Starting phenix.real_space_refine on Thu Mar 5 00:18:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nx2_49899/03_2026/9nx2_49899.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nx2_49899/03_2026/9nx2_49899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nx2_49899/03_2026/9nx2_49899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nx2_49899/03_2026/9nx2_49899.map" model { file = "/net/cci-nas-00/data/ceres_data/9nx2_49899/03_2026/9nx2_49899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nx2_49899/03_2026/9nx2_49899.cif" } resolution = 2.96 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 11131 2.51 5 N 2721 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17103 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3138 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 365} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 365} Chain breaks: 1 bond proxies already assigned to first conformer: 3216 Chain: "B" Number of atoms: 3477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3462 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 398} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3462 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 398} Chain breaks: 1 bond proxies already assigned to first conformer: 3539 Chain: "C" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 384} Chain breaks: 1 Chain: "D" Number of atoms: 3248 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3237 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 399, 3237 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 bond proxies already assigned to first conformer: 3310 Chain: "E" Number of atoms: 3344 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 387} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 387} Chain breaks: 1 bond proxies already assigned to first conformer: 3372 Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "M" 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: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'CCE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'CCE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N APHE D 227 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 227 " occ=0.50 residue: pdb=" N AARG E 125 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 125 " occ=0.50 residue: pdb=" N AMET E 299 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET E 299 " occ=0.50 Time building chain proxies: 6.32, per 1000 atoms: 0.37 Number of scatterers: 17103 At special positions: 0 Unit cell: (105.512, 113.36, 174.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 3156 8.00 N 2721 7.00 C 11131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 8 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 12 " distance=2.03 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 8 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 12 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-2 " MAN L 4 " - " MAN L 5 " ALPHA1-3 " BMA L 3 " - " MAN L 7 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " " BMA I 3 " - " MAN I 4 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 6 " " BMA M 3 " - " MAN M 4 " " MAN M 4 " - " MAN M 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG E 501 " - " ASN E 68 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN B 143 " " NAG J 1 " - " ASN B 208 " " NAG K 1 " - " ASN C 141 " " NAG L 1 " - " ASN D 141 " " NAG M 1 " - " ASN E 141 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3984 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 20 sheets defined 39.8% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.543A pdb=" N CYS A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 241 through 261 Processing helix chain 'A' and resid 272 through 300 removed outlier: 3.616A pdb=" N HIS A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.627A pdb=" N VAL A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 419 removed outlier: 4.164A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.550A pdb=" N CYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.515A pdb=" N LEU B 245 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 Processing helix chain 'B' and resid 286 through 314 removed outlier: 3.668A pdb=" N PHE B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 418 through 474 removed outlier: 3.638A pdb=" N GLU B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.689A pdb=" N CYS C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 247 through 267 removed outlier: 3.597A pdb=" N LEU C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 306 removed outlier: 3.697A pdb=" N HIS C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.727A pdb=" N ARG C 319 " --> pdb=" O PRO C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.969A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 458 removed outlier: 4.414A pdb=" N VAL C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.645A pdb=" N ASP D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL D 85 " --> pdb=" O SER D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'D' and resid 212 through 229 removed outlier: 4.878A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 230 through 235 removed outlier: 4.002A pdb=" N PHE D 233 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 262 removed outlier: 3.695A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 300 removed outlier: 3.676A pdb=" N LYS D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.808A pdb=" N ASP D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 324 removed outlier: 4.171A pdb=" N ASN D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 323 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 324' Processing helix chain 'D' and resid 369 through 424 removed outlier: 4.137A pdb=" N LYS D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS D 412 " --> pdb=" O HIS D 408 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 424 " --> pdb=" O ILE D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 427 No H-bonds generated for 'chain 'D' and resid 425 through 427' Processing helix chain 'D' and resid 428 through 434 removed outlier: 3.733A pdb=" N SER D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 removed outlier: 4.406A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 removed outlier: 4.085A pdb=" N SER E 66 " --> pdb=" O TYR E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.665A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 Processing helix chain 'E' and resid 281 through 308 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'E' and resid 410 through 432 removed outlier: 3.628A pdb=" N SER E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL E 417 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU E 418 " --> pdb=" O LYS E 414 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 419 " --> pdb=" O SER E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 470 removed outlier: 3.637A pdb=" N GLU E 438 " --> pdb=" O GLY E 434 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA E 450 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.225A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.225A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 42 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ARG A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLN A 36 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ILE A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N THR A 32 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.463A pdb=" N TYR A 198 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP A 200 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY A 183 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N HIS A 204 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR A 181 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 206 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 7.044A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 61 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 129 removed outlier: 7.044A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 61 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ILE B 178 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 37 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.616A pdb=" N ILE B 221 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.616A pdb=" N ILE B 221 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.380A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 127 removed outlier: 3.508A pdb=" N ALA C 122 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 54 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N VAL C 174 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 35 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.532A pdb=" N LYS C 147 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.532A pdb=" N LYS C 147 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 206 " --> pdb=" O ASN C 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 78 removed outlier: 3.952A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 78 removed outlier: 3.952A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 49 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER D 42 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.554A pdb=" N GLY D 147 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 80 removed outlier: 4.019A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP E 60 " --> pdb=" O MET E 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 80 removed outlier: 4.019A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP E 60 " --> pdb=" O MET E 116 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.351A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.351A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 830 hydrogen bonds defined for protein. 2416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5210 1.34 - 1.47: 4393 1.47 - 1.59: 7795 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 17548 Sorted by residual: bond pdb=" C5 CCE D 601 " pdb=" O4 CCE D 601 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" C1 MAN H 5 " pdb=" C2 MAN H 5 " ideal model delta sigma weight residual 1.526 1.573 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C5 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C1 MAN L 6 " pdb=" C2 MAN L 6 " ideal model delta sigma weight residual 1.526 1.570 -0.044 2.00e-02 2.50e+03 4.79e+00 ... (remaining 17543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 23529 1.78 - 3.57: 325 3.57 - 5.35: 66 5.35 - 7.14: 16 7.14 - 8.92: 5 Bond angle restraints: 23941 Sorted by residual: angle pdb=" N GLU E 183 " pdb=" CA GLU E 183 " pdb=" C GLU E 183 " ideal model delta sigma weight residual 114.04 109.81 4.23 1.24e+00 6.50e-01 1.16e+01 angle pdb=" C3 MAN L 4 " pdb=" C2 MAN L 4 " pdb=" O2 MAN L 4 " ideal model delta sigma weight residual 111.77 102.85 8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" N6 CCE D 601 " pdb=" C5 CCE D 601 " pdb=" O4 CCE D 601 " ideal model delta sigma weight residual 110.79 119.34 -8.55 3.00e+00 1.11e-01 8.12e+00 angle pdb=" C3 CCE D 601 " pdb=" C2 CCE D 601 " pdb=" N1 CCE D 601 " ideal model delta sigma weight residual 116.95 109.01 7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" N VAL D 103 " pdb=" CA VAL D 103 " pdb=" C VAL D 103 " ideal model delta sigma weight residual 111.90 109.80 2.10 8.10e-01 1.52e+00 6.70e+00 ... (remaining 23936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.93: 10371 23.93 - 47.85: 297 47.85 - 71.78: 61 71.78 - 95.71: 46 95.71 - 119.64: 32 Dihedral angle restraints: 10807 sinusoidal: 4687 harmonic: 6120 Sorted by residual: dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual 180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PHE B 473 " pdb=" C PHE B 473 " pdb=" N VAL B 474 " pdb=" CA VAL B 474 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual 180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 10804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2407 0.061 - 0.121: 403 0.121 - 0.182: 25 0.182 - 0.243: 1 0.243 - 0.303: 6 Chirality restraints: 2842 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2839 not shown) Planarity restraints: 2944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 149 " -0.007 2.00e-02 2.50e+03 2.16e-02 1.17e+01 pdb=" CG TRP D 149 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP D 149 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP D 149 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 149 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP D 149 " -0.062 2.00e-02 2.50e+03 pdb=" CE3 TRP D 149 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 149 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 149 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 149 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 20 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO E 21 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 21 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 21 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 327 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO C 328 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 328 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 328 " -0.022 5.00e-02 4.00e+02 ... (remaining 2941 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2688 2.77 - 3.30: 15387 3.30 - 3.83: 25772 3.83 - 4.37: 28864 4.37 - 4.90: 53187 Nonbonded interactions: 125898 Sorted by model distance: nonbonded pdb=" OD1 ASP A 111 " pdb=" OG1 THR A 113 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR C 24 " pdb=" OD1 ASP C 27 " model vdw 2.247 3.040 nonbonded pdb=" O ALA C 22 " pdb=" OG SER D 1 " model vdw 2.273 3.040 nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.274 3.040 nonbonded pdb=" O4 MAN L 6 " pdb=" O6 MAN L 6 " model vdw 2.307 3.040 ... (remaining 125893 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 226 or resid 228 through 301 or resid 303 throug \ h 331 or resid 368 through 601)) selection = (chain 'D' and (resid 1 through 226 or resid 228 through 301 or resid 303 throug \ h 331 or resid 368 through 421 or resid 601)) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'M' } 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=0.30 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.200 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.004 0.108 17589 Z= 0.177 Angle : 0.584 8.919 24047 Z= 0.276 Chirality : 0.045 0.303 2842 Planarity : 0.004 0.042 2936 Dihedral : 14.838 119.637 6790 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.36 % Allowed : 6.31 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 2042 helix: 3.40 (0.19), residues: 719 sheet: 0.66 (0.26), residues: 438 loop : -1.42 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 6 TYR 0.010 0.001 TYR E 15 PHE 0.014 0.001 PHE D 284 TRP 0.062 0.001 TRP D 149 HIS 0.003 0.000 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00354 (17548) covalent geometry : angle 0.56915 (23941) SS BOND : bond 0.00613 ( 11) SS BOND : angle 1.40247 ( 22) hydrogen bonds : bond 0.19117 ( 759) hydrogen bonds : angle 5.38212 ( 2416) Misc. bond : bond 0.00336 ( 2) link_ALPHA1-2 : bond 0.00269 ( 1) link_ALPHA1-2 : angle 3.03704 ( 3) link_ALPHA1-3 : bond 0.00456 ( 1) link_ALPHA1-3 : angle 2.26672 ( 3) link_ALPHA1-6 : bond 0.00902 ( 7) link_ALPHA1-6 : angle 2.32980 ( 21) link_BETA1-4 : bond 0.00683 ( 11) link_BETA1-4 : angle 2.34155 ( 33) link_NAG-ASN : bond 0.00480 ( 8) link_NAG-ASN : angle 1.72656 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: B 272 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8248 (mt) REVERT: C 397 LEU cc_start: 0.2439 (OUTLIER) cc_final: 0.2188 (tm) outliers start: 63 outliers final: 9 residues processed: 249 average time/residue: 0.5080 time to fit residues: 143.0145 Evaluate side-chains 111 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 140 GLN B 451 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.055180 restraints weight = 115005.017| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 5.40 r_work: 0.2556 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17589 Z= 0.140 Angle : 0.608 9.103 24047 Z= 0.304 Chirality : 0.045 0.262 2842 Planarity : 0.005 0.041 2936 Dihedral : 13.835 106.181 2799 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.21 % Allowed : 11.72 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 2042 helix: 3.21 (0.18), residues: 745 sheet: 0.75 (0.26), residues: 440 loop : -1.38 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 168 TYR 0.012 0.001 TYR A 127 PHE 0.014 0.001 PHE B 473 TRP 0.014 0.001 TRP A 60 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00282 (17548) covalent geometry : angle 0.59225 (23941) SS BOND : bond 0.00625 ( 11) SS BOND : angle 2.06611 ( 22) hydrogen bonds : bond 0.07518 ( 759) hydrogen bonds : angle 4.16560 ( 2416) Misc. bond : bond 0.00028 ( 2) link_ALPHA1-2 : bond 0.00864 ( 1) link_ALPHA1-2 : angle 3.04516 ( 3) link_ALPHA1-3 : bond 0.00776 ( 1) link_ALPHA1-3 : angle 1.77834 ( 3) link_ALPHA1-6 : bond 0.00748 ( 7) link_ALPHA1-6 : angle 2.23991 ( 21) link_BETA1-4 : bond 0.00515 ( 11) link_BETA1-4 : angle 2.44002 ( 33) link_NAG-ASN : bond 0.00437 ( 8) link_NAG-ASN : angle 1.44958 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8846 (pp) REVERT: A 305 THR cc_start: 0.8639 (p) cc_final: 0.8089 (t) REVERT: B 95 GLN cc_start: 0.9195 (mt0) cc_final: 0.8988 (mt0) REVERT: C 466 ASN cc_start: 0.8775 (t0) cc_final: 0.8543 (t0) REVERT: E 275 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8298 (tm-30) outliers start: 41 outliers final: 15 residues processed: 148 average time/residue: 0.4914 time to fit residues: 82.9283 Evaluate side-chains 115 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 167 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN B 267 GLN B 451 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.052973 restraints weight = 126180.658| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 5.46 r_work: 0.2492 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17589 Z= 0.161 Angle : 0.599 9.242 24047 Z= 0.298 Chirality : 0.045 0.262 2842 Planarity : 0.004 0.043 2936 Dihedral : 10.969 97.711 2791 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.47 % Allowed : 12.04 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 2042 helix: 3.15 (0.18), residues: 747 sheet: 0.77 (0.26), residues: 441 loop : -1.38 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 9 TYR 0.011 0.001 TYR A 203 PHE 0.016 0.001 PHE D 284 TRP 0.019 0.001 TRP D 149 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00367 (17548) covalent geometry : angle 0.58316 (23941) SS BOND : bond 0.00669 ( 11) SS BOND : angle 1.50784 ( 22) hydrogen bonds : bond 0.07865 ( 759) hydrogen bonds : angle 4.00937 ( 2416) Misc. bond : bond 0.00018 ( 2) link_ALPHA1-2 : bond 0.00994 ( 1) link_ALPHA1-2 : angle 3.52662 ( 3) link_ALPHA1-3 : bond 0.01192 ( 1) link_ALPHA1-3 : angle 1.63459 ( 3) link_ALPHA1-6 : bond 0.00836 ( 7) link_ALPHA1-6 : angle 2.41657 ( 21) link_BETA1-4 : bond 0.00472 ( 11) link_BETA1-4 : angle 2.64551 ( 33) link_NAG-ASN : bond 0.00412 ( 8) link_NAG-ASN : angle 1.33724 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9147 (m-30) cc_final: 0.8661 (t0) REVERT: A 305 THR cc_start: 0.8617 (p) cc_final: 0.8035 (t) REVERT: B 95 GLN cc_start: 0.9212 (mt0) cc_final: 0.8989 (mt0) REVERT: C 89 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8108 (t0) REVERT: C 436 ASP cc_start: 0.8762 (t0) cc_final: 0.8457 (t0) REVERT: C 466 ASN cc_start: 0.8800 (t0) cc_final: 0.8552 (t0) REVERT: D 404 MET cc_start: 0.8893 (tmm) cc_final: 0.8677 (ttt) REVERT: E 275 GLU cc_start: 0.9368 (mt-10) cc_final: 0.8275 (tm-30) outliers start: 46 outliers final: 20 residues processed: 136 average time/residue: 0.4907 time to fit residues: 75.7376 Evaluate side-chains 117 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 193 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 152 optimal weight: 0.0050 chunk 134 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN B 451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.055514 restraints weight = 132451.899| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 5.62 r_work: 0.2552 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17589 Z= 0.120 Angle : 0.545 9.341 24047 Z= 0.268 Chirality : 0.043 0.254 2842 Planarity : 0.004 0.043 2936 Dihedral : 9.590 95.706 2791 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.79 % Allowed : 12.93 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.19), residues: 2042 helix: 3.29 (0.18), residues: 753 sheet: 0.84 (0.26), residues: 439 loop : -1.21 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 168 TYR 0.010 0.001 TYR E 15 PHE 0.014 0.001 PHE A 414 TRP 0.013 0.001 TRP A 60 HIS 0.003 0.000 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00237 (17548) covalent geometry : angle 0.53064 (23941) SS BOND : bond 0.00572 ( 11) SS BOND : angle 1.35622 ( 22) hydrogen bonds : bond 0.06533 ( 759) hydrogen bonds : angle 3.70934 ( 2416) Misc. bond : bond 0.00073 ( 2) link_ALPHA1-2 : bond 0.01452 ( 1) link_ALPHA1-2 : angle 3.25760 ( 3) link_ALPHA1-3 : bond 0.01093 ( 1) link_ALPHA1-3 : angle 1.72449 ( 3) link_ALPHA1-6 : bond 0.00981 ( 7) link_ALPHA1-6 : angle 2.30188 ( 21) link_BETA1-4 : bond 0.00522 ( 11) link_BETA1-4 : angle 2.28492 ( 33) link_NAG-ASN : bond 0.00434 ( 8) link_NAG-ASN : angle 1.40321 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9126 (m-30) cc_final: 0.8728 (t0) REVERT: A 305 THR cc_start: 0.8593 (p) cc_final: 0.8022 (t) REVERT: B 95 GLN cc_start: 0.9196 (mt0) cc_final: 0.8978 (mt0) REVERT: B 267 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: B 497 HIS cc_start: 0.8937 (OUTLIER) cc_final: 0.8445 (m-70) REVERT: C 89 ASP cc_start: 0.8379 (m-30) cc_final: 0.8152 (t0) REVERT: C 133 MET cc_start: 0.9356 (ttm) cc_final: 0.9136 (ttp) REVERT: C 168 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8394 (mpp80) REVERT: C 436 ASP cc_start: 0.8756 (t0) cc_final: 0.8478 (t0) REVERT: C 466 ASN cc_start: 0.8762 (t0) cc_final: 0.8371 (t0) REVERT: D 117 MET cc_start: 0.8880 (ttp) cc_final: 0.8623 (tpp) REVERT: D 404 MET cc_start: 0.8873 (tmm) cc_final: 0.8564 (ttt) outliers start: 33 outliers final: 14 residues processed: 136 average time/residue: 0.5215 time to fit residues: 80.1850 Evaluate side-chains 116 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 99 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 0.0030 chunk 200 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.055199 restraints weight = 116069.696| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 5.40 r_work: 0.2543 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17589 Z= 0.121 Angle : 0.547 9.372 24047 Z= 0.268 Chirality : 0.043 0.257 2842 Planarity : 0.004 0.042 2936 Dihedral : 9.043 93.702 2791 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.74 % Allowed : 13.14 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 2042 helix: 3.31 (0.18), residues: 753 sheet: 0.81 (0.26), residues: 436 loop : -1.17 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 182 TYR 0.008 0.001 TYR B 439 PHE 0.014 0.001 PHE B 473 TRP 0.011 0.001 TRP A 60 HIS 0.003 0.000 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00251 (17548) covalent geometry : angle 0.53235 (23941) SS BOND : bond 0.00581 ( 11) SS BOND : angle 1.34700 ( 22) hydrogen bonds : bond 0.06463 ( 759) hydrogen bonds : angle 3.65160 ( 2416) Misc. bond : bond 0.00008 ( 2) link_ALPHA1-2 : bond 0.01335 ( 1) link_ALPHA1-2 : angle 3.46220 ( 3) link_ALPHA1-3 : bond 0.01050 ( 1) link_ALPHA1-3 : angle 1.62670 ( 3) link_ALPHA1-6 : bond 0.00975 ( 7) link_ALPHA1-6 : angle 2.44040 ( 21) link_BETA1-4 : bond 0.00493 ( 11) link_BETA1-4 : angle 2.25776 ( 33) link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 1.37804 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9107 (m-30) cc_final: 0.8714 (t0) REVERT: B 95 GLN cc_start: 0.9173 (mt0) cc_final: 0.8949 (mt0) REVERT: B 305 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8315 (t0) REVERT: B 497 HIS cc_start: 0.8906 (OUTLIER) cc_final: 0.8416 (m-70) REVERT: C 89 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8109 (t0) REVERT: C 133 MET cc_start: 0.9324 (ttm) cc_final: 0.9090 (ttp) REVERT: C 436 ASP cc_start: 0.8709 (t0) cc_final: 0.8465 (t0) REVERT: C 466 ASN cc_start: 0.8674 (t0) cc_final: 0.8319 (t0) REVERT: D 117 MET cc_start: 0.8829 (ttp) cc_final: 0.8556 (tpp) REVERT: E 275 GLU cc_start: 0.9336 (mt-10) cc_final: 0.8257 (tm-30) outliers start: 32 outliers final: 17 residues processed: 127 average time/residue: 0.5118 time to fit residues: 73.9420 Evaluate side-chains 118 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 79 optimal weight: 0.0050 chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 84 optimal weight: 0.0070 chunk 140 optimal weight: 0.4980 chunk 200 optimal weight: 20.0000 overall best weight: 0.4612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057401 restraints weight = 132786.535| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 5.72 r_work: 0.2590 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17589 Z= 0.110 Angle : 0.522 9.375 24047 Z= 0.254 Chirality : 0.042 0.251 2842 Planarity : 0.004 0.041 2936 Dihedral : 7.880 89.644 2791 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.74 % Allowed : 13.56 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 2042 helix: 3.40 (0.18), residues: 749 sheet: 0.88 (0.26), residues: 437 loop : -1.08 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 168 TYR 0.010 0.001 TYR E 15 PHE 0.011 0.001 PHE B 473 TRP 0.014 0.001 TRP D 60 HIS 0.003 0.000 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00215 (17548) covalent geometry : angle 0.50869 (23941) SS BOND : bond 0.00560 ( 11) SS BOND : angle 1.20294 ( 22) hydrogen bonds : bond 0.05538 ( 759) hydrogen bonds : angle 3.44015 ( 2416) Misc. bond : bond 0.00001 ( 2) link_ALPHA1-2 : bond 0.01758 ( 1) link_ALPHA1-2 : angle 2.58849 ( 3) link_ALPHA1-3 : bond 0.00948 ( 1) link_ALPHA1-3 : angle 1.53945 ( 3) link_ALPHA1-6 : bond 0.01208 ( 7) link_ALPHA1-6 : angle 2.25549 ( 21) link_BETA1-4 : bond 0.00564 ( 11) link_BETA1-4 : angle 2.04435 ( 33) link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 1.33450 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9102 (m-30) cc_final: 0.8694 (t0) REVERT: A 404 MET cc_start: 0.8329 (ttp) cc_final: 0.8043 (tmt) REVERT: A 407 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8015 (t0) REVERT: B 95 GLN cc_start: 0.9155 (mt0) cc_final: 0.8955 (mt0) REVERT: B 305 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8210 (t0) REVERT: B 497 HIS cc_start: 0.8847 (OUTLIER) cc_final: 0.8375 (m-70) REVERT: C 89 ASP cc_start: 0.8344 (m-30) cc_final: 0.8139 (t0) REVERT: C 133 MET cc_start: 0.9338 (ttm) cc_final: 0.9134 (ttp) REVERT: C 168 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8400 (mpp80) REVERT: C 436 ASP cc_start: 0.8680 (t0) cc_final: 0.8455 (t0) REVERT: C 466 ASN cc_start: 0.8651 (t0) cc_final: 0.8302 (t0) REVERT: D 117 MET cc_start: 0.8834 (ttp) cc_final: 0.8518 (tpp) REVERT: D 310 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8665 (tm-30) REVERT: E 275 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8340 (tm-30) outliers start: 32 outliers final: 13 residues processed: 142 average time/residue: 0.4875 time to fit residues: 78.8383 Evaluate side-chains 121 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 158 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.055363 restraints weight = 129705.187| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 5.62 r_work: 0.2541 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17589 Z= 0.128 Angle : 0.540 9.384 24047 Z= 0.265 Chirality : 0.043 0.256 2842 Planarity : 0.004 0.041 2936 Dihedral : 7.555 87.159 2791 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.42 % Allowed : 13.99 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 2042 helix: 3.40 (0.18), residues: 748 sheet: 0.83 (0.26), residues: 438 loop : -1.07 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.011 0.001 TYR A 112 PHE 0.012 0.001 PHE B 473 TRP 0.009 0.001 TRP D 149 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00283 (17548) covalent geometry : angle 0.52605 (23941) SS BOND : bond 0.00569 ( 11) SS BOND : angle 1.33258 ( 22) hydrogen bonds : bond 0.06049 ( 759) hydrogen bonds : angle 3.53480 ( 2416) Misc. bond : bond 0.00008 ( 2) link_ALPHA1-2 : bond 0.01307 ( 1) link_ALPHA1-2 : angle 2.77282 ( 3) link_ALPHA1-3 : bond 0.00946 ( 1) link_ALPHA1-3 : angle 1.51714 ( 3) link_ALPHA1-6 : bond 0.01036 ( 7) link_ALPHA1-6 : angle 2.39782 ( 21) link_BETA1-4 : bond 0.00496 ( 11) link_BETA1-4 : angle 2.12763 ( 33) link_NAG-ASN : bond 0.00344 ( 8) link_NAG-ASN : angle 1.33174 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9136 (m-30) cc_final: 0.8760 (t0) REVERT: A 404 MET cc_start: 0.8363 (ttp) cc_final: 0.8096 (tmt) REVERT: A 407 ASP cc_start: 0.8415 (m-30) cc_final: 0.8075 (t0) REVERT: B 95 GLN cc_start: 0.9158 (mt0) cc_final: 0.8934 (mt0) REVERT: B 159 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8590 (p) REVERT: B 305 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8215 (t0) REVERT: B 497 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8405 (m-70) REVERT: C 89 ASP cc_start: 0.8342 (m-30) cc_final: 0.8112 (t0) REVERT: C 133 MET cc_start: 0.9329 (ttm) cc_final: 0.9121 (ttp) REVERT: C 436 ASP cc_start: 0.8668 (t0) cc_final: 0.8445 (t0) REVERT: C 466 ASN cc_start: 0.8683 (t0) cc_final: 0.8314 (t0) REVERT: D 117 MET cc_start: 0.8885 (ttp) cc_final: 0.8602 (tpp) REVERT: D 310 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8668 (tm-30) REVERT: E 275 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8299 (tm-30) outliers start: 26 outliers final: 16 residues processed: 124 average time/residue: 0.5029 time to fit residues: 70.6597 Evaluate side-chains 120 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.054909 restraints weight = 137753.806| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 5.75 r_work: 0.2526 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17589 Z= 0.123 Angle : 0.536 9.386 24047 Z= 0.265 Chirality : 0.043 0.257 2842 Planarity : 0.004 0.041 2936 Dihedral : 7.131 87.640 2791 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.63 % Allowed : 13.99 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 2042 helix: 3.34 (0.18), residues: 754 sheet: 0.82 (0.26), residues: 437 loop : -1.04 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 9 TYR 0.009 0.001 TYR B 439 PHE 0.012 0.001 PHE B 473 TRP 0.011 0.001 TRP A 60 HIS 0.003 0.000 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00267 (17548) covalent geometry : angle 0.52313 (23941) SS BOND : bond 0.00575 ( 11) SS BOND : angle 1.32681 ( 22) hydrogen bonds : bond 0.06152 ( 759) hydrogen bonds : angle 3.55636 ( 2416) Misc. bond : bond 0.00010 ( 2) link_ALPHA1-2 : bond 0.01009 ( 1) link_ALPHA1-2 : angle 1.99038 ( 3) link_ALPHA1-3 : bond 0.00914 ( 1) link_ALPHA1-3 : angle 1.50213 ( 3) link_ALPHA1-6 : bond 0.01131 ( 7) link_ALPHA1-6 : angle 2.19420 ( 21) link_BETA1-4 : bond 0.00494 ( 11) link_BETA1-4 : angle 2.07068 ( 33) link_NAG-ASN : bond 0.00370 ( 8) link_NAG-ASN : angle 1.38311 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9160 (m-30) cc_final: 0.8786 (t0) REVERT: A 404 MET cc_start: 0.8378 (ttp) cc_final: 0.8107 (tmt) REVERT: B 95 GLN cc_start: 0.9138 (mt0) cc_final: 0.8931 (mt0) REVERT: B 159 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8585 (p) REVERT: B 163 MET cc_start: 0.9040 (tpt) cc_final: 0.8828 (tpp) REVERT: B 305 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8238 (t0) REVERT: B 497 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8470 (m-70) REVERT: C 89 ASP cc_start: 0.8314 (m-30) cc_final: 0.8084 (t0) REVERT: C 133 MET cc_start: 0.9320 (ttm) cc_final: 0.9106 (ttp) REVERT: C 436 ASP cc_start: 0.8685 (t0) cc_final: 0.8468 (t0) REVERT: C 466 ASN cc_start: 0.8648 (t0) cc_final: 0.8268 (t0) REVERT: D 117 MET cc_start: 0.8852 (ttp) cc_final: 0.8562 (tpp) REVERT: D 310 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8664 (tm-30) REVERT: E 275 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8262 (tm-30) outliers start: 30 outliers final: 19 residues processed: 129 average time/residue: 0.5110 time to fit residues: 74.7136 Evaluate side-chains 122 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 155 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.077128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.054339 restraints weight = 132952.882| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 5.73 r_work: 0.2509 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17589 Z= 0.133 Angle : 0.546 9.896 24047 Z= 0.271 Chirality : 0.043 0.259 2842 Planarity : 0.004 0.041 2936 Dihedral : 6.886 88.806 2791 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.42 % Allowed : 14.35 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 2042 helix: 3.34 (0.18), residues: 754 sheet: 0.77 (0.26), residues: 441 loop : -1.05 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.010 0.001 TYR B 439 PHE 0.019 0.001 PHE B 473 TRP 0.011 0.001 TRP D 149 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00297 (17548) covalent geometry : angle 0.53351 (23941) SS BOND : bond 0.00571 ( 11) SS BOND : angle 1.36999 ( 22) hydrogen bonds : bond 0.06419 ( 759) hydrogen bonds : angle 3.62004 ( 2416) Misc. bond : bond 0.00011 ( 2) link_ALPHA1-2 : bond 0.00739 ( 1) link_ALPHA1-2 : angle 2.14247 ( 3) link_ALPHA1-3 : bond 0.00905 ( 1) link_ALPHA1-3 : angle 1.52266 ( 3) link_ALPHA1-6 : bond 0.01010 ( 7) link_ALPHA1-6 : angle 2.21998 ( 21) link_BETA1-4 : bond 0.00470 ( 11) link_BETA1-4 : angle 2.10947 ( 33) link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 1.38281 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9168 (m-30) cc_final: 0.8819 (t0) REVERT: A 404 MET cc_start: 0.8425 (ttp) cc_final: 0.8107 (tmt) REVERT: A 407 ASP cc_start: 0.8457 (t0) cc_final: 0.8019 (t0) REVERT: B 95 GLN cc_start: 0.9150 (mt0) cc_final: 0.8937 (mt0) REVERT: B 159 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 305 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8266 (t0) REVERT: B 497 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8205 (m-70) REVERT: C 89 ASP cc_start: 0.8347 (m-30) cc_final: 0.8119 (t0) REVERT: C 133 MET cc_start: 0.9335 (ttm) cc_final: 0.9123 (ttp) REVERT: C 238 VAL cc_start: 0.8750 (t) cc_final: 0.8543 (t) REVERT: C 436 ASP cc_start: 0.8717 (t0) cc_final: 0.8470 (t0) REVERT: C 466 ASN cc_start: 0.8679 (t0) cc_final: 0.8310 (t0) REVERT: D 19 ILE cc_start: 0.9189 (pt) cc_final: 0.8825 (pp) REVERT: D 117 MET cc_start: 0.8884 (ttp) cc_final: 0.8608 (tpp) REVERT: D 310 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8681 (tm-30) REVERT: E 275 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8276 (tm-30) REVERT: E 323 HIS cc_start: 0.9142 (t70) cc_final: 0.8660 (t-90) outliers start: 26 outliers final: 19 residues processed: 127 average time/residue: 0.5141 time to fit residues: 74.4661 Evaluate side-chains 122 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 38 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.052212 restraints weight = 152715.460| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 5.88 r_work: 0.2462 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17589 Z= 0.161 Angle : 0.574 9.412 24047 Z= 0.287 Chirality : 0.044 0.301 2842 Planarity : 0.004 0.041 2936 Dihedral : 6.798 88.727 2791 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.10 % Allowed : 14.77 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 2042 helix: 3.26 (0.18), residues: 747 sheet: 0.70 (0.26), residues: 439 loop : -1.15 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 9 TYR 0.012 0.001 TYR B 439 PHE 0.016 0.001 PHE D 284 TRP 0.014 0.001 TRP D 149 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00378 (17548) covalent geometry : angle 0.56143 (23941) SS BOND : bond 0.00600 ( 11) SS BOND : angle 1.47731 ( 22) hydrogen bonds : bond 0.07166 ( 759) hydrogen bonds : angle 3.80000 ( 2416) Misc. bond : bond 0.00013 ( 2) link_ALPHA1-2 : bond 0.00653 ( 1) link_ALPHA1-2 : angle 1.98896 ( 3) link_ALPHA1-3 : bond 0.00940 ( 1) link_ALPHA1-3 : angle 1.55207 ( 3) link_ALPHA1-6 : bond 0.01128 ( 7) link_ALPHA1-6 : angle 1.96503 ( 21) link_BETA1-4 : bond 0.00467 ( 11) link_BETA1-4 : angle 2.25957 ( 33) link_NAG-ASN : bond 0.00399 ( 8) link_NAG-ASN : angle 1.49296 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9158 (m-30) cc_final: 0.8784 (t0) REVERT: A 404 MET cc_start: 0.8381 (ttp) cc_final: 0.8145 (ttt) REVERT: A 407 ASP cc_start: 0.8512 (t0) cc_final: 0.8198 (t0) REVERT: B 159 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8585 (p) REVERT: B 163 MET cc_start: 0.9086 (tpt) cc_final: 0.8867 (tpp) REVERT: C 89 ASP cc_start: 0.8360 (m-30) cc_final: 0.8113 (t0) REVERT: C 133 MET cc_start: 0.9300 (ttm) cc_final: 0.9069 (ttp) REVERT: C 436 ASP cc_start: 0.8714 (t0) cc_final: 0.8484 (t0) REVERT: C 466 ASN cc_start: 0.8675 (t0) cc_final: 0.8298 (t0) REVERT: D 19 ILE cc_start: 0.9205 (pt) cc_final: 0.8824 (pp) REVERT: D 117 MET cc_start: 0.8889 (ttp) cc_final: 0.8600 (tpp) REVERT: D 310 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8685 (tm-30) REVERT: E 323 HIS cc_start: 0.9140 (t70) cc_final: 0.8678 (t-90) outliers start: 20 outliers final: 15 residues processed: 121 average time/residue: 0.5391 time to fit residues: 73.6226 Evaluate side-chains 114 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 2 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 167 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.077242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.054425 restraints weight = 130654.177| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 5.58 r_work: 0.2518 rms_B_bonded: 5.30 restraints_weight: 2.0000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17589 Z= 0.120 Angle : 0.534 9.370 24047 Z= 0.266 Chirality : 0.042 0.256 2842 Planarity : 0.004 0.042 2936 Dihedral : 6.531 89.214 2791 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.05 % Allowed : 14.98 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.19), residues: 2042 helix: 3.31 (0.18), residues: 753 sheet: 0.70 (0.26), residues: 440 loop : -1.06 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 9 TYR 0.009 0.001 TYR B 439 PHE 0.011 0.001 PHE D 284 TRP 0.013 0.001 TRP D 60 HIS 0.002 0.000 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00255 (17548) covalent geometry : angle 0.52247 (23941) SS BOND : bond 0.00572 ( 11) SS BOND : angle 1.30525 ( 22) hydrogen bonds : bond 0.06291 ( 759) hydrogen bonds : angle 3.62864 ( 2416) Misc. bond : bond 0.00005 ( 2) link_ALPHA1-2 : bond 0.00760 ( 1) link_ALPHA1-2 : angle 1.68468 ( 3) link_ALPHA1-3 : bond 0.00920 ( 1) link_ALPHA1-3 : angle 1.54454 ( 3) link_ALPHA1-6 : bond 0.01083 ( 7) link_ALPHA1-6 : angle 1.81252 ( 21) link_BETA1-4 : bond 0.00521 ( 11) link_BETA1-4 : angle 2.04428 ( 33) link_NAG-ASN : bond 0.00407 ( 8) link_NAG-ASN : angle 1.45282 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4756.42 seconds wall clock time: 81 minutes 46.77 seconds (4906.77 seconds total)