Starting phenix.real_space_refine on Tue Aug 26 20:16:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dms_47014/08_2025/9dms_47014_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dms_47014/08_2025/9dms_47014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dms_47014/08_2025/9dms_47014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dms_47014/08_2025/9dms_47014.map" model { file = "/net/cci-nas-00/data/ceres_data/9dms_47014/08_2025/9dms_47014_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dms_47014/08_2025/9dms_47014_trim.cif" } resolution = 1.92 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= 0.010 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 86 5.16 5 C 13243 2.51 5 N 3253 2.21 5 O 3839 1.98 5 H 19683 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s 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: 40108 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 6433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6433 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "C" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6486 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 380} Chain breaks: 1 Chain: "E" Number of atoms: 6575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6575 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7053 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 6480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6480 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "F" Number of atoms: 3262 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 3240 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 218, 3240 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 bond proxies already assigned to first conformer: 3258 Chain: "G" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3128 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 198} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'CLR': 2, 'NAG': 1, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'CLR': 2, 'NAG': 1, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG F 133 " occ=0.50 ... (42 atoms not shown) pdb="HH22BARG F 133 " occ=0.50 Time building chain proxies: 6.44, per 1000 atoms: 0.16 Number of scatterers: 40108 At special positions: 0 Unit cell: (99.11, 109.395, 231.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 4 15.00 O 3839 8.00 N 3253 7.00 C 13243 6.00 H 19683 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 127 " distance=2.33 Simple disulfide: pdb=" SG CYS F 182 " - pdb=" SG CYS F 238 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 106 " distance=2.04 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA K 3 " - " MAN K 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 " - " BMA L 3 " BETA1-6 " BMA L 3 " - " BMA L 5 " NAG-ASN " NAG B 501 " - " ASN B 66 " " NAG D 502 " - " ASN D 76 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN C 141 " " NAG J 1 " - " ASN E 141 " " NAG K 1 " - " ASN D 143 " " NAG L 1 " - " ASN B 141 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 956.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 30 sheets defined 38.9% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.663A pdb=" N PHE A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.019A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.885A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.783A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.074A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 324' Processing helix chain 'A' and resid 369 through 436 removed outlier: 3.647A pdb=" N TRP A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.965A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 231 removed outlier: 3.948A pdb=" N GLY C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 241 through 264 removed outlier: 4.085A pdb=" N LEU C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.552A pdb=" N ASP C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 removed outlier: 4.034A pdb=" N ASN C 322 " --> pdb=" O ASP C 318 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 323' Processing helix chain 'C' and resid 369 through 435 removed outlier: 3.717A pdb=" N LYS C 373 " --> pdb=" O HIS C 369 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 72 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 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 273 removed outlier: 4.173A pdb=" N ASP E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 328 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.858A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 469 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.508A pdb=" N VAL D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.562A pdb=" N GLY D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.919A pdb=" N LYS D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.685A pdb=" N GLU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 409 through 473 Proline residue: D 416 - end of helix Proline residue: D 458 - end of helix removed outlier: 3.840A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.653A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.090A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.752A pdb=" N GLN B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.817A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 459 removed outlier: 3.642A pdb=" N TRP B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 63 removed outlier: 3.935A pdb=" N TYR F 63 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.507A pdb=" N THR F 122 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 229 through 231 No H-bonds generated for 'chain 'F' and resid 229 through 231' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 202 through 208 removed outlier: 3.623A pdb=" N HIS G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.072A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.072A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN A 36 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N THR A 32 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.756A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A 196 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TYR A 190 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.084A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.084A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 49 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL C 43 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 51 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG C 55 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU C 37 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS C 57 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU C 35 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN C 59 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL C 33 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL C 61 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL C 31 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL C 29 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 31 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.797A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR C 196 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR C 190 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 180 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN C 208 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE C 178 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.035A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.035A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU E 43 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU E 37 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU E 35 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU E 59 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL E 33 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N THR E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL E 31 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N TYR E 63 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL E 29 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.922A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.922A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.922A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 51 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER D 44 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR D 53 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU D 42 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN D 55 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR D 63 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP D 32 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 94 removed outlier: 6.899A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 167 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.634A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.634A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 43 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 51 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU B 37 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY B 57 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL B 35 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASP B 59 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU B 33 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N GLN B 61 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE B 31 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.102A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.102A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 34 through 38 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 removed outlier: 5.966A pdb=" N ARG F 69 " --> pdb=" O TRP F 78 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TRP F 78 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'F' and resid 162 through 166 removed outlier: 3.708A pdb=" N GLY F 181 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR F 218 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 162 through 166 removed outlier: 3.708A pdb=" N GLY F 181 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR F 218 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 193 through 196 removed outlier: 4.298A pdb=" N TYR F 236 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 28 through 31 removed outlier: 6.559A pdb=" N TRP G 53 " --> pdb=" O VAL G 65 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 28 through 31 Processing sheet with id=AD1, first strand: chain 'G' and resid 37 through 42 Processing sheet with id=AD2, first strand: chain 'G' and resid 133 through 137 removed outlier: 5.228A pdb=" N SER G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU G 200 " --> pdb=" O SER G 150 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL G 152 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU G 198 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU G 154 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER G 196 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN G 156 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU G 194 " --> pdb=" O ASN G 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 163 through 169 1116 hydrogen bonds defined for protein. 3132 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: 8.92 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 19664 1.04 - 1.23: 604 1.23 - 1.43: 8055 1.43 - 1.63: 12130 1.63 - 1.82: 133 Bond restraints: 40586 Sorted by residual: bond pdb=" N AARG F 133 " pdb=" CA AARG F 133 " ideal model delta sigma weight residual 1.458 1.524 -0.067 1.33e-02 5.65e+03 2.51e+01 bond pdb=" NZ LYS D 167 " pdb=" HZ3 LYS D 167 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS A 125 " pdb=" HZ3 LYS A 125 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS C 10 " pdb=" HZ2 LYS C 10 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 69 " pdb=" HZ2 LYS B 69 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 40581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.13: 73188 13.13 - 26.27: 6 26.27 - 39.40: 0 39.40 - 52.53: 4 52.53 - 65.67: 2 Bond angle restraints: 73200 Sorted by residual: angle pdb=" CA LYS A 368 " pdb=" N LYS A 368 " pdb=" H LYS A 368 " ideal model delta sigma weight residual 114.00 179.67 -65.67 3.00e+00 1.11e-01 4.79e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 178.07 -64.07 3.00e+00 1.11e-01 4.56e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 166.01 -52.01 3.00e+00 1.11e-01 3.01e+02 angle pdb=" CA GLN D 408 " pdb=" N GLN D 408 " pdb=" H GLN D 408 " ideal model delta sigma weight residual 114.00 163.28 -49.28 3.00e+00 1.11e-01 2.70e+02 angle pdb=" CA GLY E 168 " pdb=" N GLY E 168 " pdb=" H GLY E 168 " ideal model delta sigma weight residual 114.00 162.53 -48.53 3.00e+00 1.11e-01 2.62e+02 ... (remaining 73195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.13: 18848 26.13 - 52.26: 818 52.26 - 78.39: 193 78.39 - 104.51: 49 104.51 - 130.64: 15 Dihedral angle restraints: 19923 sinusoidal: 11199 harmonic: 8724 Sorted by residual: dihedral pdb=" CD ARG F 103 " pdb=" NE ARG F 103 " pdb=" CZ ARG F 103 " pdb=" NH1 ARG F 103 " ideal model delta sinusoidal sigma weight residual 0.00 39.59 -39.59 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CA LYS E 221 " pdb=" C LYS E 221 " pdb=" N PRO E 222 " pdb=" CA PRO E 222 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C29 POV D 503 " pdb="C210 POV D 503 " pdb="C211 POV D 503 " pdb="C212 POV D 503 " ideal model delta sinusoidal sigma weight residual 112.25 -117.11 -130.64 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 19920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 3364 0.948 - 1.895: 0 1.895 - 2.843: 1 2.843 - 3.790: 0 3.790 - 4.738: 1 Chirality restraints: 3366 Sorted by residual: chirality pdb=" C1 BMA L 5 " pdb=" O6 BMA L 3 " pdb=" C2 BMA L 5 " pdb=" O5 BMA L 5 " both_signs ideal model delta sigma weight residual False -2.40 2.34 -4.74 2.00e-02 2.50e+03 5.61e+04 chirality pdb=" C2 BMA L 5 " pdb=" C1 BMA L 5 " pdb=" C3 BMA L 5 " pdb=" O2 BMA L 5 " both_signs ideal model delta sigma weight residual False 2.47 -0.03 2.50 2.00e-01 2.50e+01 1.57e+02 chirality pdb=" C1 MAN L 4 " pdb=" O3 BMA L 3 " pdb=" C2 MAN L 4 " pdb=" O5 MAN L 4 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 3363 not shown) Planarity restraints: 5832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG F 133 " -0.040 9.50e-02 1.11e+02 2.87e-01 1.85e+03 pdb=" NE BARG F 133 " -0.276 2.00e-02 2.50e+03 pdb=" CZ BARG F 133 " -0.069 2.00e-02 2.50e+03 pdb=" NH1BARG F 133 " 0.015 2.00e-02 2.50e+03 pdb=" NH2BARG F 133 " 0.049 2.00e-02 2.50e+03 pdb="HH11BARG F 133 " 0.601 2.00e-02 2.50e+03 pdb="HH12BARG F 133 " -0.507 2.00e-02 2.50e+03 pdb="HH21BARG F 133 " 0.196 2.00e-02 2.50e+03 pdb="HH22BARG F 133 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.281 2.00e-02 2.50e+03 2.43e-01 7.39e+02 pdb=" C7 NAG B 501 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.004 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.417 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " -0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.228 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" C7 NAG I 1 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.324 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.175 2.00e-02 2.50e+03 ... (remaining 5829 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 172 1.95 - 2.61: 44330 2.61 - 3.27: 122569 3.27 - 3.94: 162424 3.94 - 4.60: 249913 Nonbonded interactions: 579408 Sorted by model distance: nonbonded pdb=" HG SER A 1 " pdb=" OH TYR E 63 " model vdw 1.287 2.450 nonbonded pdb=" HH TYR F 91 " pdb=" H ILE F 101 " model vdw 1.292 2.100 nonbonded pdb=" HH TYR E 15 " pdb=" H TRP E 86 " model vdw 1.292 2.100 nonbonded pdb="HD22 ASN B 301 " pdb=" HB3 CYS B 438 " model vdw 1.378 2.270 nonbonded pdb=" HH TYR B 15 " pdb=" H TRP B 86 " model vdw 1.498 2.100 ... (remaining 579403 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 436) selection = (chain 'C' and (resid 1 through 330 or resid 369 through 436)) } ncs_group { reference = (chain 'H' and resid 1 through 4) selection = (chain 'I' and resid 1 through 4) selection = (chain 'J' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) } 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: 4.080 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: 0.170 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 32.210 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 20940 Z= 0.342 Angle : 0.912 25.908 28608 Z= 0.482 Chirality : 0.108 4.738 3366 Planarity : 0.012 0.299 3503 Dihedral : 17.017 130.642 8304 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.88 % Rotamer: Outliers : 0.31 % Allowed : 8.45 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.26 (0.17), residues: 2451 helix: 2.34 (0.18), residues: 797 sheet: 0.05 (0.20), residues: 624 loop : 0.26 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 125 TYR 0.014 0.001 TYR G 159 PHE 0.021 0.002 PHE D 294 TRP 0.013 0.001 TRP B 55 HIS 0.011 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00566 (20903) covalent geometry : angle 0.88274 (28507) SS BOND : bond 0.09410 ( 10) SS BOND : angle 4.60643 ( 20) hydrogen bonds : bond 0.12200 ( 1006) hydrogen bonds : angle 5.71339 ( 3132) link_ALPHA1-3 : bond 0.00456 ( 5) link_ALPHA1-3 : angle 1.71409 ( 15) link_ALPHA1-6 : bond 0.00193 ( 4) link_ALPHA1-6 : angle 1.07917 ( 12) link_BETA1-4 : bond 0.00461 ( 10) link_BETA1-4 : angle 1.77835 ( 30) link_BETA1-6 : bond 0.00114 ( 1) link_BETA1-6 : angle 0.89668 ( 3) link_NAG-ASN : bond 0.13416 ( 7) link_NAG-ASN : angle 6.89239 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 244 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.8946 (mtt) cc_final: 0.8740 (mtt) REVERT: C 329 MET cc_start: 0.5955 (tmm) cc_final: 0.5302 (mtm) REVERT: D 470 GLN cc_start: 0.8796 (mm110) cc_final: 0.8571 (mm110) REVERT: G 153 CYS cc_start: 0.3589 (OUTLIER) cc_final: 0.2356 (t) outliers start: 7 outliers final: 4 residues processed: 250 average time/residue: 1.3977 time to fit residues: 390.9688 Evaluate side-chains 228 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 223 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain G residue 153 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 297 ASN A 306 HIS E 318 GLN E 325 GLN B 272 GLN B 301 ASN B 408 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN G 45 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108544 restraints weight = 56942.645| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.41 r_work: 0.3197 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20940 Z= 0.149 Angle : 0.594 8.514 28608 Z= 0.300 Chirality : 0.044 0.234 3366 Planarity : 0.005 0.077 3503 Dihedral : 12.611 120.492 3677 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 0.89 % Allowed : 8.72 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.43 (0.17), residues: 2451 helix: 2.45 (0.18), residues: 803 sheet: 0.23 (0.20), residues: 630 loop : 0.31 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 125 TYR 0.011 0.001 TYR D 119 PHE 0.018 0.002 PHE E 267 TRP 0.011 0.001 TRP D 176 HIS 0.009 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00314 (20903) covalent geometry : angle 0.57959 (28507) SS BOND : bond 0.00496 ( 10) SS BOND : angle 1.17294 ( 20) hydrogen bonds : bond 0.05065 ( 1006) hydrogen bonds : angle 4.68119 ( 3132) link_ALPHA1-3 : bond 0.00936 ( 5) link_ALPHA1-3 : angle 3.30091 ( 15) link_ALPHA1-6 : bond 0.00937 ( 4) link_ALPHA1-6 : angle 1.81991 ( 12) link_BETA1-4 : bond 0.00542 ( 10) link_BETA1-4 : angle 2.36860 ( 30) link_BETA1-6 : bond 0.00495 ( 1) link_BETA1-6 : angle 2.67880 ( 3) link_NAG-ASN : bond 0.00498 ( 7) link_NAG-ASN : angle 2.33105 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: C 329 MET cc_start: 0.6022 (tmm) cc_final: 0.5453 (ttp) REVERT: C 416 LEU cc_start: 0.8677 (tp) cc_final: 0.8380 (tt) REVERT: D 28 GLU cc_start: 0.8220 (mm-30) cc_final: 0.8005 (pm20) REVERT: D 437 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7663 (tp30) REVERT: B 196 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7887 (mtt90) REVERT: F 44 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: G 153 CYS cc_start: 0.3492 (OUTLIER) cc_final: 0.1780 (t) outliers start: 20 outliers final: 10 residues processed: 238 average time/residue: 1.3634 time to fit residues: 362.7669 Evaluate side-chains 230 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain G residue 153 CYS Chi-restraints excluded: chain G residue 154 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 198 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS C 186 HIS B 272 GLN B 408 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.149748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106632 restraints weight = 55356.010| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.50 r_work: 0.3162 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20940 Z= 0.161 Angle : 0.591 6.180 28608 Z= 0.304 Chirality : 0.045 0.259 3366 Planarity : 0.005 0.064 3503 Dihedral : 10.956 86.122 3674 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Rotamer: Outliers : 1.07 % Allowed : 8.72 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.41 (0.17), residues: 2451 helix: 2.43 (0.18), residues: 804 sheet: 0.28 (0.20), residues: 635 loop : 0.25 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 81 TYR 0.013 0.002 TYR G 21 PHE 0.020 0.002 PHE D 291 TRP 0.015 0.001 TRP D 176 HIS 0.010 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00339 (20903) covalent geometry : angle 0.57915 (28507) SS BOND : bond 0.00473 ( 10) SS BOND : angle 1.26778 ( 20) hydrogen bonds : bond 0.05287 ( 1006) hydrogen bonds : angle 4.64184 ( 3132) link_ALPHA1-3 : bond 0.00899 ( 5) link_ALPHA1-3 : angle 1.72025 ( 15) link_ALPHA1-6 : bond 0.00895 ( 4) link_ALPHA1-6 : angle 1.93657 ( 12) link_BETA1-4 : bond 0.00669 ( 10) link_BETA1-4 : angle 2.54975 ( 30) link_BETA1-6 : bond 0.00520 ( 1) link_BETA1-6 : angle 2.87001 ( 3) link_NAG-ASN : bond 0.00308 ( 7) link_NAG-ASN : angle 2.08047 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8216 (tt) REVERT: C 324 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.5501 (mtt) REVERT: C 329 MET cc_start: 0.5963 (tmm) cc_final: 0.5474 (ttp) REVERT: C 416 LEU cc_start: 0.8694 (tp) cc_final: 0.8392 (tt) REVERT: D 60 HIS cc_start: 0.9458 (OUTLIER) cc_final: 0.8528 (m-70) REVERT: D 301 MET cc_start: 0.8586 (mtp) cc_final: 0.8354 (mtp) REVERT: D 446 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8127 (mtp85) REVERT: D 475 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: B 196 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7890 (mtt90) REVERT: F 44 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: F 190 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7498 (mt-10) outliers start: 24 outliers final: 15 residues processed: 245 average time/residue: 1.3134 time to fit residues: 361.1648 Evaluate side-chains 248 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain G residue 153 CYS Chi-restraints excluded: chain G residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 217 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN D 13 GLN B 272 GLN B 408 ASN F 116 ASN G 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105977 restraints weight = 53632.256| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.50 r_work: 0.3154 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20940 Z= 0.182 Angle : 0.595 8.774 28608 Z= 0.309 Chirality : 0.045 0.248 3366 Planarity : 0.005 0.067 3503 Dihedral : 10.552 83.927 3674 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Rotamer: Outliers : 1.34 % Allowed : 8.41 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.37 (0.17), residues: 2451 helix: 2.40 (0.18), residues: 803 sheet: 0.28 (0.20), residues: 637 loop : 0.22 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 81 TYR 0.013 0.002 TYR A 198 PHE 0.023 0.002 PHE E 267 TRP 0.016 0.002 TRP D 176 HIS 0.010 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00388 (20903) covalent geometry : angle 0.58257 (28507) SS BOND : bond 0.00562 ( 10) SS BOND : angle 1.37686 ( 20) hydrogen bonds : bond 0.05394 ( 1006) hydrogen bonds : angle 4.67304 ( 3132) link_ALPHA1-3 : bond 0.00854 ( 5) link_ALPHA1-3 : angle 2.40803 ( 15) link_ALPHA1-6 : bond 0.00866 ( 4) link_ALPHA1-6 : angle 2.12706 ( 12) link_BETA1-4 : bond 0.00573 ( 10) link_BETA1-4 : angle 2.44839 ( 30) link_BETA1-6 : bond 0.00379 ( 1) link_BETA1-6 : angle 1.69527 ( 3) link_NAG-ASN : bond 0.00358 ( 7) link_NAG-ASN : angle 2.15857 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 231 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8706 (mm) REVERT: A 274 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8252 (tt) REVERT: C 324 MET cc_start: 0.5735 (OUTLIER) cc_final: 0.5525 (mtt) REVERT: C 329 MET cc_start: 0.6065 (tmm) cc_final: 0.5556 (ttp) REVERT: C 416 LEU cc_start: 0.8679 (tp) cc_final: 0.8360 (tt) REVERT: D 60 HIS cc_start: 0.9470 (OUTLIER) cc_final: 0.8447 (m-70) REVERT: D 301 MET cc_start: 0.8591 (mtp) cc_final: 0.8363 (mtp) REVERT: D 475 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: B 196 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7832 (mtt90) REVERT: F 44 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7520 (mp10) outliers start: 30 outliers final: 15 residues processed: 249 average time/residue: 1.3327 time to fit residues: 374.3384 Evaluate side-chains 245 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain G residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 239 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN B 272 GLN B 408 ASN F 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107474 restraints weight = 52883.905| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.37 r_work: 0.3180 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20940 Z= 0.128 Angle : 0.536 4.978 28608 Z= 0.276 Chirality : 0.043 0.253 3366 Planarity : 0.004 0.043 3503 Dihedral : 9.934 83.525 3673 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.76 % Favored : 98.20 % Rotamer: Outliers : 1.39 % Allowed : 8.36 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.49 (0.17), residues: 2451 helix: 2.54 (0.18), residues: 803 sheet: 0.32 (0.20), residues: 633 loop : 0.25 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.011 0.001 TYR D 119 PHE 0.017 0.001 PHE C 284 TRP 0.012 0.001 TRP D 176 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00267 (20903) covalent geometry : angle 0.52623 (28507) SS BOND : bond 0.00321 ( 10) SS BOND : angle 1.15428 ( 20) hydrogen bonds : bond 0.04845 ( 1006) hydrogen bonds : angle 4.49639 ( 3132) link_ALPHA1-3 : bond 0.00889 ( 5) link_ALPHA1-3 : angle 1.82865 ( 15) link_ALPHA1-6 : bond 0.00873 ( 4) link_ALPHA1-6 : angle 1.77642 ( 12) link_BETA1-4 : bond 0.00391 ( 10) link_BETA1-4 : angle 2.07193 ( 30) link_BETA1-6 : bond 0.00367 ( 1) link_BETA1-6 : angle 1.98780 ( 3) link_NAG-ASN : bond 0.00169 ( 7) link_NAG-ASN : angle 1.93739 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8724 (mm) REVERT: A 274 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8231 (tt) REVERT: A 407 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7933 (t0) REVERT: C 324 MET cc_start: 0.5735 (OUTLIER) cc_final: 0.5525 (mtt) REVERT: C 329 MET cc_start: 0.6097 (tmm) cc_final: 0.5600 (ttp) REVERT: C 416 LEU cc_start: 0.8701 (tp) cc_final: 0.8396 (tt) REVERT: D 60 HIS cc_start: 0.9442 (OUTLIER) cc_final: 0.8488 (m-70) REVERT: D 301 MET cc_start: 0.8588 (mtp) cc_final: 0.8353 (mtp) REVERT: D 475 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: B 196 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7850 (mtt90) REVERT: F 44 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: G 153 CYS cc_start: 0.3689 (OUTLIER) cc_final: 0.1476 (t) outliers start: 31 outliers final: 14 residues processed: 253 average time/residue: 1.2953 time to fit residues: 370.8497 Evaluate side-chains 249 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain G residue 153 CYS Chi-restraints excluded: chain G residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 230 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 91 optimal weight: 0.0050 chunk 129 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 ASN D 13 GLN B 272 GLN B 408 ASN F 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108558 restraints weight = 53851.744| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.39 r_work: 0.3195 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20940 Z= 0.111 Angle : 0.513 6.007 28608 Z= 0.263 Chirality : 0.043 0.251 3366 Planarity : 0.004 0.041 3503 Dihedral : 9.300 84.269 3673 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 1.21 % Allowed : 8.72 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.58 (0.17), residues: 2451 helix: 2.68 (0.18), residues: 803 sheet: 0.33 (0.20), residues: 626 loop : 0.29 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 125 TYR 0.010 0.001 TYR D 119 PHE 0.015 0.001 PHE C 284 TRP 0.009 0.001 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00235 (20903) covalent geometry : angle 0.50340 (28507) SS BOND : bond 0.00249 ( 10) SS BOND : angle 1.05540 ( 20) hydrogen bonds : bond 0.04478 ( 1006) hydrogen bonds : angle 4.35559 ( 3132) link_ALPHA1-3 : bond 0.00845 ( 5) link_ALPHA1-3 : angle 2.05261 ( 15) link_ALPHA1-6 : bond 0.00993 ( 4) link_ALPHA1-6 : angle 1.84736 ( 12) link_BETA1-4 : bond 0.00351 ( 10) link_BETA1-4 : angle 1.90024 ( 30) link_BETA1-6 : bond 0.00368 ( 1) link_BETA1-6 : angle 1.76809 ( 3) link_NAG-ASN : bond 0.00092 ( 7) link_NAG-ASN : angle 1.77124 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8716 (mm) REVERT: A 274 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8150 (tt) REVERT: A 301 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7966 (mtp85) REVERT: C 324 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.5525 (mtt) REVERT: C 329 MET cc_start: 0.6162 (tmm) cc_final: 0.5613 (ttp) REVERT: D 60 HIS cc_start: 0.9406 (OUTLIER) cc_final: 0.8368 (m-70) REVERT: D 301 MET cc_start: 0.8609 (mtp) cc_final: 0.8378 (mtp) REVERT: D 475 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: B 196 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7832 (mtt90) REVERT: F 44 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: G 216 THR cc_start: 0.5798 (OUTLIER) cc_final: 0.5571 (t) outliers start: 27 outliers final: 13 residues processed: 253 average time/residue: 1.3358 time to fit residues: 382.0806 Evaluate side-chains 247 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 150 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN B 272 GLN B 408 ASN F 116 ASN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105936 restraints weight = 55810.867| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.40 r_work: 0.3158 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20940 Z= 0.169 Angle : 0.573 5.919 28608 Z= 0.297 Chirality : 0.044 0.234 3366 Planarity : 0.005 0.057 3503 Dihedral : 9.535 84.358 3673 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.24 % Rotamer: Outliers : 1.30 % Allowed : 8.90 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.50 (0.17), residues: 2451 helix: 2.57 (0.18), residues: 803 sheet: 0.33 (0.20), residues: 635 loop : 0.25 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 81 TYR 0.014 0.002 TYR E 225 PHE 0.024 0.002 PHE E 267 TRP 0.016 0.001 TRP D 176 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00360 (20903) covalent geometry : angle 0.56074 (28507) SS BOND : bond 0.00537 ( 10) SS BOND : angle 1.45138 ( 20) hydrogen bonds : bond 0.05148 ( 1006) hydrogen bonds : angle 4.54623 ( 3132) link_ALPHA1-3 : bond 0.00744 ( 5) link_ALPHA1-3 : angle 1.95425 ( 15) link_ALPHA1-6 : bond 0.01162 ( 4) link_ALPHA1-6 : angle 2.45635 ( 12) link_BETA1-4 : bond 0.00457 ( 10) link_BETA1-4 : angle 2.32347 ( 30) link_BETA1-6 : bond 0.00433 ( 1) link_BETA1-6 : angle 1.99961 ( 3) link_NAG-ASN : bond 0.00282 ( 7) link_NAG-ASN : angle 2.08600 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8713 (mm) REVERT: A 274 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8258 (tt) REVERT: A 407 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7941 (t0) REVERT: C 329 MET cc_start: 0.6161 (tmm) cc_final: 0.5604 (ttp) REVERT: D 60 HIS cc_start: 0.9452 (OUTLIER) cc_final: 0.8514 (m-70) REVERT: D 475 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: B 196 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7807 (mtt90) REVERT: B 260 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8727 (mt) REVERT: F 44 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: F 118 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6623 (mtt-85) REVERT: G 216 THR cc_start: 0.5768 (OUTLIER) cc_final: 0.5528 (t) outliers start: 29 outliers final: 14 residues processed: 241 average time/residue: 1.2849 time to fit residues: 348.7713 Evaluate side-chains 245 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 216 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 207 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 174 optimal weight: 0.0970 chunk 173 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 408 ASN F 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106620 restraints weight = 53422.027| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.37 r_work: 0.3167 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20940 Z= 0.150 Angle : 0.553 6.186 28608 Z= 0.286 Chirality : 0.043 0.232 3366 Planarity : 0.005 0.052 3503 Dihedral : 9.406 84.357 3669 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.84 % Favored : 98.12 % Rotamer: Outliers : 1.16 % Allowed : 9.08 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.51 (0.17), residues: 2451 helix: 2.58 (0.18), residues: 803 sheet: 0.34 (0.20), residues: 635 loop : 0.24 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 81 TYR 0.014 0.001 TYR E 225 PHE 0.020 0.002 PHE E 267 TRP 0.014 0.001 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00317 (20903) covalent geometry : angle 0.54090 (28507) SS BOND : bond 0.00435 ( 10) SS BOND : angle 1.25003 ( 20) hydrogen bonds : bond 0.04988 ( 1006) hydrogen bonds : angle 4.51674 ( 3132) link_ALPHA1-3 : bond 0.00731 ( 5) link_ALPHA1-3 : angle 1.86473 ( 15) link_ALPHA1-6 : bond 0.01149 ( 4) link_ALPHA1-6 : angle 2.47319 ( 12) link_BETA1-4 : bond 0.00402 ( 10) link_BETA1-4 : angle 2.24265 ( 30) link_BETA1-6 : bond 0.00331 ( 1) link_BETA1-6 : angle 2.16146 ( 3) link_NAG-ASN : bond 0.00192 ( 7) link_NAG-ASN : angle 1.98228 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8258 (tt) REVERT: A 407 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7905 (t0) REVERT: C 329 MET cc_start: 0.6151 (tmm) cc_final: 0.5582 (ttp) REVERT: C 416 LEU cc_start: 0.8708 (tp) cc_final: 0.8397 (tt) REVERT: D 60 HIS cc_start: 0.9455 (OUTLIER) cc_final: 0.8528 (m-70) REVERT: D 475 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: B 260 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8740 (mt) REVERT: F 44 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: F 118 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6596 (mtt-85) REVERT: G 153 CYS cc_start: 0.2578 (OUTLIER) cc_final: 0.1484 (t) REVERT: G 216 THR cc_start: 0.5750 (OUTLIER) cc_final: 0.5508 (t) outliers start: 26 outliers final: 15 residues processed: 242 average time/residue: 1.3539 time to fit residues: 370.0950 Evaluate side-chains 246 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain G residue 153 CYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 216 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 82 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 180 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 408 ASN F 116 ASN G 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106742 restraints weight = 53545.170| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.37 r_work: 0.3169 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20940 Z= 0.142 Angle : 0.552 6.307 28608 Z= 0.285 Chirality : 0.043 0.231 3366 Planarity : 0.004 0.046 3503 Dihedral : 9.302 84.505 3669 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 1.12 % Allowed : 9.44 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.53 (0.17), residues: 2451 helix: 2.60 (0.18), residues: 803 sheet: 0.34 (0.20), residues: 635 loop : 0.26 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.013 0.001 TYR E 225 PHE 0.019 0.002 PHE E 267 TRP 0.013 0.001 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00301 (20903) covalent geometry : angle 0.54064 (28507) SS BOND : bond 0.00455 ( 10) SS BOND : angle 1.09155 ( 20) hydrogen bonds : bond 0.04927 ( 1006) hydrogen bonds : angle 4.48457 ( 3132) link_ALPHA1-3 : bond 0.00735 ( 5) link_ALPHA1-3 : angle 1.79622 ( 15) link_ALPHA1-6 : bond 0.01127 ( 4) link_ALPHA1-6 : angle 2.45980 ( 12) link_BETA1-4 : bond 0.00382 ( 10) link_BETA1-4 : angle 2.23323 ( 30) link_BETA1-6 : bond 0.00310 ( 1) link_BETA1-6 : angle 2.18403 ( 3) link_NAG-ASN : bond 0.00192 ( 7) link_NAG-ASN : angle 1.99028 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 407 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7917 (t0) REVERT: C 329 MET cc_start: 0.6161 (tmm) cc_final: 0.5570 (ttp) REVERT: C 416 LEU cc_start: 0.8706 (tp) cc_final: 0.8396 (tt) REVERT: D 60 HIS cc_start: 0.9449 (OUTLIER) cc_final: 0.8547 (m-70) REVERT: D 475 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: B 260 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8740 (mt) REVERT: F 44 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: F 118 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6608 (mtt-85) REVERT: G 153 CYS cc_start: 0.2764 (OUTLIER) cc_final: 0.1605 (t) REVERT: G 216 THR cc_start: 0.5734 (OUTLIER) cc_final: 0.5491 (t) outliers start: 25 outliers final: 14 residues processed: 241 average time/residue: 1.3569 time to fit residues: 371.0858 Evaluate side-chains 245 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain G residue 153 CYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 217 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 475 GLN B 272 GLN B 408 ASN F 116 ASN G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.149712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106998 restraints weight = 53434.839| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.37 r_work: 0.3171 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20940 Z= 0.137 Angle : 0.543 6.840 28608 Z= 0.281 Chirality : 0.043 0.227 3366 Planarity : 0.004 0.044 3503 Dihedral : 9.215 84.453 3669 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 1.07 % Allowed : 9.39 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.55 (0.17), residues: 2451 helix: 2.62 (0.18), residues: 803 sheet: 0.38 (0.20), residues: 627 loop : 0.25 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.015 0.001 TYR E 225 PHE 0.018 0.002 PHE E 267 TRP 0.013 0.001 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00291 (20903) covalent geometry : angle 0.53207 (28507) SS BOND : bond 0.00400 ( 10) SS BOND : angle 1.13158 ( 20) hydrogen bonds : bond 0.04849 ( 1006) hydrogen bonds : angle 4.46207 ( 3132) link_ALPHA1-3 : bond 0.00715 ( 5) link_ALPHA1-3 : angle 1.78073 ( 15) link_ALPHA1-6 : bond 0.01117 ( 4) link_ALPHA1-6 : angle 2.40970 ( 12) link_BETA1-4 : bond 0.00369 ( 10) link_BETA1-4 : angle 2.17839 ( 30) link_BETA1-6 : bond 0.00323 ( 1) link_BETA1-6 : angle 2.12912 ( 3) link_NAG-ASN : bond 0.00174 ( 7) link_NAG-ASN : angle 1.94140 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8226 (tt) REVERT: A 407 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7918 (t0) REVERT: C 329 MET cc_start: 0.6174 (tmm) cc_final: 0.5568 (ttp) REVERT: C 416 LEU cc_start: 0.8702 (tp) cc_final: 0.8391 (tt) REVERT: D 60 HIS cc_start: 0.9446 (OUTLIER) cc_final: 0.8518 (m-70) REVERT: B 260 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8738 (mt) REVERT: F 44 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: F 118 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6589 (mtt-85) REVERT: G 153 CYS cc_start: 0.2496 (OUTLIER) cc_final: 0.1459 (t) REVERT: G 216 THR cc_start: 0.5824 (OUTLIER) cc_final: 0.5574 (t) outliers start: 24 outliers final: 13 residues processed: 246 average time/residue: 1.2684 time to fit residues: 352.8431 Evaluate side-chains 245 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain G residue 153 CYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 209 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 190 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN C 408 HIS B 272 GLN B 408 ASN F 116 ASN G 35 GLN G 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105197 restraints weight = 55197.655| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.38 r_work: 0.3145 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20940 Z= 0.196 Angle : 0.606 6.317 28608 Z= 0.315 Chirality : 0.045 0.219 3366 Planarity : 0.005 0.072 3503 Dihedral : 9.432 83.069 3669 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Rotamer: Outliers : 1.12 % Allowed : 9.44 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.67 % 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: 1.42 (0.17), residues: 2451 helix: 2.46 (0.18), residues: 803 sheet: 0.34 (0.20), residues: 636 loop : 0.19 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 81 TYR 0.020 0.002 TYR E 225 PHE 0.027 0.002 PHE E 267 TRP 0.018 0.002 TRP D 176 HIS 0.008 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00424 (20903) covalent geometry : angle 0.59322 (28507) SS BOND : bond 0.00617 ( 10) SS BOND : angle 1.53084 ( 20) hydrogen bonds : bond 0.05478 ( 1006) hydrogen bonds : angle 4.65041 ( 3132) link_ALPHA1-3 : bond 0.00692 ( 5) link_ALPHA1-3 : angle 1.79873 ( 15) link_ALPHA1-6 : bond 0.01133 ( 4) link_ALPHA1-6 : angle 2.43272 ( 12) link_BETA1-4 : bond 0.00522 ( 10) link_BETA1-4 : angle 2.59190 ( 30) link_BETA1-6 : bond 0.00289 ( 1) link_BETA1-6 : angle 2.27416 ( 3) link_NAG-ASN : bond 0.00331 ( 7) link_NAG-ASN : angle 2.24469 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20353.86 seconds wall clock time: 343 minutes 2.92 seconds (20582.92 seconds total)