Starting phenix.real_space_refine on Sat Sep 12 21:54:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uwz_20928/09_2026/6uwz_20928.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwz_20928/09_2026/6uwz_20928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6uwz_20928/09_2026/6uwz_20928.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uwz_20928/09_2026/6uwz_20928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uwz_20928/09_2026/6uwz_20928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwz_20928/09_2026/6uwz_20928.map" model { file = "/net/cci-nas-00/data/ceres_data/6uwz_20928/09_2026/6uwz_20928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwz_20928/09_2026/6uwz_20928.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 108 5.16 5 C 11832 2.51 5 N 2857 2.21 5 O 3528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18330 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 bond proxies already assigned to first conformer: 3281 Chain: "B" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3462 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 398} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3337 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 546 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 64} Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 546 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 64} Chain: "H" 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 chiralities: 10 Chain: "I" 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 chiralities: 3 Chain: "J" 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 chiralities: 3 Chain: "K" 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 chiralities: 10 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.99, per 1000 atoms: 0.22 Number of scatterers: 18330 At special positions: 0 Unit cell: (123.12, 165.24, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 5 15.00 O 3528 8.00 N 2857 7.00 C 11832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.05 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 23 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 44 " distance=2.03 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 33 " distance=2.04 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 59 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 23 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 44 " distance=2.03 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS G 33 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 59 " distance=2.02 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 65 " 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 H 4 " - " MAN H 5 " " MAN H 5 " - " MAN H 6 " " MAN H 8 " - " MAN H 9 " " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " MAN H 7 " - " MAN H 10 " " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 10 " ALPHA1-6 " BMA H 3 " - " MAN H 7 " " MAN H 7 " - " MAN H 8 " " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 8 " " NAG L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " NAG-ASN " NAG B 604 " - " ASN B 70 " " NAG B 605 " - " ASN B 208 " " NAG E 506 " - " ASN E 68 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN B 143 " " NAG J 1 " - " ASN C 141 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 849.9 milliseconds 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4206 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 23 sheets defined 39.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.147A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.725A pdb=" N GLU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.811A pdb=" N ARG A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 371 through 425 removed outlier: 3.621A pdb=" N ILE A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.501A pdb=" N LEU B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.543A pdb=" N CYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.647A pdb=" N GLN B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 332 through 339 removed outlier: 4.002A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 478 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.823A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 217 through 238 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 247 through 268 removed outlier: 3.554A pdb=" N LEU C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.693A pdb=" N ARG C 319 " --> pdb=" O PRO C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 4.432A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.584A pdb=" N LEU D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 removed outlier: 4.015A pdb=" N ARG D 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 317 removed outlier: 3.749A pdb=" N ARG D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 371 through 425 Processing helix chain 'D' and resid 427 through 433 Processing helix chain 'E' and resid 2 through 12 removed outlier: 4.225A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.941A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 131 through 135 removed outlier: 4.291A pdb=" N TYR E 134 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.805A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 243 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.547A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'E' and resid 411 through 473 removed outlier: 3.842A pdb=" N LEU E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.257A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.257A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ARG A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLN A 36 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ILE A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N THR A 32 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.465A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 198 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP A 200 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY A 183 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N HIS A 204 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR A 181 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 206 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 19.561A pdb=" N LYS A 185 " --> pdb=" O CYS F 44 " (cutoff:3.500A) removed outlier: 17.025A pdb=" N CYS F 44 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N TRP A 187 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N LEU F 42 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR A 189 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 43 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 22 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.707A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.652A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.652A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.835A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 114 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C 33 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 161 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 127 removed outlier: 6.840A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N VAL C 174 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 35 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.339A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 139 through 140 removed outlier: 6.780A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.149A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.149A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE D 49 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER D 42 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.704A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 8.472A pdb=" N ASN E 107 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP E 118 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU E 109 " --> pdb=" O MET E 116 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET E 116 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 111 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 8.472A pdb=" N ASN E 107 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP E 118 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU E 109 " --> pdb=" O MET E 116 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET E 116 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 111 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.294A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.294A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AC3, first strand: chain 'F' and resid 2 through 5 removed outlier: 3.539A pdb=" N SER F 12 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 2 through 5 removed outlier: 3.627A pdb=" N SER G 12 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 24 through 26 removed outlier: 3.556A pdb=" N TYR G 24 " --> pdb=" O GLY G 43 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY G 43 " --> pdb=" O TYR G 24 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2664 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: 3.33 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2900 1.32 - 1.45: 5464 1.45 - 1.58: 10118 1.58 - 1.72: 10 1.72 - 1.85: 165 Bond restraints: 18657 Sorted by residual: bond pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 POV D 511 " pdb=" O31 POV D 511 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 POV C 705 " pdb=" O31 POV C 705 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C31 POV A 511 " pdb=" O31 POV A 511 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C21 POV A 511 " pdb=" O21 POV A 511 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 18652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 24929 2.51 - 5.01: 438 5.01 - 7.52: 38 7.52 - 10.03: 8 10.03 - 12.54: 10 Bond angle restraints: 25423 Sorted by residual: angle pdb=" O11 POV A 511 " pdb=" P POV A 511 " pdb=" O12 POV A 511 " ideal model delta sigma weight residual 97.67 110.21 -12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" O13 POV D 511 " pdb=" P POV D 511 " pdb=" O14 POV D 511 " ideal model delta sigma weight residual 121.11 109.00 12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O13 POV A 511 " pdb=" P POV A 511 " pdb=" O14 POV A 511 " ideal model delta sigma weight residual 121.11 109.04 12.07 3.00e+00 1.11e-01 1.62e+01 angle pdb=" O11 POV C 701 " pdb=" P POV C 701 " pdb=" O12 POV C 701 " ideal model delta sigma weight residual 97.67 109.43 -11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O13 POV C 701 " pdb=" P POV C 701 " pdb=" O14 POV C 701 " ideal model delta sigma weight residual 121.11 109.36 11.75 3.00e+00 1.11e-01 1.53e+01 ... (remaining 25418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 10555 29.05 - 58.11: 324 58.11 - 87.16: 25 87.16 - 116.22: 2 116.22 - 145.27: 2 Dihedral angle restraints: 10908 sinusoidal: 4449 harmonic: 6459 Sorted by residual: dihedral pdb=" CB CYS F 29 " pdb=" SG CYS F 29 " pdb=" SG CYS F 33 " pdb=" CB CYS F 33 " ideal model delta sinusoidal sigma weight residual 93.00 25.37 67.63 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CB CYS G 60 " pdb=" SG CYS G 60 " pdb=" SG CYS G 65 " pdb=" CB CYS G 65 " ideal model delta sinusoidal sigma weight residual 93.00 28.78 64.22 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS F 48 " pdb=" SG CYS F 48 " pdb=" SG CYS F 59 " pdb=" CB CYS F 59 " ideal model delta sinusoidal sigma weight residual 93.00 149.30 -56.30 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 10905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2494 0.071 - 0.141: 512 0.141 - 0.212: 13 0.212 - 0.282: 3 0.282 - 0.353: 3 Chirality restraints: 3025 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.37e+02 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.33e+02 chirality pdb=" C1 MAN H 6 " pdb=" O2 MAN H 5 " pdb=" C2 MAN H 6 " pdb=" O5 MAN H 6 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 3022 not shown) Planarity restraints: 3098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.138 2.00e-02 2.50e+03 1.13e-01 1.61e+02 pdb=" C7 NAG J 2 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.182 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.111 2.00e-02 2.50e+03 9.19e-02 1.06e+02 pdb=" C7 NAG I 2 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.147 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.087 2.00e-02 2.50e+03 7.14e-02 6.38e+01 pdb=" C7 NAG J 1 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.114 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.015 2.00e-02 2.50e+03 ... (remaining 3095 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 8 2.18 - 2.86: 6685 2.86 - 3.54: 25392 3.54 - 4.22: 47127 4.22 - 4.90: 81032 Nonbonded interactions: 160244 Sorted by model distance: nonbonded pdb=" OD2 ASP E 483 " pdb=" OH TYR E 487 " model vdw 1.501 3.040 nonbonded pdb=" O SER A 327 " pdb=" O13 POV A 511 " model vdw 2.020 3.040 nonbonded pdb=" OD2 ASP B 214 " pdb=" OG1 THR B 216 " model vdw 2.044 3.040 nonbonded pdb=" OE1 GLU B 280 " pdb=" OH TYR C 220 " model vdw 2.060 3.040 nonbonded pdb=" O VAL C 277 " pdb=" NH1 ARG C 282 " model vdw 2.074 3.120 ... (remaining 160239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 65 or resid 67 through 511)) selection = (chain 'D' and (resid 1 through 65 or resid 67 through 433 or (resid 511 and (na \ me N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C2 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name O11 or name O12 or name O13 or name O14 or name O21 or nam \ e O22 or name O31 or name O32 or name P )))) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.330 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.216 18708 Z= 0.466 Angle : 0.924 20.198 25557 Z= 0.412 Chirality : 0.053 0.353 3025 Planarity : 0.006 0.113 3090 Dihedral : 13.949 145.270 6654 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.16), residues: 2152 helix: -0.79 (0.16), residues: 792 sheet: -2.00 (0.21), residues: 461 loop : -2.40 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 55 TYR 0.013 0.002 TYR F 24 PHE 0.027 0.001 PHE A 284 TRP 0.010 0.001 TRP A 60 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.01081 / 0.43 (18657) covalent geometry : angle 0.82102 / 0.39 (25423) SS BOND : bond 0.00845 / 0.54 ( 16) SS BOND : angle 2.39512 / 1.62 ( 32) hydrogen bonds : bond 0.12939 / 8.73 ( 859) hydrogen bonds : angle 6.78205 / 4.68 ( 2664) Misc. bond : bond 0.21597 / 11.37 ( 1) link_ALPHA1-2 : bond 0.05294 / 3.04 ( 6) link_ALPHA1-2 : angle 8.96097 / 5.22 ( 18) link_ALPHA1-3 : bond 0.06489 / 3.25 ( 4) link_ALPHA1-3 : angle 6.43035 / 3.89 ( 12) link_ALPHA1-6 : bond 0.03840 / 1.97 ( 6) link_ALPHA1-6 : angle 8.60410 / 4.56 ( 18) link_BETA1-4 : bond 0.04196 / 2.80 ( 10) link_BETA1-4 : angle 4.61089 / 2.64 ( 30) link_NAG-ASN : bond 0.02367 / 1.21 ( 8) link_NAG-ASN : angle 4.88125 / 3.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.738 Fit side-chains REVERT: A 330 LYS cc_start: 0.7131 (ttpt) cc_final: 0.6854 (tttm) REVERT: A 415 MET cc_start: 0.7103 (mmt) cc_final: 0.6653 (mmp) REVERT: B 477 ASN cc_start: 0.6989 (t0) cc_final: 0.6698 (t160) REVERT: C 107 ASN cc_start: 0.7803 (p0) cc_final: 0.7295 (m-40) REVERT: C 244 ASP cc_start: 0.7200 (m-30) cc_final: 0.6697 (t0) REVERT: D 77 LYS cc_start: 0.8632 (mttm) cc_final: 0.8365 (mttt) REVERT: D 323 VAL cc_start: 0.8273 (t) cc_final: 0.7936 (t) REVERT: D 387 LYS cc_start: 0.7152 (ptpt) cc_final: 0.6779 (ptmm) REVERT: E 174 ASP cc_start: 0.7389 (t0) cc_final: 0.6492 (t0) REVERT: E 314 THR cc_start: 0.7669 (p) cc_final: 0.7398 (p) REVERT: E 471 HIS cc_start: 0.7412 (t-90) cc_final: 0.7172 (t-90) REVERT: G 26 LYS cc_start: 0.8405 (mtpt) cc_final: 0.7847 (mtmm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.6452 time to fit residues: 223.8952 Evaluate side-chains 229 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 95 ASN A 186 HIS A 394 ASN B 26 HIS B 95 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 140 GLN C 159 GLN C 310 ASN C 316 ASN C 320 GLN D 58 GLN D 139 GLN D 140 GLN D 208 GLN D 408 HIS E 27 HIS E 140 GLN E 188 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110176 restraints weight = 32674.269| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.11 r_work: 0.3126 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18708 Z= 0.149 Angle : 0.618 10.985 25557 Z= 0.311 Chirality : 0.044 0.326 3025 Planarity : 0.005 0.044 3090 Dihedral : 8.293 116.912 2443 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 1.45 % Allowed : 9.98 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2152 helix: 1.04 (0.18), residues: 778 sheet: -1.49 (0.21), residues: 460 loop : -1.54 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 313 TYR 0.011 0.001 TYR E 117 PHE 0.011 0.001 PHE B 473 TRP 0.014 0.001 TRP D 60 HIS 0.004 0.001 HIS F 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (18657) covalent geometry : angle 0.59745 / 0.31 (25423) SS BOND : bond 0.00686 / 0.45 ( 16) SS BOND : angle 3.01735 / 2.10 ( 32) hydrogen bonds : bond 0.04589 / 3.04 ( 859) hydrogen bonds : angle 4.95726 / 3.50 ( 2664) Misc. bond : bond 0.00427 / 0.22 ( 1) link_ALPHA1-2 : bond 0.00562 / 0.29 ( 6) link_ALPHA1-2 : angle 1.99582 / 1.23 ( 18) link_ALPHA1-3 : bond 0.00495 / 0.25 ( 4) link_ALPHA1-3 : angle 1.15909 / 0.70 ( 12) link_ALPHA1-6 : bond 0.00243 / 0.13 ( 6) link_ALPHA1-6 : angle 1.57112 / 0.98 ( 18) link_BETA1-4 : bond 0.00316 / 0.18 ( 10) link_BETA1-4 : angle 1.80565 / 1.23 ( 30) link_NAG-ASN : bond 0.00438 / 0.28 ( 8) link_NAG-ASN : angle 2.60623 / 1.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.696 Fit side-chains REVERT: A 415 MET cc_start: 0.7674 (mmt) cc_final: 0.7200 (mmp) REVERT: B 186 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: B 477 ASN cc_start: 0.7052 (t0) cc_final: 0.6724 (t160) REVERT: C 50 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8089 (ttm) REVERT: C 107 ASN cc_start: 0.8409 (p0) cc_final: 0.7654 (m-40) REVERT: C 413 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7185 (tp30) REVERT: D 323 VAL cc_start: 0.8101 (t) cc_final: 0.7748 (t) REVERT: D 324 MET cc_start: 0.7470 (mtt) cc_final: 0.7203 (mtt) REVERT: D 330 LYS cc_start: 0.8336 (tttm) cc_final: 0.8098 (ttpt) REVERT: E 174 ASP cc_start: 0.7660 (t0) cc_final: 0.7325 (t0) REVERT: E 224 ILE cc_start: 0.8495 (pt) cc_final: 0.8287 (pp) REVERT: E 471 HIS cc_start: 0.7516 (t-90) cc_final: 0.7131 (t-90) REVERT: F 55 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8560 (mt-10) REVERT: G 26 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7796 (mtmm) REVERT: G 52 LYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5058 (mtmt) outliers start: 29 outliers final: 8 residues processed: 258 average time/residue: 0.5745 time to fit residues: 167.5913 Evaluate side-chains 234 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 202 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN A 297 ASN B 26 HIS B 187 ASN C 111 GLN C 310 ASN C 316 ASN D 186 HIS D 208 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104315 restraints weight = 22602.401| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.69 r_work: 0.3135 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18708 Z= 0.188 Angle : 0.608 9.185 25557 Z= 0.304 Chirality : 0.044 0.225 3025 Planarity : 0.005 0.041 3090 Dihedral : 7.891 94.920 2443 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.90 % Allowed : 11.47 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2152 helix: 1.56 (0.19), residues: 783 sheet: -1.20 (0.22), residues: 446 loop : -1.16 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 313 TYR 0.016 0.001 TYR D 381 PHE 0.013 0.001 PHE A 256 TRP 0.010 0.001 TRP D 60 HIS 0.005 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (18657) covalent geometry : angle 0.58856 / 0.30 (25423) SS BOND : bond 0.00995 / 0.72 ( 16) SS BOND : angle 2.48285 / 1.70 ( 32) hydrogen bonds : bond 0.04486 / 2.99 ( 859) hydrogen bonds : angle 4.70760 / 3.35 ( 2664) Misc. bond : bond 0.00076 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00264 / 0.14 ( 6) link_ALPHA1-2 : angle 1.80692 / 1.14 ( 18) link_ALPHA1-3 : bond 0.00140 / 0.07 ( 4) link_ALPHA1-3 : angle 1.84289 / 1.06 ( 12) link_ALPHA1-6 : bond 0.00207 / 0.11 ( 6) link_ALPHA1-6 : angle 1.73789 / 1.08 ( 18) link_BETA1-4 : bond 0.00428 / 0.27 ( 10) link_BETA1-4 : angle 1.93158 / 1.29 ( 30) link_NAG-ASN : bond 0.00523 / 0.35 ( 8) link_NAG-ASN : angle 2.72951 / 1.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.732 Fit side-chains REVERT: A 313 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7860 (ttp-110) REVERT: A 415 MET cc_start: 0.7745 (mmt) cc_final: 0.7022 (mmp) REVERT: B 186 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: B 322 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8305 (tp) REVERT: B 437 ASN cc_start: 0.8591 (m-40) cc_final: 0.8381 (m110) REVERT: B 441 GLU cc_start: 0.8123 (tp30) cc_final: 0.7858 (tm-30) REVERT: B 477 ASN cc_start: 0.7091 (t0) cc_final: 0.6885 (t160) REVERT: C 50 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: C 167 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6063 (mp0) REVERT: C 214 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8577 (tp40) REVERT: C 316 ASN cc_start: 0.8053 (m-40) cc_final: 0.7587 (m110) REVERT: C 413 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7157 (tp30) REVERT: D 323 VAL cc_start: 0.8227 (t) cc_final: 0.7883 (t) REVERT: D 324 MET cc_start: 0.7672 (mtt) cc_final: 0.7427 (mtt) REVERT: D 330 LYS cc_start: 0.8305 (tttm) cc_final: 0.8025 (ttpt) REVERT: E 174 ASP cc_start: 0.7814 (t0) cc_final: 0.7520 (t0) REVERT: E 183 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: E 471 HIS cc_start: 0.7562 (t-90) cc_final: 0.7154 (t-90) REVERT: F 62 THR cc_start: 0.7698 (m) cc_final: 0.7464 (t) REVERT: G 26 LYS cc_start: 0.8419 (mtpt) cc_final: 0.7888 (mtmm) outliers start: 38 outliers final: 11 residues processed: 255 average time/residue: 0.5636 time to fit residues: 163.3172 Evaluate side-chains 234 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 159 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 144 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS B 26 HIS B 103 HIS B 200 ASN B 213 GLN C 107 ASN C 111 GLN C 183 ASN C 310 ASN C 466 ASN D 208 GLN E 250 GLN E 271 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105381 restraints weight = 25165.372| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.86 r_work: 0.3098 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 18708 Z= 0.153 Angle : 0.569 9.541 25557 Z= 0.286 Chirality : 0.043 0.221 3025 Planarity : 0.004 0.059 3090 Dihedral : 7.559 89.164 2443 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 2.39 % Allowed : 12.47 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2152 helix: 1.84 (0.19), residues: 777 sheet: -1.04 (0.22), residues: 453 loop : -0.96 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.009 0.001 TYR E 241 PHE 0.011 0.001 PHE D 256 TRP 0.011 0.001 TRP G 28 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (18657) covalent geometry : angle 0.55022 / 0.28 (25423) SS BOND : bond 0.00883 / 0.63 ( 16) SS BOND : angle 2.65683 / 1.82 ( 32) hydrogen bonds : bond 0.04162 / 2.77 ( 859) hydrogen bonds : angle 4.57381 / 3.26 ( 2664) Misc. bond : bond 0.00090 / 0.05 ( 1) link_ALPHA1-2 : bond 0.00403 / 0.21 ( 6) link_ALPHA1-2 : angle 1.50411 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00321 / 0.16 ( 4) link_ALPHA1-3 : angle 1.48747 / 0.86 ( 12) link_ALPHA1-6 : bond 0.00186 / 0.10 ( 6) link_ALPHA1-6 : angle 1.57537 / 0.98 ( 18) link_BETA1-4 : bond 0.00401 / 0.24 ( 10) link_BETA1-4 : angle 1.71732 / 1.15 ( 30) link_NAG-ASN : bond 0.00389 / 0.26 ( 8) link_NAG-ASN : angle 2.50129 / 1.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7971 (tpt) cc_final: 0.7282 (tpt) REVERT: A 313 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7783 (ttp-110) REVERT: A 384 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7210 (tp30) REVERT: A 415 MET cc_start: 0.7683 (mmt) cc_final: 0.6962 (mmp) REVERT: B 186 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: B 441 GLU cc_start: 0.8248 (tp30) cc_final: 0.7923 (tm-30) REVERT: B 477 ASN cc_start: 0.7137 (t0) cc_final: 0.6851 (t160) REVERT: C 50 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8318 (ttm) REVERT: C 214 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8596 (tp40) REVERT: C 316 ASN cc_start: 0.8137 (m-40) cc_final: 0.7648 (m110) REVERT: C 413 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7115 (tp30) REVERT: D 117 MET cc_start: 0.9223 (tpp) cc_final: 0.8941 (tpp) REVERT: D 323 VAL cc_start: 0.8216 (t) cc_final: 0.7869 (t) REVERT: D 324 MET cc_start: 0.7631 (mtt) cc_final: 0.7392 (mtp) REVERT: D 330 LYS cc_start: 0.8289 (tttm) cc_final: 0.7985 (ttpt) REVERT: D 387 LYS cc_start: 0.7420 (ptmm) cc_final: 0.6847 (ptpt) REVERT: D 416 LEU cc_start: 0.8025 (tp) cc_final: 0.7171 (mm) REVERT: E 174 ASP cc_start: 0.7964 (t0) cc_final: 0.7606 (t0) REVERT: E 176 GLU cc_start: 0.6985 (pm20) cc_final: 0.6776 (pm20) REVERT: E 183 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: E 464 LEU cc_start: 0.8095 (tp) cc_final: 0.7846 (tm) REVERT: E 471 HIS cc_start: 0.7503 (t-90) cc_final: 0.7094 (t-90) REVERT: F 62 THR cc_start: 0.7620 (m) cc_final: 0.7334 (t) REVERT: G 26 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7719 (mtmm) outliers start: 48 outliers final: 20 residues processed: 259 average time/residue: 0.5539 time to fit residues: 162.7965 Evaluate side-chains 243 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 161 optimal weight: 0.4980 chunk 210 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS B 213 GLN C 53 ASN C 111 GLN C 310 ASN C 466 ASN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106362 restraints weight = 25322.369| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.84 r_work: 0.3093 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 18708 Z= 0.136 Angle : 0.562 13.245 25557 Z= 0.281 Chirality : 0.043 0.208 3025 Planarity : 0.004 0.061 3090 Dihedral : 7.323 88.774 2443 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 2.24 % Allowed : 13.77 % Favored : 83.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2152 helix: 2.00 (0.19), residues: 777 sheet: -0.93 (0.22), residues: 453 loop : -0.86 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.012 0.001 TYR C 410 PHE 0.011 0.001 PHE D 256 TRP 0.011 0.001 TRP G 28 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (18657) covalent geometry : angle 0.54138 / 0.27 (25423) SS BOND : bond 0.00861 / 0.62 ( 16) SS BOND : angle 3.00135 / 2.05 ( 32) hydrogen bonds : bond 0.03998 / 2.66 ( 859) hydrogen bonds : angle 4.46718 / 3.20 ( 2664) Misc. bond : bond 0.00047 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00386 / 0.20 ( 6) link_ALPHA1-2 : angle 1.49536 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00342 / 0.17 ( 4) link_ALPHA1-3 : angle 1.48332 / 0.86 ( 12) link_ALPHA1-6 : bond 0.00229 / 0.12 ( 6) link_ALPHA1-6 : angle 1.54295 / 0.96 ( 18) link_BETA1-4 : bond 0.00393 / 0.23 ( 10) link_BETA1-4 : angle 1.67517 / 1.12 ( 30) link_NAG-ASN : bond 0.00328 / 0.22 ( 8) link_NAG-ASN : angle 2.40983 / 1.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7945 (tpt) cc_final: 0.7175 (tpt) REVERT: A 313 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7917 (ttm-80) REVERT: A 384 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7180 (tp30) REVERT: A 415 MET cc_start: 0.7662 (mmt) cc_final: 0.6943 (mmp) REVERT: B 186 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: B 322 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8349 (tp) REVERT: B 436 LYS cc_start: 0.7668 (tttm) cc_final: 0.7302 (ttpt) REVERT: B 441 GLU cc_start: 0.8277 (tp30) cc_final: 0.7899 (tm-30) REVERT: B 477 ASN cc_start: 0.7096 (t0) cc_final: 0.6831 (t160) REVERT: C 50 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8324 (ttm) REVERT: C 214 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8626 (tp40) REVERT: C 244 ASP cc_start: 0.7605 (m-30) cc_final: 0.7001 (t0) REVERT: C 316 ASN cc_start: 0.8144 (m-40) cc_final: 0.7649 (m110) REVERT: C 331 TRP cc_start: 0.7507 (m100) cc_final: 0.6851 (m-90) REVERT: C 413 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7100 (tp30) REVERT: D 117 MET cc_start: 0.9231 (tpp) cc_final: 0.8957 (tpp) REVERT: D 164 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8106 (mtm180) REVERT: D 262 GLU cc_start: 0.6284 (tt0) cc_final: 0.5458 (tp30) REVERT: D 330 LYS cc_start: 0.8319 (tttm) cc_final: 0.7968 (ttpt) REVERT: D 387 LYS cc_start: 0.7393 (ptmm) cc_final: 0.6846 (ptpt) REVERT: D 416 LEU cc_start: 0.7949 (tp) cc_final: 0.7099 (mm) REVERT: E 174 ASP cc_start: 0.7969 (t0) cc_final: 0.7566 (t0) REVERT: E 464 LEU cc_start: 0.8058 (tp) cc_final: 0.7848 (tm) REVERT: E 471 HIS cc_start: 0.7523 (t-90) cc_final: 0.7116 (t-90) REVERT: F 62 THR cc_start: 0.7568 (m) cc_final: 0.7273 (t) REVERT: G 26 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7698 (mtmm) REVERT: G 41 GLU cc_start: 0.8005 (tt0) cc_final: 0.7669 (tt0) outliers start: 45 outliers final: 15 residues processed: 264 average time/residue: 0.5509 time to fit residues: 165.7307 Evaluate side-chains 245 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 103 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 58 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS B 213 GLN C 107 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN C 414 GLN C 466 ASN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107060 restraints weight = 32052.785| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.16 r_work: 0.3013 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 18708 Z= 0.150 Angle : 0.571 18.464 25557 Z= 0.283 Chirality : 0.043 0.204 3025 Planarity : 0.004 0.066 3090 Dihedral : 7.112 79.403 2443 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 2.04 % Allowed : 14.86 % Favored : 83.09 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2152 helix: 2.08 (0.19), residues: 777 sheet: -0.79 (0.23), residues: 459 loop : -0.79 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 222 TYR 0.018 0.001 TYR D 381 PHE 0.011 0.001 PHE B 473 TRP 0.009 0.001 TRP G 28 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (18657) covalent geometry : angle 0.54486 / 0.27 (25423) SS BOND : bond 0.01067 / 0.79 ( 16) SS BOND : angle 3.77690 / 2.57 ( 32) hydrogen bonds : bond 0.03971 / 2.64 ( 859) hydrogen bonds : angle 4.43784 / 3.18 ( 2664) Misc. bond : bond 0.00056 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00360 / 0.19 ( 6) link_ALPHA1-2 : angle 1.49783 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00281 / 0.14 ( 4) link_ALPHA1-3 : angle 1.58262 / 0.91 ( 12) link_ALPHA1-6 : bond 0.00192 / 0.10 ( 6) link_ALPHA1-6 : angle 1.56464 / 0.98 ( 18) link_BETA1-4 : bond 0.00337 / 0.20 ( 10) link_BETA1-4 : angle 1.67738 / 1.12 ( 30) link_NAG-ASN : bond 0.00349 / 0.23 ( 8) link_NAG-ASN : angle 2.40820 / 1.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7944 (ttm-80) REVERT: A 415 MET cc_start: 0.7732 (mmt) cc_final: 0.7028 (mmp) REVERT: B 186 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8343 (mt-10) REVERT: B 213 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: B 305 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7674 (t0) REVERT: B 441 GLU cc_start: 0.8433 (tp30) cc_final: 0.8044 (tm-30) REVERT: B 477 ASN cc_start: 0.7134 (t0) cc_final: 0.6856 (t160) REVERT: C 50 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8431 (ttm) REVERT: C 214 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8671 (tp40) REVERT: C 244 ASP cc_start: 0.7690 (m-30) cc_final: 0.7070 (t0) REVERT: C 316 ASN cc_start: 0.8196 (m-40) cc_final: 0.7693 (m110) REVERT: C 331 TRP cc_start: 0.7497 (m100) cc_final: 0.6831 (m-90) REVERT: C 413 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7101 (tp30) REVERT: D 117 MET cc_start: 0.9263 (tpp) cc_final: 0.9033 (tpp) REVERT: D 164 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8128 (mtm180) REVERT: D 262 GLU cc_start: 0.6304 (tt0) cc_final: 0.5470 (tp30) REVERT: D 291 ILE cc_start: 0.8274 (mt) cc_final: 0.8054 (tp) REVERT: D 330 LYS cc_start: 0.8408 (tttm) cc_final: 0.8064 (ttpt) REVERT: D 387 LYS cc_start: 0.7480 (ptmm) cc_final: 0.6661 (pttp) REVERT: D 410 LEU cc_start: 0.8455 (mt) cc_final: 0.8231 (mp) REVERT: D 416 LEU cc_start: 0.7979 (tp) cc_final: 0.7155 (mm) REVERT: E 174 ASP cc_start: 0.8032 (t0) cc_final: 0.7605 (t0) REVERT: E 176 GLU cc_start: 0.6982 (pm20) cc_final: 0.6742 (pm20) REVERT: E 259 LEU cc_start: 0.8199 (tp) cc_final: 0.7967 (mt) REVERT: E 471 HIS cc_start: 0.7529 (t-90) cc_final: 0.7121 (t-90) REVERT: F 62 THR cc_start: 0.7565 (m) cc_final: 0.7234 (t) REVERT: G 26 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7759 (mtmm) REVERT: G 41 GLU cc_start: 0.8122 (tt0) cc_final: 0.7808 (tt0) outliers start: 41 outliers final: 19 residues processed: 253 average time/residue: 0.5753 time to fit residues: 165.1581 Evaluate side-chains 249 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 37 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 53 ASN C 107 ASN C 111 GLN C 310 ASN C 414 GLN C 466 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108134 restraints weight = 31959.655| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.04 r_work: 0.3108 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 18708 Z= 0.141 Angle : 0.570 19.255 25557 Z= 0.281 Chirality : 0.042 0.202 3025 Planarity : 0.004 0.101 3090 Dihedral : 6.975 77.132 2443 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 2.04 % Allowed : 15.66 % Favored : 82.29 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2152 helix: 2.15 (0.19), residues: 777 sheet: -0.76 (0.23), residues: 459 loop : -0.74 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.015 0.001 TYR C 410 PHE 0.011 0.001 PHE B 473 TRP 0.009 0.001 TRP D 60 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (18657) covalent geometry : angle 0.54269 / 0.27 (25423) SS BOND : bond 0.00909 / 0.66 ( 16) SS BOND : angle 3.87497 / 2.64 ( 32) hydrogen bonds : bond 0.03894 / 2.59 ( 859) hydrogen bonds : angle 4.39966 / 3.15 ( 2664) Misc. bond : bond 0.00052 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00353 / 0.18 ( 6) link_ALPHA1-2 : angle 1.46080 / 0.95 ( 18) link_ALPHA1-3 : bond 0.00329 / 0.17 ( 4) link_ALPHA1-3 : angle 1.51967 / 0.88 ( 12) link_ALPHA1-6 : bond 0.00226 / 0.12 ( 6) link_ALPHA1-6 : angle 1.53895 / 0.96 ( 18) link_BETA1-4 : bond 0.00371 / 0.22 ( 10) link_BETA1-4 : angle 1.67601 / 1.11 ( 30) link_NAG-ASN : bond 0.00325 / 0.22 ( 8) link_NAG-ASN : angle 2.36844 / 1.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7989 (ttm-80) REVERT: A 415 MET cc_start: 0.7773 (mmt) cc_final: 0.7460 (mmp) REVERT: B 186 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: B 305 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 441 GLU cc_start: 0.8385 (tp30) cc_final: 0.8007 (tm-30) REVERT: B 477 ASN cc_start: 0.7130 (t0) cc_final: 0.6851 (t160) REVERT: C 50 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8348 (ttm) REVERT: C 214 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8673 (tp40) REVERT: C 244 ASP cc_start: 0.7695 (m-30) cc_final: 0.7114 (t0) REVERT: C 316 ASN cc_start: 0.8163 (m-40) cc_final: 0.7677 (m110) REVERT: C 331 TRP cc_start: 0.7485 (m100) cc_final: 0.6904 (m-90) REVERT: C 413 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7119 (tp30) REVERT: D 117 MET cc_start: 0.9269 (tpp) cc_final: 0.9045 (tpp) REVERT: D 164 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8120 (mtm180) REVERT: D 262 GLU cc_start: 0.6342 (tt0) cc_final: 0.5513 (tp30) REVERT: D 264 ILE cc_start: 0.7408 (pt) cc_final: 0.7127 (pt) REVERT: D 291 ILE cc_start: 0.8237 (mt) cc_final: 0.8032 (tp) REVERT: D 330 LYS cc_start: 0.8418 (tttm) cc_final: 0.8102 (ttpt) REVERT: D 387 LYS cc_start: 0.7500 (ptmm) cc_final: 0.6688 (pttp) REVERT: D 416 LEU cc_start: 0.8027 (tp) cc_final: 0.7215 (mm) REVERT: E 26 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6989 (p0) REVERT: E 174 ASP cc_start: 0.8002 (t0) cc_final: 0.7612 (t0) REVERT: E 176 GLU cc_start: 0.7005 (pm20) cc_final: 0.6780 (pm20) REVERT: E 183 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: E 259 LEU cc_start: 0.8189 (tp) cc_final: 0.7965 (mt) REVERT: E 471 HIS cc_start: 0.7566 (t-90) cc_final: 0.7152 (t-90) REVERT: F 62 THR cc_start: 0.7587 (m) cc_final: 0.7302 (t) REVERT: G 26 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7722 (mtmm) REVERT: G 41 GLU cc_start: 0.8136 (tt0) cc_final: 0.7823 (tt0) outliers start: 41 outliers final: 18 residues processed: 258 average time/residue: 0.5583 time to fit residues: 163.4426 Evaluate side-chains 252 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 207 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN A 140 GLN B 26 HIS B 213 GLN C 53 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 466 ASN D 208 GLN D 394 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104056 restraints weight = 26998.014| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.86 r_work: 0.3036 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 18708 Z= 0.200 Angle : 0.614 19.048 25557 Z= 0.304 Chirality : 0.044 0.215 3025 Planarity : 0.005 0.089 3090 Dihedral : 7.076 74.834 2443 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 2.09 % Allowed : 16.11 % Favored : 81.80 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2152 helix: 2.05 (0.19), residues: 778 sheet: -0.74 (0.23), residues: 454 loop : -0.79 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.017 0.001 TYR D 381 PHE 0.013 0.001 PHE E 467 TRP 0.006 0.001 TRP B 176 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (18657) covalent geometry : angle 0.58549 / 0.29 (25423) SS BOND : bond 0.00956 / 0.69 ( 16) SS BOND : angle 4.02587 / 2.74 ( 32) hydrogen bonds : bond 0.04210 / 2.80 ( 859) hydrogen bonds : angle 4.51525 / 3.23 ( 2664) Misc. bond : bond 0.00059 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00272 / 0.14 ( 6) link_ALPHA1-2 : angle 1.58090 / 1.02 ( 18) link_ALPHA1-3 : bond 0.00149 / 0.08 ( 4) link_ALPHA1-3 : angle 1.81328 / 1.04 ( 12) link_ALPHA1-6 : bond 0.00183 / 0.09 ( 6) link_ALPHA1-6 : angle 1.69362 / 1.05 ( 18) link_BETA1-4 : bond 0.00412 / 0.27 ( 10) link_BETA1-4 : angle 1.86608 / 1.24 ( 30) link_NAG-ASN : bond 0.00502 / 0.33 ( 8) link_NAG-ASN : angle 2.57167 / 1.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8088 (tpt) cc_final: 0.7318 (tpt) REVERT: A 313 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7938 (ttm-80) REVERT: A 380 LYS cc_start: 0.8310 (mtmt) cc_final: 0.8076 (mtmm) REVERT: A 415 MET cc_start: 0.7725 (mmt) cc_final: 0.7397 (mmp) REVERT: B 186 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: B 305 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7598 (t0) REVERT: B 441 GLU cc_start: 0.8356 (tp30) cc_final: 0.7949 (tm-30) REVERT: B 477 ASN cc_start: 0.7159 (t0) cc_final: 0.6865 (t160) REVERT: C 50 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8427 (ttm) REVERT: C 107 ASN cc_start: 0.8649 (p0) cc_final: 0.8085 (p0) REVERT: C 214 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8594 (tp40) REVERT: C 316 ASN cc_start: 0.8172 (m-40) cc_final: 0.7512 (m110) REVERT: C 320 GLN cc_start: 0.7626 (tt0) cc_final: 0.7215 (mt0) REVERT: C 331 TRP cc_start: 0.7488 (m100) cc_final: 0.6861 (m-90) REVERT: C 413 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7131 (tp30) REVERT: C 415 LEU cc_start: 0.8003 (mp) cc_final: 0.7576 (mp) REVERT: D 164 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8130 (mtm180) REVERT: D 262 GLU cc_start: 0.6319 (tt0) cc_final: 0.5487 (tp30) REVERT: D 264 ILE cc_start: 0.7438 (pt) cc_final: 0.7173 (pt) REVERT: D 291 ILE cc_start: 0.8215 (mt) cc_final: 0.7986 (tp) REVERT: D 330 LYS cc_start: 0.8375 (tttm) cc_final: 0.8020 (ttpt) REVERT: D 387 LYS cc_start: 0.7491 (ptmm) cc_final: 0.6656 (pttp) REVERT: D 416 LEU cc_start: 0.7966 (tp) cc_final: 0.7132 (mm) REVERT: E 174 ASP cc_start: 0.8003 (t0) cc_final: 0.7599 (t0) REVERT: E 176 GLU cc_start: 0.6972 (pm20) cc_final: 0.6748 (pm20) REVERT: E 183 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: E 471 HIS cc_start: 0.7555 (t-90) cc_final: 0.7100 (t-90) REVERT: F 62 THR cc_start: 0.7513 (m) cc_final: 0.7246 (t) REVERT: G 26 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7818 (mtmm) REVERT: G 41 GLU cc_start: 0.8082 (tt0) cc_final: 0.7673 (tt0) outliers start: 42 outliers final: 22 residues processed: 259 average time/residue: 0.5645 time to fit residues: 165.7551 Evaluate side-chains 258 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 30 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 89 optimal weight: 0.0770 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS B 213 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107218 restraints weight = 23017.055| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.71 r_work: 0.3109 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 18708 Z= 0.132 Angle : 0.578 19.316 25557 Z= 0.286 Chirality : 0.042 0.208 3025 Planarity : 0.004 0.087 3090 Dihedral : 6.802 73.684 2443 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 1.35 % Allowed : 16.81 % Favored : 81.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2152 helix: 2.20 (0.19), residues: 782 sheet: -0.72 (0.23), residues: 454 loop : -0.70 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.013 0.001 TYR C 410 PHE 0.010 0.001 PHE B 473 TRP 0.011 0.001 TRP D 60 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (18657) covalent geometry : angle 0.54868 / 0.28 (25423) SS BOND : bond 0.00873 / 0.64 ( 16) SS BOND : angle 4.20252 / 3.01 ( 32) hydrogen bonds : bond 0.03823 / 2.55 ( 859) hydrogen bonds : angle 4.37272 / 3.14 ( 2664) Misc. bond : bond 0.00049 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00419 / 0.22 ( 6) link_ALPHA1-2 : angle 1.39003 / 0.91 ( 18) link_ALPHA1-3 : bond 0.00415 / 0.21 ( 4) link_ALPHA1-3 : angle 1.39364 / 0.81 ( 12) link_ALPHA1-6 : bond 0.00267 / 0.14 ( 6) link_ALPHA1-6 : angle 1.49908 / 0.94 ( 18) link_BETA1-4 : bond 0.00352 / 0.19 ( 10) link_BETA1-4 : angle 1.59195 / 1.05 ( 30) link_NAG-ASN : bond 0.00294 / 0.19 ( 8) link_NAG-ASN : angle 2.32864 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 308 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7699 (tpp) REVERT: A 313 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7560 (ttm-80) REVERT: A 380 LYS cc_start: 0.8323 (mtmt) cc_final: 0.8095 (mtmm) REVERT: A 415 MET cc_start: 0.7727 (mmt) cc_final: 0.7420 (mmp) REVERT: B 186 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: B 283 LEU cc_start: 0.8677 (mt) cc_final: 0.8422 (mm) REVERT: B 441 GLU cc_start: 0.8312 (tp30) cc_final: 0.7936 (tm-30) REVERT: B 477 ASN cc_start: 0.7168 (t0) cc_final: 0.6887 (t160) REVERT: C 50 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8257 (ttm) REVERT: C 107 ASN cc_start: 0.8335 (p0) cc_final: 0.7772 (m110) REVERT: C 214 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8610 (tp40) REVERT: C 244 ASP cc_start: 0.7606 (m-30) cc_final: 0.7079 (t0) REVERT: C 316 ASN cc_start: 0.8106 (m-40) cc_final: 0.7614 (m110) REVERT: C 331 TRP cc_start: 0.7409 (m100) cc_final: 0.6906 (m-90) REVERT: C 413 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7117 (tp30) REVERT: D 164 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8088 (mtm180) REVERT: D 262 GLU cc_start: 0.6315 (tt0) cc_final: 0.5503 (tp30) REVERT: D 264 ILE cc_start: 0.7404 (pt) cc_final: 0.7108 (pt) REVERT: D 387 LYS cc_start: 0.7492 (ptmm) cc_final: 0.7162 (mtmt) REVERT: D 416 LEU cc_start: 0.7977 (tp) cc_final: 0.7167 (mm) REVERT: E 174 ASP cc_start: 0.7963 (t0) cc_final: 0.7672 (t0) REVERT: E 176 GLU cc_start: 0.6960 (pm20) cc_final: 0.6727 (pm20) REVERT: E 259 LEU cc_start: 0.8121 (tp) cc_final: 0.7896 (mt) REVERT: E 471 HIS cc_start: 0.7559 (t-90) cc_final: 0.7129 (t-90) REVERT: F 62 THR cc_start: 0.7528 (m) cc_final: 0.7251 (t) REVERT: G 41 GLU cc_start: 0.8046 (tt0) cc_final: 0.7612 (tt0) outliers start: 27 outliers final: 12 residues processed: 252 average time/residue: 0.5408 time to fit residues: 155.3443 Evaluate side-chains 247 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 157 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS B 213 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107586 restraints weight = 32193.337| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.04 r_work: 0.3043 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.185 18708 Z= 0.142 Angle : 0.576 19.292 25557 Z= 0.286 Chirality : 0.042 0.195 3025 Planarity : 0.004 0.085 3090 Dihedral : 6.742 76.435 2443 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.00 % Allowed : 17.01 % Favored : 82.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2152 helix: 2.18 (0.19), residues: 790 sheet: -0.73 (0.23), residues: 447 loop : -0.61 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 182 TYR 0.019 0.001 TYR D 381 PHE 0.011 0.001 PHE B 473 TRP 0.019 0.001 TRP G 28 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (18657) covalent geometry : angle 0.54911 / 0.28 (25423) SS BOND : bond 0.00889 / 0.65 ( 16) SS BOND : angle 3.92268 / 2.69 ( 32) hydrogen bonds : bond 0.03863 / 2.58 ( 859) hydrogen bonds : angle 4.37365 / 3.14 ( 2664) Misc. bond : bond 0.00051 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00321 / 0.17 ( 6) link_ALPHA1-2 : angle 1.47984 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00301 / 0.15 ( 4) link_ALPHA1-3 : angle 1.59074 / 0.92 ( 12) link_ALPHA1-6 : bond 0.00215 / 0.11 ( 6) link_ALPHA1-6 : angle 1.55166 / 0.97 ( 18) link_BETA1-4 : bond 0.00369 / 0.22 ( 10) link_BETA1-4 : angle 1.64764 / 1.09 ( 30) link_NAG-ASN : bond 0.00314 / 0.21 ( 8) link_NAG-ASN : angle 2.32621 / 1.61 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 308 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7742 (tpp) REVERT: A 313 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7582 (ttm-80) REVERT: A 380 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8103 (mtmm) REVERT: A 407 ASP cc_start: 0.8651 (m-30) cc_final: 0.8437 (t0) REVERT: A 415 MET cc_start: 0.7759 (mmt) cc_final: 0.7439 (mmp) REVERT: B 186 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: B 283 LEU cc_start: 0.8692 (mt) cc_final: 0.8419 (mm) REVERT: B 441 GLU cc_start: 0.8435 (tp30) cc_final: 0.8047 (tm-30) REVERT: B 457 SER cc_start: 0.8752 (t) cc_final: 0.8400 (m) REVERT: B 477 ASN cc_start: 0.7159 (t0) cc_final: 0.6863 (t160) REVERT: C 50 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8373 (ttm) REVERT: C 107 ASN cc_start: 0.8526 (p0) cc_final: 0.7985 (m110) REVERT: C 214 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8666 (tp40) REVERT: C 244 ASP cc_start: 0.7719 (m-30) cc_final: 0.7134 (t0) REVERT: C 316 ASN cc_start: 0.8162 (m-40) cc_final: 0.7520 (m110) REVERT: C 320 GLN cc_start: 0.7698 (tt0) cc_final: 0.7279 (mt0) REVERT: C 331 TRP cc_start: 0.7461 (m100) cc_final: 0.6928 (m-90) REVERT: C 413 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7203 (tp30) REVERT: C 415 LEU cc_start: 0.8062 (mp) cc_final: 0.7736 (mt) REVERT: D 164 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8122 (mtm180) REVERT: D 262 GLU cc_start: 0.6324 (tt0) cc_final: 0.5510 (tp30) REVERT: D 264 ILE cc_start: 0.7459 (pt) cc_final: 0.7154 (pt) REVERT: D 387 LYS cc_start: 0.7493 (ptmm) cc_final: 0.7154 (mtmt) REVERT: D 390 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: D 416 LEU cc_start: 0.7960 (tp) cc_final: 0.7160 (mm) REVERT: E 174 ASP cc_start: 0.8009 (t0) cc_final: 0.7685 (t0) REVERT: E 176 GLU cc_start: 0.7026 (pm20) cc_final: 0.6764 (pm20) REVERT: E 259 LEU cc_start: 0.8185 (tp) cc_final: 0.7967 (mt) REVERT: E 471 HIS cc_start: 0.7567 (t-90) cc_final: 0.7130 (t-90) REVERT: F 62 THR cc_start: 0.7534 (m) cc_final: 0.7202 (p) REVERT: G 26 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7830 (mtmm) REVERT: G 41 GLU cc_start: 0.8174 (tt0) cc_final: 0.7885 (tt0) outliers start: 20 outliers final: 11 residues processed: 252 average time/residue: 0.5551 time to fit residues: 158.9015 Evaluate side-chains 252 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 235 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 202 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS B 213 GLN C 53 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105166 restraints weight = 30695.369| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.04 r_work: 0.3017 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 18708 Z= 0.172 Angle : 0.599 19.194 25557 Z= 0.297 Chirality : 0.043 0.206 3025 Planarity : 0.004 0.083 3090 Dihedral : 6.830 79.538 2443 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 1.20 % Allowed : 17.11 % Favored : 81.70 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2152 helix: 2.11 (0.19), residues: 790 sheet: -0.73 (0.23), residues: 442 loop : -0.63 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 182 TYR 0.013 0.001 TYR C 410 PHE 0.012 0.001 PHE B 473 TRP 0.007 0.001 TRP D 187 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (18657) covalent geometry : angle 0.57114 / 0.29 (25423) SS BOND : bond 0.00915 / 0.66 ( 16) SS BOND : angle 4.03130 / 2.76 ( 32) hydrogen bonds : bond 0.04054 / 2.70 ( 859) hydrogen bonds : angle 4.44887 / 3.19 ( 2664) Misc. bond : bond 0.00049 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00297 / 0.16 ( 6) link_ALPHA1-2 : angle 1.52934 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00168 / 0.09 ( 4) link_ALPHA1-3 : angle 1.73080 / 0.99 ( 12) link_ALPHA1-6 : bond 0.00167 / 0.08 ( 6) link_ALPHA1-6 : angle 1.63696 / 1.02 ( 18) link_BETA1-4 : bond 0.00376 / 0.24 ( 10) link_BETA1-4 : angle 1.76550 / 1.17 ( 30) link_NAG-ASN : bond 0.00419 / 0.28 ( 8) link_NAG-ASN : angle 2.48310 / 1.74 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7588.58 seconds wall clock time: 129 minutes 55.35 seconds (7795.35 seconds total)