Starting phenix.real_space_refine on Sun Aug 24 09:15:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uwz_20928/08_2025/6uwz_20928.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwz_20928/08_2025/6uwz_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 { model { file = "/net/cci-nas-00/data/ceres_data/6uwz_20928/08_2025/6uwz_20928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwz_20928/08_2025/6uwz_20928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uwz_20928/08_2025/6uwz_20928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwz_20928/08_2025/6uwz_20928.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 30 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 30 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 3 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: 5.09, per 1000 atoms: 0.28 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: 2.12 Conformation dependent library (CDL) restraints added in 859.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.72 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: 3.75 Time building geometry restraints manager: 2.58 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: 11187 29.05 - 58.11: 353 58.11 - 87.16: 52 87.16 - 116.22: 18 116.22 - 145.27: 2 Dihedral angle restraints: 11612 sinusoidal: 5153 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 11609 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: 4.090 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: 0.560 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.560 Find NCS groups from input model: 0.310 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:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 15.212 145.270 7358 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 aren 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 covalent geometry : bond 0.01081 (18657) covalent geometry : angle 0.82102 (25423) SS BOND : bond 0.00845 ( 16) SS BOND : angle 2.39512 ( 32) hydrogen bonds : bond 0.12939 ( 859) hydrogen bonds : angle 6.78205 ( 2664) Misc. bond : bond 0.21597 ( 1) link_ALPHA1-2 : bond 0.05294 ( 6) link_ALPHA1-2 : angle 8.96097 ( 18) link_ALPHA1-3 : bond 0.06489 ( 4) link_ALPHA1-3 : angle 6.43035 ( 12) link_ALPHA1-6 : bond 0.03840 ( 6) link_ALPHA1-6 : angle 8.60410 ( 18) link_BETA1-4 : bond 0.04196 ( 10) link_BETA1-4 : angle 4.61089 ( 30) link_NAG-ASN : bond 0.02367 ( 8) link_NAG-ASN : angle 4.88125 ( 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 : 0.810 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: 0.7050 time to fit residues: 243.3060 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 : 0.759 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110204 restraints weight = 32701.938| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.10 r_work: 0.3128 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 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 = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18708 Z= 0.147 Angle : 0.628 9.751 25557 Z= 0.314 Chirality : 0.045 0.315 3025 Planarity : 0.005 0.046 3090 Dihedral : 10.861 111.865 3147 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 1.45 % Allowed : 10.07 % Favored : 88.48 % 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 aren not related in a simple way. whole: -0.90 (0.17), residues: 2152 helix: 1.03 (0.18), residues: 784 sheet: -1.51 (0.21), residues: 440 loop : -1.52 (0.19), residues: 928 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 0.013 0.001 TRP D 60 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00329 (18657) covalent geometry : angle 0.60787 (25423) SS BOND : bond 0.00649 ( 16) SS BOND : angle 2.66286 ( 32) hydrogen bonds : bond 0.04506 ( 859) hydrogen bonds : angle 4.94359 ( 2664) Misc. bond : bond 0.00208 ( 1) link_ALPHA1-2 : bond 0.00736 ( 6) link_ALPHA1-2 : angle 2.12000 ( 18) link_ALPHA1-3 : bond 0.00979 ( 4) link_ALPHA1-3 : angle 1.27157 ( 12) link_ALPHA1-6 : bond 0.00302 ( 6) link_ALPHA1-6 : angle 1.62559 ( 18) link_BETA1-4 : bond 0.00392 ( 10) link_BETA1-4 : angle 2.12144 ( 30) link_NAG-ASN : bond 0.00430 ( 8) link_NAG-ASN : angle 2.58299 ( 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 276 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.783 Fit side-chains REVERT: A 415 MET cc_start: 0.7682 (mmt) cc_final: 0.7212 (mmp) REVERT: B 186 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: B 187 ASN cc_start: 0.8390 (t0) cc_final: 0.8106 (t160) REVERT: B 477 ASN cc_start: 0.7075 (t0) cc_final: 0.6747 (t160) REVERT: C 50 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8054 (ttm) REVERT: C 107 ASN cc_start: 0.8399 (p0) cc_final: 0.7650 (m-40) REVERT: C 413 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7185 (tp30) REVERT: D 323 VAL cc_start: 0.8110 (t) cc_final: 0.7753 (t) REVERT: D 324 MET cc_start: 0.7497 (mtt) cc_final: 0.7292 (mtt) REVERT: D 330 LYS cc_start: 0.8344 (tttm) cc_final: 0.8046 (ttpt) REVERT: E 174 ASP cc_start: 0.7681 (t0) cc_final: 0.7354 (t0) REVERT: E 224 ILE cc_start: 0.8501 (pt) cc_final: 0.8295 (pp) REVERT: E 471 HIS cc_start: 0.7528 (t-90) cc_final: 0.7149 (t-90) REVERT: F 55 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8554 (mt-10) REVERT: G 26 LYS cc_start: 0.8419 (mtpt) cc_final: 0.7820 (mtmm) REVERT: G 52 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5062 (mtmt) outliers start: 29 outliers final: 8 residues processed: 258 average time/residue: 0.6527 time to fit residues: 189.3456 Evaluate side-chains 232 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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: 2.9990 chunk 196 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 204 HIS A 297 ASN B 26 HIS C 53 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110011 restraints weight = 22657.602| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.72 r_work: 0.3183 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18708 Z= 0.134 Angle : 0.564 8.648 25557 Z= 0.281 Chirality : 0.044 0.213 3025 Planarity : 0.004 0.040 3090 Dihedral : 9.353 89.172 3147 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.65 % Allowed : 11.47 % Favored : 86.88 % 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 aren not related in a simple way. whole: -0.10 (0.18), residues: 2152 helix: 1.77 (0.19), residues: 777 sheet: -1.13 (0.22), residues: 444 loop : -1.08 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.010 0.001 TYR E 195 PHE 0.009 0.001 PHE E 467 TRP 0.011 0.001 TRP D 60 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00301 (18657) covalent geometry : angle 0.54411 (25423) SS BOND : bond 0.00911 ( 16) SS BOND : angle 2.38376 ( 32) hydrogen bonds : bond 0.04138 ( 859) hydrogen bonds : angle 4.57152 ( 2664) Misc. bond : bond 0.00093 ( 1) link_ALPHA1-2 : bond 0.00358 ( 6) link_ALPHA1-2 : angle 1.82095 ( 18) link_ALPHA1-3 : bond 0.00641 ( 4) link_ALPHA1-3 : angle 1.82400 ( 12) link_ALPHA1-6 : bond 0.00230 ( 6) link_ALPHA1-6 : angle 1.74522 ( 18) link_BETA1-4 : bond 0.00477 ( 10) link_BETA1-4 : angle 1.92140 ( 30) link_NAG-ASN : bond 0.00347 ( 8) link_NAG-ASN : angle 2.44685 ( 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 276 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.781 Fit side-chains REVERT: A 313 ARG cc_start: 0.8188 (ttm110) cc_final: 0.7701 (ttp-110) REVERT: A 415 MET cc_start: 0.7627 (mmt) cc_final: 0.6890 (mmp) REVERT: B 186 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: B 187 ASN cc_start: 0.8400 (t0) cc_final: 0.8181 (t160) REVERT: B 276 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: B 322 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8206 (tp) REVERT: B 437 ASN cc_start: 0.8505 (m-40) cc_final: 0.8286 (m110) REVERT: B 477 ASN cc_start: 0.6976 (t0) cc_final: 0.6701 (t160) REVERT: C 50 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8026 (ttm) REVERT: C 107 ASN cc_start: 0.8281 (p0) cc_final: 0.7591 (m-40) REVERT: C 167 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: C 316 ASN cc_start: 0.8000 (m-40) cc_final: 0.7565 (m110) REVERT: D 330 LYS cc_start: 0.8292 (tttm) cc_final: 0.8023 (ttpt) REVERT: D 387 LYS cc_start: 0.7244 (ptmm) cc_final: 0.6555 (ptpt) REVERT: E 101 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8169 (mp0) REVERT: E 174 ASP cc_start: 0.7741 (t0) cc_final: 0.7452 (t0) REVERT: E 176 GLU cc_start: 0.6795 (pm20) cc_final: 0.6581 (pm20) REVERT: E 224 ILE cc_start: 0.8427 (pt) cc_final: 0.8153 (pp) REVERT: E 464 LEU cc_start: 0.7982 (tp) cc_final: 0.7728 (tm) REVERT: E 471 HIS cc_start: 0.7437 (t-90) cc_final: 0.7077 (t-90) REVERT: F 62 THR cc_start: 0.7669 (m) cc_final: 0.7393 (t) REVERT: G 26 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7770 (mtmm) outliers start: 33 outliers final: 6 residues processed: 261 average time/residue: 0.6413 time to fit residues: 188.4489 Evaluate side-chains 225 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 276 GLN 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 D residue 42 SER Chi-restraints excluded: chain D residue 142 CYS 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: 6.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS B 103 HIS ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 107 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 310 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN E 216 GLN E 250 GLN E 271 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102698 restraints weight = 24728.742| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.83 r_work: 0.3051 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 18708 Z= 0.224 Angle : 0.651 10.396 25557 Z= 0.323 Chirality : 0.046 0.234 3025 Planarity : 0.005 0.055 3090 Dihedral : 9.450 89.579 3147 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 2.69 % Allowed : 12.27 % Favored : 85.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.02 (0.18), residues: 2152 helix: 1.70 (0.19), residues: 783 sheet: -0.98 (0.22), residues: 446 loop : -0.98 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 313 TYR 0.015 0.002 TYR B 74 PHE 0.016 0.002 PHE A 256 TRP 0.010 0.001 TRP E 197 HIS 0.005 0.001 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00534 (18657) covalent geometry : angle 0.62708 (25423) SS BOND : bond 0.00920 ( 16) SS BOND : angle 3.08520 ( 32) hydrogen bonds : bond 0.04604 ( 859) hydrogen bonds : angle 4.73234 ( 2664) Misc. bond : bond 0.00091 ( 1) link_ALPHA1-2 : bond 0.00379 ( 6) link_ALPHA1-2 : angle 1.75660 ( 18) link_ALPHA1-3 : bond 0.00478 ( 4) link_ALPHA1-3 : angle 2.05739 ( 12) link_ALPHA1-6 : bond 0.00233 ( 6) link_ALPHA1-6 : angle 1.95602 ( 18) link_BETA1-4 : bond 0.00516 ( 10) link_BETA1-4 : angle 2.22326 ( 30) link_NAG-ASN : bond 0.00681 ( 8) link_NAG-ASN : angle 2.87520 ( 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 284 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8035 (tpt) cc_final: 0.7217 (tpt) REVERT: A 313 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7807 (ttp-110) REVERT: A 384 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7263 (tp30) REVERT: A 415 MET cc_start: 0.7709 (mmt) cc_final: 0.6998 (mmp) REVERT: B 186 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: B 436 LYS cc_start: 0.7681 (tttm) cc_final: 0.7293 (ttpt) REVERT: B 441 GLU cc_start: 0.8289 (tp30) cc_final: 0.7909 (tm-30) REVERT: B 477 ASN cc_start: 0.7077 (t0) cc_final: 0.6854 (t160) REVERT: C 50 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8429 (ttm) REVERT: C 172 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8103 (pp20) REVERT: C 214 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8538 (tp40) REVERT: C 316 ASN cc_start: 0.8141 (m-40) cc_final: 0.7612 (m110) REVERT: C 331 TRP cc_start: 0.7553 (m100) cc_final: 0.6860 (m-90) REVERT: C 413 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7160 (tp30) REVERT: D 330 LYS cc_start: 0.8310 (tttm) cc_final: 0.7969 (ttpt) REVERT: D 387 LYS cc_start: 0.7282 (ptmm) cc_final: 0.6683 (ptpt) REVERT: E 101 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8342 (mp0) REVERT: E 174 ASP cc_start: 0.8007 (t0) cc_final: 0.7576 (t0) REVERT: E 183 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: E 471 HIS cc_start: 0.7521 (t-90) cc_final: 0.7085 (t-90) REVERT: F 62 THR cc_start: 0.7595 (m) cc_final: 0.7288 (t) REVERT: G 26 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7784 (mtmm) outliers start: 54 outliers final: 21 residues processed: 261 average time/residue: 0.6460 time to fit residues: 189.8506 Evaluate side-chains 246 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 107 ASN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS 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 52 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 161 optimal weight: 0.7980 chunk 210 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 0.0010 chunk 157 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 30 optimal weight: 10.0000 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS B 200 ASN B 213 GLN C 111 GLN ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 466 ASN D 139 GLN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106316 restraints weight = 25343.335| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.87 r_work: 0.3092 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 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 = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 18708 Z= 0.125 Angle : 0.559 10.861 25557 Z= 0.279 Chirality : 0.043 0.232 3025 Planarity : 0.004 0.062 3090 Dihedral : 8.793 87.255 3147 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.14 % Allowed : 14.11 % Favored : 83.74 % 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 aren not related in a simple way. whole: 0.27 (0.18), residues: 2152 helix: 2.02 (0.19), residues: 777 sheet: -0.92 (0.23), residues: 446 loop : -0.81 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.010 0.001 TYR C 410 PHE 0.010 0.001 PHE E 467 TRP 0.011 0.001 TRP G 28 HIS 0.005 0.001 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00289 (18657) covalent geometry : angle 0.53915 (25423) SS BOND : bond 0.00849 ( 16) SS BOND : angle 2.77508 ( 32) hydrogen bonds : bond 0.03968 ( 859) hydrogen bonds : angle 4.47084 ( 2664) Misc. bond : bond 0.00050 ( 1) link_ALPHA1-2 : bond 0.00480 ( 6) link_ALPHA1-2 : angle 1.56764 ( 18) link_ALPHA1-3 : bond 0.00805 ( 4) link_ALPHA1-3 : angle 1.76416 ( 12) link_ALPHA1-6 : bond 0.00375 ( 6) link_ALPHA1-6 : angle 1.76793 ( 18) link_BETA1-4 : bond 0.00425 ( 10) link_BETA1-4 : angle 1.68115 ( 30) link_NAG-ASN : bond 0.00299 ( 8) link_NAG-ASN : angle 2.42058 ( 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 281 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.774 Fit side-chains REVERT: A 313 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7744 (ttp-110) REVERT: A 384 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7233 (tp30) REVERT: A 415 MET cc_start: 0.7755 (mmt) cc_final: 0.7049 (mmp) REVERT: B 186 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: B 436 LYS cc_start: 0.7742 (tttm) cc_final: 0.7374 (ttpt) REVERT: B 441 GLU cc_start: 0.8309 (tp30) cc_final: 0.7941 (tm-30) REVERT: B 477 ASN cc_start: 0.7184 (t0) cc_final: 0.6912 (t160) REVERT: C 50 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8338 (ttm) REVERT: C 214 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8634 (tp40) REVERT: C 244 ASP cc_start: 0.7622 (m-30) cc_final: 0.7064 (t0) REVERT: C 316 ASN cc_start: 0.8153 (m-40) cc_final: 0.7651 (m110) REVERT: C 331 TRP cc_start: 0.7513 (m100) cc_final: 0.6879 (m-90) REVERT: C 413 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7119 (tp30) REVERT: D 117 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8978 (tpp) REVERT: D 262 GLU cc_start: 0.6291 (tt0) cc_final: 0.5448 (tp30) REVERT: D 330 LYS cc_start: 0.8373 (tttm) cc_final: 0.8057 (ttpt) REVERT: D 387 LYS cc_start: 0.7331 (ptmm) cc_final: 0.6782 (ptpt) REVERT: D 416 LEU cc_start: 0.8027 (tp) cc_final: 0.7187 (mm) REVERT: E 101 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8397 (mp0) REVERT: E 174 ASP cc_start: 0.7929 (t0) cc_final: 0.7580 (t0) REVERT: E 176 GLU cc_start: 0.6987 (pm20) cc_final: 0.6754 (pm20) REVERT: E 259 LEU cc_start: 0.8184 (tp) cc_final: 0.7967 (mt) REVERT: E 464 LEU cc_start: 0.8109 (tp) cc_final: 0.7901 (tm) REVERT: E 471 HIS cc_start: 0.7519 (t-90) cc_final: 0.7121 (t-90) REVERT: F 62 THR cc_start: 0.7638 (m) cc_final: 0.7334 (t) REVERT: G 41 GLU cc_start: 0.8000 (tt0) cc_final: 0.7633 (tt0) outliers start: 43 outliers final: 12 residues processed: 263 average time/residue: 0.6139 time to fit residues: 182.8954 Evaluate side-chains 240 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 391 GLU 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 D residue 117 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 171 MET 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 50 SER 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: 3.9990 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN B 26 HIS B 213 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104661 restraints weight = 31799.660| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.09 r_work: 0.2993 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 18708 Z= 0.196 Angle : 0.627 19.600 25557 Z= 0.309 Chirality : 0.045 0.226 3025 Planarity : 0.005 0.091 3090 Dihedral : 9.041 76.339 3147 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 2.24 % Allowed : 14.51 % Favored : 83.24 % 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 aren not related in a simple way. whole: 0.26 (0.18), residues: 2152 helix: 1.92 (0.19), residues: 780 sheet: -0.86 (0.23), residues: 444 loop : -0.77 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 222 TYR 0.016 0.001 TYR D 381 PHE 0.013 0.001 PHE A 256 TRP 0.009 0.001 TRP G 28 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00478 (18657) covalent geometry : angle 0.59610 (25423) SS BOND : bond 0.00874 ( 16) SS BOND : angle 4.18406 ( 32) hydrogen bonds : bond 0.04286 ( 859) hydrogen bonds : angle 4.56297 ( 2664) Misc. bond : bond 0.00054 ( 1) link_ALPHA1-2 : bond 0.00333 ( 6) link_ALPHA1-2 : angle 1.69286 ( 18) link_ALPHA1-3 : bond 0.00473 ( 4) link_ALPHA1-3 : angle 2.00762 ( 12) link_ALPHA1-6 : bond 0.00242 ( 6) link_ALPHA1-6 : angle 1.88473 ( 18) link_BETA1-4 : bond 0.00452 ( 10) link_BETA1-4 : angle 1.98377 ( 30) link_NAG-ASN : bond 0.00555 ( 8) link_NAG-ASN : angle 2.65908 ( 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 277 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8147 (tpt) cc_final: 0.7413 (tpt) REVERT: A 415 MET cc_start: 0.7760 (mmt) cc_final: 0.7443 (mmp) REVERT: B 186 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: B 436 LYS cc_start: 0.7844 (tttm) cc_final: 0.7462 (ttpt) REVERT: B 441 GLU cc_start: 0.8449 (tp30) cc_final: 0.8046 (tm-30) REVERT: B 477 ASN cc_start: 0.7248 (t0) cc_final: 0.6939 (t160) REVERT: C 50 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8517 (ttm) REVERT: C 214 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8641 (tp40) REVERT: C 244 ASP cc_start: 0.7738 (m-30) cc_final: 0.7130 (t0) REVERT: C 316 ASN cc_start: 0.8232 (m-40) cc_final: 0.7704 (m110) REVERT: C 331 TRP cc_start: 0.7574 (m100) cc_final: 0.6918 (m-90) REVERT: C 413 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7192 (tp30) REVERT: D 164 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8136 (mtm180) REVERT: D 330 LYS cc_start: 0.8437 (tttm) cc_final: 0.8081 (ttpt) REVERT: D 387 LYS cc_start: 0.7334 (ptmm) cc_final: 0.6747 (ptpt) REVERT: E 101 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8452 (mp0) REVERT: E 174 ASP cc_start: 0.8069 (t0) cc_final: 0.7658 (t0) REVERT: E 176 GLU cc_start: 0.7031 (pm20) cc_final: 0.6788 (pm20) REVERT: E 183 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: E 471 HIS cc_start: 0.7546 (t-90) cc_final: 0.7090 (t-90) REVERT: F 62 THR cc_start: 0.7641 (m) cc_final: 0.7365 (t) REVERT: G 41 GLU cc_start: 0.8166 (tt0) cc_final: 0.7790 (tt0) outliers start: 45 outliers final: 20 residues processed: 257 average time/residue: 0.6330 time to fit residues: 183.3678 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 : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR 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 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 D residue 292 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2747 > 50: distance: 21 - 27: 24.070 distance: 27 - 28: 16.098 distance: 28 - 29: 13.682 distance: 28 - 31: 7.758 distance: 29 - 30: 19.296 distance: 29 - 35: 10.968 distance: 31 - 32: 24.222 distance: 31 - 33: 12.651 distance: 32 - 34: 20.548 distance: 35 - 36: 13.750 distance: 36 - 37: 43.325 distance: 36 - 39: 10.230 distance: 37 - 38: 16.832 distance: 37 - 43: 36.753 distance: 39 - 40: 26.439 distance: 39 - 41: 17.980 distance: 40 - 42: 14.534 distance: 43 - 44: 23.839 distance: 44 - 45: 17.553 distance: 44 - 47: 13.141 distance: 45 - 46: 23.364 distance: 45 - 50: 9.749 distance: 47 - 48: 18.221 distance: 47 - 49: 10.223 distance: 50 - 51: 5.279 distance: 51 - 52: 15.390 distance: 51 - 54: 18.148 distance: 52 - 53: 5.807 distance: 52 - 57: 22.165 distance: 54 - 55: 15.959 distance: 54 - 56: 20.948 distance: 57 - 58: 9.792 distance: 58 - 59: 10.925 distance: 58 - 61: 3.746 distance: 59 - 60: 11.389 distance: 59 - 67: 6.220 distance: 62 - 63: 7.778 distance: 62 - 64: 5.539 distance: 63 - 65: 9.264 distance: 64 - 66: 7.422 distance: 65 - 66: 7.240 distance: 67 - 68: 13.984 distance: 68 - 69: 20.136 distance: 68 - 71: 10.849 distance: 69 - 70: 15.775 distance: 69 - 78: 14.439 distance: 71 - 72: 8.258 distance: 72 - 73: 7.944 distance: 72 - 74: 4.795 distance: 73 - 75: 6.896 distance: 74 - 76: 6.728 distance: 75 - 77: 3.264 distance: 76 - 77: 3.546 distance: 78 - 79: 18.366 distance: 78 - 84: 20.263 distance: 79 - 80: 36.544 distance: 79 - 82: 8.880 distance: 80 - 81: 45.011 distance: 80 - 85: 43.614 distance: 82 - 83: 25.277 distance: 83 - 84: 18.037 distance: 85 - 86: 15.945 distance: 86 - 87: 23.923 distance: 86 - 89: 18.253 distance: 87 - 88: 16.284 distance: 87 - 96: 12.326 distance: 89 - 90: 19.760 distance: 90 - 91: 21.861 distance: 90 - 92: 6.701 distance: 91 - 93: 23.657 distance: 92 - 94: 12.655 distance: 93 - 95: 23.154 distance: 94 - 95: 24.638 distance: 96 - 97: 7.361 distance: 97 - 98: 17.904 distance: 97 - 100: 3.366 distance: 98 - 99: 10.757 distance: 98 - 104: 15.163 distance: 100 - 101: 10.002 distance: 101 - 102: 6.797 distance: 101 - 103: 13.285 distance: 104 - 105: 12.505 distance: 105 - 106: 4.243 distance: 105 - 108: 5.814 distance: 106 - 113: 8.264 distance: 108 - 109: 8.119 distance: 109 - 110: 6.197 distance: 110 - 111: 4.568 distance: 110 - 112: 7.492