D 346 ASN E 318 HIS 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 = 0.3498 r_free = 0.3498 target = 0.106559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.073247 restraints weight = 29674.167| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.60 r_work: 0.2785 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1806 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= 0.131 Angle : 0.592 13.061 24433 Z= 0.292 Chirality : 0.043 0.446 2807 Planarity : 0.004 0.050 2988 Dihedral : 8.248 79.542 2857 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.92 % Allowed : 13.86 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 2103 helix: 2.93 (0.20), residues: 590 sheet: -0.09 (0.20), residues: 653 loop : -0.11 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 319 HIS 0.004 0.001 HIS E 163 PHE 0.018 0.001 PHE C 330 TYR 0.029 0.001 TYR L 49 ARG 0.004 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 7) link_NAG-ASN : angle 4.70713 ( 21) link_ALPHA1-6 : bond 0.00354 ( 2) link_ALPHA1-6 : angle 1.60949 ( 6) link_BETA1-4 : bond 0.00499 ( 9) link_BETA1-4 : angle 2.04190 ( 27) link_ALPHA1-2 : bond 0.00517 ( 3) link_ALPHA1-2 : angle 1.54386 ( 9) link_ALPHA1-3 : bond 0.01051 ( 2) link_ALPHA1-3 : angle 1.16303 ( 6) hydrogen bonds : bond 0.04155 ( 686) hydrogen bonds : angle 4.41802 ( 1917) SS BOND : bond 0.00286 ( 9) SS BOND : angle 0.60009 ( 18) covalent geometry : bond 0.00295 (17899) covalent geometry : angle 0.57107 (24346) Misc. bond : bond 0.00049 ( 1) *********************** 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 332 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9067 (tpt) cc_final: 0.8720 (tpt) REVERT: B 277 LEU cc_start: 0.7574 (pt) cc_final: 0.7361 (pp) REVERT: C 185 GLN cc_start: 0.8193 (pt0) cc_final: 0.7472 (pt0) REVERT: D 190 GLN cc_start: 0.8712 (pt0) cc_final: 0.8303 (pt0) REVERT: D 242 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.6392 (mp-120) REVERT: E 296 MET cc_start: 0.7032 (ppp) cc_final: 0.6602 (pp-130) REVERT: E 304 PHE cc_start: 0.8740 (t80) cc_final: 0.8519 (t80) REVERT: E 332 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: E 336 ARG cc_start: 0.7083 (mtm110) cc_final: 0.6596 (mtt180) REVERT: I 11 MET cc_start: 0.8677 (ppp) cc_final: 0.8423 (ppp) REVERT: I 81 GLU cc_start: 0.7931 (pp20) cc_final: 0.7274 (pm20) REVERT: J 52 ASP cc_start: 0.8361 (t0) cc_final: 0.8009 (t0) REVERT: L 13 MET cc_start: 0.7742 (pp-130) cc_final: 0.7521 (ppp) REVERT: L 24 LYS cc_start: 0.8632 (tttp) cc_final: 0.8063 (mtpp) REVERT: L 61 ARG cc_start: 0.7949 (ptt-90) cc_final: 0.7698 (ptp-170) REVERT: L 79 GLN cc_start: 0.7802 (mp10) cc_final: 0.7542 (mm-40) REVERT: L 83 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8789 (pt) REVERT: K 63 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8680 (mmtm) REVERT: K 73 ASP cc_start: 0.8227 (t0) cc_final: 0.7715 (t0) outliers start: 55 outliers final: 26 residues processed: 304 average time/residue: 1.3204 time to fit residues: 448.0397 Evaluate side-chains 282 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET 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 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 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 19 VAL 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 11 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 23 optimal weight: 0.1980 chunk 134 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN D 229 GLN D 346 ASN K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.074115 restraints weight = 30180.714| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.57 r_work: 0.2802 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1997 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= 0.121 Angle : 0.577 12.303 24433 Z= 0.283 Chirality : 0.042 0.395 2807 Planarity : 0.004 0.046 2988 Dihedral : 7.621 79.978 2857 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.08 % Allowed : 15.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 2103 helix: 2.98 (0.21), residues: 588 sheet: 0.03 (0.20), residues: 656 loop : -0.03 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 319 HIS 0.004 0.001 HIS E 163 PHE 0.018 0.001 PHE E 308 TYR 0.033 0.001 TYR L 49 ARG 0.007 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 7) link_NAG-ASN : angle 4.34922 ( 21) link_ALPHA1-6 : bond 0.00307 ( 2) link_ALPHA1-6 : angle 1.69037 ( 6) link_BETA1-4 : bond 0.00465 ( 9) link_BETA1-4 : angle 1.83203 ( 27) link_ALPHA1-2 : bond 0.00435 ( 3) link_ALPHA1-2 : angle 1.57323 ( 9) link_ALPHA1-3 : bond 0.01009 ( 2) link_ALPHA1-3 : angle 1.17706 ( 6) hydrogen bonds : bond 0.03745 ( 686) hydrogen bonds : angle 4.21929 ( 1917) SS BOND : bond 0.00282 ( 9) SS BOND : angle 0.56264 ( 18) covalent geometry : bond 0.00274 (17899) covalent geometry : angle 0.55878 (24346) Misc. bond : bond 0.00009 ( 1) *********************** 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 325 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8157 (tp30) cc_final: 0.7955 (tm-30) REVERT: B 90 MET cc_start: 0.9056 (tpt) cc_final: 0.8714 (tpt) REVERT: B 277 LEU cc_start: 0.7565 (pt) cc_final: 0.7355 (pp) REVERT: C 81 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8917 (pp) REVERT: C 185 GLN cc_start: 0.8228 (pt0) cc_final: 0.7514 (pt0) REVERT: D 190 GLN cc_start: 0.8715 (pt0) cc_final: 0.8298 (pt0) REVERT: D 242 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: E 211 GLU cc_start: 0.8186 (pt0) cc_final: 0.7919 (tt0) REVERT: E 332 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: E 343 PHE cc_start: 0.8052 (t80) cc_final: 0.7795 (t80) REVERT: J 52 ASP cc_start: 0.8321 (t0) cc_final: 0.7963 (t0) REVERT: L 24 LYS cc_start: 0.8635 (tttp) cc_final: 0.8044 (mtpp) REVERT: L 61 ARG cc_start: 0.7977 (ptt-90) cc_final: 0.7765 (ptp-170) REVERT: L 83 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8777 (pt) REVERT: K 63 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8686 (mmtm) REVERT: K 73 ASP cc_start: 0.8324 (t0) cc_final: 0.7889 (t0) outliers start: 58 outliers final: 32 residues processed: 299 average time/residue: 1.2445 time to fit residues: 416.2369 Evaluate side-chains 294 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 81 LEU 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 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 269 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 E residue 332 ASP Chi-restraints excluded: chain I residue 19 VAL 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 18 VAL Chi-restraints excluded: chain K residue 30 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 89 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3511 r_free = 0.3511 target = 0.107245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.074016 restraints weight = 30038.377| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.61 r_work: 0.2801 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2104 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= 0.127 Angle : 0.580 11.454 24433 Z= 0.284 Chirality : 0.042 0.308 2807 Planarity : 0.004 0.046 2988 Dihedral : 7.366 80.563 2857 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.51 % Allowed : 15.19 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 2103 helix: 2.93 (0.21), residues: 590 sheet: 0.07 (0.20), residues: 658 loop : -0.07 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 319 HIS 0.003 0.001 HIS B 110 PHE 0.020 0.001 PHE C 330 TYR 0.032 0.001 TYR L 49 ARG 0.004 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 7) link_NAG-ASN : angle 4.20020 ( 21) link_ALPHA1-6 : bond 0.00249 ( 2) link_ALPHA1-6 : angle 1.73223 ( 6) link_BETA1-4 : bond 0.00481 ( 9) link_BETA1-4 : angle 1.79489 ( 27) link_ALPHA1-2 : bond 0.00446 ( 3) link_ALPHA1-2 : angle 1.56844 ( 9) link_ALPHA1-3 : bond 0.01106 ( 2) link_ALPHA1-3 : angle 1.16847 ( 6) hydrogen bonds : bond 0.03642 ( 686) hydrogen bonds : angle 4.15667 ( 1917) SS BOND : bond 0.00290 ( 9) SS BOND : angle 0.57284 ( 18) covalent geometry : bond 0.00293 (17899) covalent geometry : angle 0.56220 (24346) Misc. bond : bond 0.00011 ( 1) *********************** 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 330 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8197 (tp30) cc_final: 0.7988 (tm-30) REVERT: B 90 MET cc_start: 0.9064 (tpt) cc_final: 0.8732 (tpt) REVERT: B 277 LEU cc_start: 0.7536 (pt) cc_final: 0.7328 (pp) REVERT: C 48 ASP cc_start: 0.8117 (m-30) cc_final: 0.7902 (m-30) REVERT: C 81 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8839 (pp) REVERT: C 185 GLN cc_start: 0.8179 (pt0) cc_final: 0.7405 (pt0) REVERT: C 259 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7205 (mm) REVERT: D 133 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8394 (pp) REVERT: D 190 GLN cc_start: 0.8714 (pt0) cc_final: 0.8282 (pt0) REVERT: D 242 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: D 294 TYR cc_start: 0.8616 (t80) cc_final: 0.8282 (t80) REVERT: E 211 GLU cc_start: 0.8189 (pt0) cc_final: 0.7923 (tt0) REVERT: E 318 HIS cc_start: 0.8199 (t70) cc_final: 0.7960 (t70) REVERT: E 332 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: I 11 MET cc_start: 0.8619 (ppp) cc_final: 0.8330 (ppp) REVERT: J 52 ASP cc_start: 0.8332 (t0) cc_final: 0.7991 (t0) REVERT: L 24 LYS cc_start: 0.8640 (tttp) cc_final: 0.8050 (mtpp) REVERT: L 61 ARG cc_start: 0.7958 (ptt-90) cc_final: 0.7714 (ptp-170) REVERT: L 79 GLN cc_start: 0.7674 (mp10) cc_final: 0.7459 (mm-40) REVERT: L 83 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8763 (pt) REVERT: L 104 GLU cc_start: 0.5450 (tt0) cc_final: 0.5125 (tt0) REVERT: K 63 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8683 (mmtm) REVERT: K 73 ASP cc_start: 0.8385 (t0) cc_final: 0.7892 (t0) REVERT: K 89 GLU cc_start: 0.7961 (mp0) cc_final: 0.7726 (mp0) outliers start: 66 outliers final: 37 residues processed: 295 average time/residue: 1.2414 time to fit residues: 410.2456 Evaluate side-chains 299 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain C residue 81 LEU 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 269 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 E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL 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 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 MET 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 18 VAL Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 145 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 242 GLN 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 = 0.3511 r_free = 0.3511 target = 0.107246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073294 restraints weight = 29826.236| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.36 r_work: 0.2813 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17932 Z= 0.130 Angle : 0.581 11.449 24433 Z= 0.286 Chirality : 0.042 0.308 2807 Planarity : 0.004 0.045 2988 Dihedral : 7.145 80.645 2857 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.19 % Allowed : 16.09 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 2103 helix: 2.94 (0.21), residues: 588 sheet: 0.11 (0.20), residues: 660 loop : -0.04 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 319 HIS 0.003 0.001 HIS E 163 PHE 0.021 0.001 PHE C 330 TYR 0.033 0.001 TYR L 49 ARG 0.005 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 7) link_NAG-ASN : angle 4.07429 ( 21) link_ALPHA1-6 : bond 0.00223 ( 2) link_ALPHA1-6 : angle 1.78288 ( 6) link_BETA1-4 : bond 0.00529 ( 9) link_BETA1-4 : angle 1.77105 ( 27) link_ALPHA1-2 : bond 0.00426 ( 3) link_ALPHA1-2 : angle 1.59172 ( 9) link_ALPHA1-3 : bond 0.01080 ( 2) link_ALPHA1-3 : angle 1.17089 ( 6) hydrogen bonds : bond 0.03594 ( 686) hydrogen bonds : angle 4.10976 ( 1917) SS BOND : bond 0.00294 ( 9) SS BOND : angle 0.56073 ( 18) covalent geometry : bond 0.00302 (17899) covalent geometry : angle 0.56467 (24346) Misc. bond : bond 0.00013 ( 1) *********************** 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 323 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9052 (tpt) cc_final: 0.8715 (tpt) REVERT: B 213 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8815 (mmp) REVERT: C 48 ASP cc_start: 0.8112 (m-30) cc_final: 0.7887 (m-30) REVERT: C 185 GLN cc_start: 0.8171 (pt0) cc_final: 0.7410 (pt0) REVERT: C 259 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7170 (mm) REVERT: D 133 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8373 (pp) REVERT: D 190 GLN cc_start: 0.8695 (pt0) cc_final: 0.8309 (pt0) REVERT: D 242 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: D 294 TYR cc_start: 0.8596 (t80) cc_final: 0.8286 (t80) REVERT: E 211 GLU cc_start: 0.8204 (pt0) cc_final: 0.7919 (tt0) REVERT: E 296 MET cc_start: 0.6935 (ppp) cc_final: 0.6519 (pp-130) REVERT: E 318 HIS cc_start: 0.8085 (t70) cc_final: 0.7845 (t70) REVERT: I 11 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8380 (ppp) REVERT: I 24 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8241 (mtpt) REVERT: J 52 ASP cc_start: 0.8319 (t0) cc_final: 0.7995 (t0) REVERT: L 13 MET cc_start: 0.7874 (pp-130) cc_final: 0.7646 (ppp) REVERT: L 24 LYS cc_start: 0.8692 (tttp) cc_final: 0.8135 (mtpp) REVERT: L 61 ARG cc_start: 0.7965 (ptt-90) cc_final: 0.7746 (ptp-170) REVERT: L 83 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8569 (pt) REVERT: K 3 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7802 (tm-30) REVERT: K 63 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8700 (mmtm) REVERT: K 73 ASP cc_start: 0.8362 (t0) cc_final: 0.7865 (t0) REVERT: K 89 GLU cc_start: 0.7937 (mp0) cc_final: 0.7691 (mp0) outliers start: 60 outliers final: 38 residues processed: 297 average time/residue: 1.2280 time to fit residues: 408.0683 Evaluate side-chains 303 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 294 MET 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 241 SER Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 258 PHE 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 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 269 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 11 MET Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 24 LYS 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 11 MET 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 Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.107539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074665 restraints weight = 29798.786| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.52 r_work: 0.2810 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2258 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= 0.122 Angle : 0.582 11.725 24433 Z= 0.286 Chirality : 0.042 0.273 2807 Planarity : 0.004 0.044 2988 Dihedral : 7.011 80.730 2857 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.24 % Allowed : 16.46 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 2103 helix: 2.97 (0.21), residues: 586 sheet: 0.17 (0.20), residues: 652 loop : -0.03 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 319 HIS 0.003 0.001 HIS E 163 PHE 0.021 0.001 PHE C 330 TYR 0.033 0.001 TYR L 49 ARG 0.004 0.000 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 7) link_NAG-ASN : angle 3.87649 ( 21) link_ALPHA1-6 : bond 0.00233 ( 2) link_ALPHA1-6 : angle 1.77950 ( 6) link_BETA1-4 : bond 0.00482 ( 9) link_BETA1-4 : angle 1.71238 ( 27) link_ALPHA1-2 : bond 0.00435 ( 3) link_ALPHA1-2 : angle 1.56378 ( 9) link_ALPHA1-3 : bond 0.01161 ( 2) link_ALPHA1-3 : angle 1.18825 ( 6) hydrogen bonds : bond 0.03487 ( 686) hydrogen bonds : angle 4.09438 ( 1917) SS BOND : bond 0.00278 ( 9) SS BOND : angle 0.51184 ( 18) covalent geometry : bond 0.00280 (17899) covalent geometry : angle 0.56700 (24346) Misc. bond : bond 0.00004 ( 1) *********************** 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 323 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 262 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9052 (tpt) cc_final: 0.8716 (tpt) REVERT: B 213 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8817 (mmp) REVERT: B 277 LEU cc_start: 0.7462 (pt) cc_final: 0.7227 (pp) REVERT: C 48 ASP cc_start: 0.8147 (m-30) cc_final: 0.7905 (m-30) REVERT: C 185 GLN cc_start: 0.8177 (pt0) cc_final: 0.7425 (pt0) REVERT: C 259 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7180 (mm) REVERT: D 133 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8357 (pp) REVERT: D 190 GLN cc_start: 0.8706 (pt0) cc_final: 0.8323 (pt0) REVERT: D 242 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: D 294 TYR cc_start: 0.8644 (t80) cc_final: 0.8310 (t80) REVERT: E 211 GLU cc_start: 0.8212 (pt0) cc_final: 0.7940 (tt0) REVERT: E 296 MET cc_start: 0.6913 (ppp) cc_final: 0.6519 (pp-130) REVERT: E 334 TYR cc_start: 0.7916 (m-80) cc_final: 0.7567 (m-80) REVERT: I 11 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8402 (ppp) REVERT: I 24 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8300 (mtpt) REVERT: J 52 ASP cc_start: 0.8336 (t0) cc_final: 0.8023 (t0) REVERT: L 13 MET cc_start: 0.7854 (pp-130) cc_final: 0.7607 (ppp) REVERT: L 24 LYS cc_start: 0.8748 (tttp) cc_final: 0.8129 (mtpp) REVERT: L 61 ARG cc_start: 0.7974 (ptt-90) cc_final: 0.7758 (ptp-170) REVERT: L 83 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8738 (pt) REVERT: K 3 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7694 (tm-30) REVERT: K 73 ASP cc_start: 0.8375 (t0) cc_final: 0.7876 (t0) REVERT: K 89 GLU cc_start: 0.7908 (mp0) cc_final: 0.7620 (mp0) outliers start: 61 outliers final: 43 residues processed: 293 average time/residue: 1.3037 time to fit residues: 426.5404 Evaluate side-chains 305 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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 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 241 SER Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain C residue 80 ASN 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 269 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 11 MET Chi-restraints excluded: chain I residue 19 VAL 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 11 MET 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 Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 160 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 139 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- 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 K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.073656 restraints weight = 30142.124| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.52 r_work: 0.2792 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17932 Z= 0.160 Angle : 0.610 11.911 24433 Z= 0.300 Chirality : 0.043 0.266 2807 Planarity : 0.004 0.045 2988 Dihedral : 7.013 80.742 2857 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.13 % Allowed : 17.05 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2103 helix: 2.87 (0.21), residues: 588 sheet: 0.11 (0.20), residues: 657 loop : -0.03 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 319 HIS 0.004 0.001 HIS B 110 PHE 0.022 0.001 PHE C 330 TYR 0.034 0.001 TYR L 49 ARG 0.004 0.000 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 7) link_NAG-ASN : angle 4.00248 ( 21) link_ALPHA1-6 : bond 0.00073 ( 2) link_ALPHA1-6 : angle 1.92811 ( 6) link_BETA1-4 : bond 0.00491 ( 9) link_BETA1-4 : angle 1.81744 ( 27) link_ALPHA1-2 : bond 0.00390 ( 3) link_ALPHA1-2 : angle 1.68702 ( 9) link_ALPHA1-3 : bond 0.01170 ( 2) link_ALPHA1-3 : angle 1.25789 ( 6) hydrogen bonds : bond 0.03691 ( 686) hydrogen bonds : angle 4.15417 ( 1917) SS BOND : bond 0.00337 ( 9) SS BOND : angle 0.65731 ( 18) covalent geometry : bond 0.00378 (17899) covalent geometry : angle 0.59386 (24346) Misc. bond : bond 0.00028 ( 1) *********************** 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 321 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 262 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: B 90 MET cc_start: 0.9050 (tpt) cc_final: 0.8720 (tpt) REVERT: B 213 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8810 (mmp) REVERT: C 48 ASP cc_start: 0.8129 (m-30) cc_final: 0.7897 (m-30) REVERT: C 185 GLN cc_start: 0.8183 (pt0) cc_final: 0.7417 (pt0) REVERT: C 259 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7193 (mm) REVERT: D 133 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8397 (pp) REVERT: D 190 GLN cc_start: 0.8706 (pt0) cc_final: 0.8331 (pt0) REVERT: D 242 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: E 211 GLU cc_start: 0.8215 (pt0) cc_final: 0.7950 (tt0) REVERT: E 296 MET cc_start: 0.6934 (ppp) cc_final: 0.6540 (pp-130) REVERT: E 332 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: E 334 TYR cc_start: 0.7949 (m-80) cc_final: 0.7552 (m-80) REVERT: I 11 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8366 (ppp) REVERT: J 34 MET cc_start: 0.9192 (tpp) cc_final: 0.8650 (mpp) REVERT: J 52 ASP cc_start: 0.8376 (t0) cc_final: 0.8078 (t0) REVERT: L 11 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7017 (tpp) REVERT: L 24 LYS cc_start: 0.8764 (tttp) cc_final: 0.8168 (mtpp) REVERT: L 61 ARG cc_start: 0.7997 (ptt-90) cc_final: 0.7769 (ptp-170) REVERT: L 83 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8577 (pt) REVERT: K 3 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7729 (tm-30) REVERT: K 73 ASP cc_start: 0.8361 (t0) cc_final: 0.7857 (t0) REVERT: K 89 GLU cc_start: 0.7911 (mp0) cc_final: 0.7627 (mp0) outliers start: 59 outliers final: 38 residues processed: 294 average time/residue: 1.3664 time to fit residues: 457.5478 Evaluate side-chains 304 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 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 241 SER Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain C residue 80 ASN 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 269 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 E residue 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 19 VAL 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 11 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 116 optimal weight: 0.0170 chunk 123 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 146 optimal weight: 0.1980 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.074845 restraints weight = 29863.999| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.32 r_work: 0.2846 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17932 Z= 0.109 Angle : 0.587 12.090 24433 Z= 0.288 Chirality : 0.041 0.265 2807 Planarity : 0.003 0.044 2988 Dihedral : 6.885 85.967 2857 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.60 % Allowed : 17.68 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 2103 helix: 2.94 (0.21), residues: 587 sheet: 0.15 (0.20), residues: 658 loop : 0.04 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 319 HIS 0.003 0.001 HIS E 163 PHE 0.023 0.001 PHE C 330 TYR 0.034 0.001 TYR L 49 ARG 0.004 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 7) link_NAG-ASN : angle 3.60433 ( 21) link_ALPHA1-6 : bond 0.00308 ( 2) link_ALPHA1-6 : angle 1.70852 ( 6) link_BETA1-4 : bond 0.00502 ( 9) link_BETA1-4 : angle 1.57815 ( 27) link_ALPHA1-2 : bond 0.00492 ( 3) link_ALPHA1-2 : angle 1.48693 ( 9) link_ALPHA1-3 : bond 0.01297 ( 2) link_ALPHA1-3 : angle 1.18512 ( 6) hydrogen bonds : bond 0.03301 ( 686) hydrogen bonds : angle 4.05367 ( 1917) SS BOND : bond 0.00229 ( 9) SS BOND : angle 0.44754 ( 18) covalent geometry : bond 0.00242 (17899) covalent geometry : angle 0.57404 (24346) Misc. bond : bond 0.00014 ( 1) ********************** 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 321 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8764 (mm-30) REVERT: B 90 MET cc_start: 0.9030 (tpt) cc_final: 0.8690 (tpt) REVERT: B 277 LEU cc_start: 0.7440 (pt) cc_final: 0.7200 (pp) REVERT: C 185 GLN cc_start: 0.8155 (pt0) cc_final: 0.7400 (pt0) REVERT: D 190 GLN cc_start: 0.8665 (pt0) cc_final: 0.8271 (pt0) REVERT: D 242 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: D 294 TYR cc_start: 0.8603 (t80) cc_final: 0.8341 (t80) REVERT: E 211 GLU cc_start: 0.8172 (pt0) cc_final: 0.7924 (tt0) REVERT: E 229 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7092 (pp) REVERT: E 296 MET cc_start: 0.6865 (ppp) cc_final: 0.6477 (pp-130) REVERT: E 332 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: E 334 TYR cc_start: 0.7866 (m-80) cc_final: 0.7504 (m-80) REVERT: I 11 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8314 (ppp) REVERT: J 52 ASP cc_start: 0.8296 (t0) cc_final: 0.8000 (t0) REVERT: L 24 LYS cc_start: 0.8779 (tttp) cc_final: 0.8200 (mtpp) REVERT: L 61 ARG cc_start: 0.7880 (ptt-90) cc_final: 0.7637 (ptp-170) REVERT: L 79 GLN cc_start: 0.7581 (mp10) cc_final: 0.7368 (mm-40) REVERT: L 83 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8716 (pt) REVERT: K 73 ASP cc_start: 0.8388 (t0) cc_final: 0.7887 (t0) REVERT: K 89 GLU cc_start: 0.7889 (mp0) cc_final: 0.7599 (mp0) outliers start: 49 outliers final: 28 residues processed: 300 average time/residue: 1.2024 time to fit residues: 404.0067 Evaluate side-chains 299 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 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 242 GLN Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 227 MET 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 264 LEU Chi-restraints excluded: chain D residue 269 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 332 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 19 VAL 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 11 MET 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 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 100 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** 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 = 0.3523 r_free = 0.3523 target = 0.107989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.074042 restraints weight = 29811.665| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.38 r_work: 0.2833 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17932 Z= 0.125 Angle : 0.600 12.467 24433 Z= 0.296 Chirality : 0.042 0.261 2807 Planarity : 0.004 0.044 2988 Dihedral : 6.882 85.939 2857 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.18 % Allowed : 18.37 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 2103 helix: 2.88 (0.21), residues: 587 sheet: 0.13 (0.19), residues: 678 loop : 0.06 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 319 HIS 0.003 0.001 HIS E 163 PHE 0.038 0.001 PHE C 323 TYR 0.042 0.001 TYR E 235 ARG 0.004 0.000 ARG D 136 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 7) link_NAG-ASN : angle 3.64731 ( 21) link_ALPHA1-6 : bond 0.00206 ( 2) link_ALPHA1-6 : angle 1.80066 ( 6) link_BETA1-4 : bond 0.00517 ( 9) link_BETA1-4 : angle 1.61741 ( 27) link_ALPHA1-2 : bond 0.00406 ( 3) link_ALPHA1-2 : angle 1.54917 ( 9) link_ALPHA1-3 : bond 0.01303 ( 2) link_ALPHA1-3 : angle 1.22538 ( 6) hydrogen bonds : bond 0.03336 ( 686) hydrogen bonds : angle 4.06675 ( 1917) SS BOND : bond 0.00275 ( 9) SS BOND : angle 0.51986 ( 18) covalent geometry : bond 0.00290 (17899) covalent geometry : angle 0.58695 (24346) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13907.75 seconds wall clock time: 239 minutes 47.93 seconds (14387.93 seconds total)