Starting phenix.real_space_refine on Mon Apr 6 04:30:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjf_45630/04_2026/9cjf_45630.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjf_45630/04_2026/9cjf_45630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjf_45630/04_2026/9cjf_45630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjf_45630/04_2026/9cjf_45630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjf_45630/04_2026/9cjf_45630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjf_45630/04_2026/9cjf_45630.map" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 32 7.16 5 S 134 5.16 5 C 9757 2.51 5 N 2575 2.21 5 O 3512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16012 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3054 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 366} Chain breaks: 3 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2969 Classifications: {'peptide': 376} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 357} Chain breaks: 4 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "E" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 85} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' FE': 1, '1N7': 1, 'CLF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' FE': 1, '1N7': 1, 'CLF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "B" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 248 Classifications: {'water': 248} Link IDs: {None: 247} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 256 Classifications: {'water': 256} Link IDs: {None: 255} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1728 SG CYS A 275 31.851 58.797 124.860 1.00 51.63 S ATOM 809 SG CYS A 154 51.451 48.170 126.656 1.00 25.04 S ATOM 3813 SG CYS B 95 50.306 45.172 122.499 1.00 33.46 S ATOM 104 SG CYS A 62 46.061 50.339 123.618 1.00 21.88 S ATOM 291 SG CYS A 88 52.046 50.581 120.643 1.00 30.60 S ATOM 291 SG CYS A 88 52.046 50.581 120.643 1.00 30.60 S ATOM 4266 SG CYS B 153 54.961 47.092 123.513 1.00 36.24 S ATOM 3633 SG CYS B 70 53.641 45.295 116.651 1.00 36.07 S ATOM 3813 SG CYS B 95 50.306 45.172 122.499 1.00 33.46 S ATOM 8956 SG CYS C 275 51.383 59.963 50.580 1.00 47.49 S ATOM 8037 SG CYS C 154 33.528 46.796 48.791 1.00 30.96 S ATOM 10956 SG CYS D 95 35.131 43.971 52.954 1.00 32.65 S ATOM 7332 SG CYS C 62 38.550 49.588 51.927 1.00 20.97 S ATOM 7519 SG CYS C 88 32.399 48.995 54.823 1.00 30.93 S ATOM 7519 SG CYS C 88 32.399 48.995 54.823 1.00 30.93 S ATOM 11409 SG CYS D 153 30.126 45.145 51.974 1.00 37.95 S ATOM 10776 SG CYS D 70 31.740 43.574 58.832 1.00 33.34 S ATOM 10956 SG CYS D 95 35.131 43.971 52.954 1.00 32.65 S Time building chain proxies: 4.02, per 1000 atoms: 0.25 Number of scatterers: 16012 At special positions: 0 Unit cell: (85.15, 98.15, 149.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 134 16.00 O 3512 8.00 N 2575 7.00 C 9757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 681.9 milliseconds 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3482 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 13 sheets defined 56.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 85 through 93 removed outlier: 4.684A pdb=" N GLY A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.533A pdb=" N GLY A 157 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.757A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.239A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.391A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.666A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.863A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 424 through 434 removed outlier: 3.941A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.600A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.920A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.969A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.781A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.029A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.919A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.290A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 85 through 92 removed outlier: 4.603A pdb=" N GLY C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.205A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.590A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.251A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.506A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.800A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.929A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 316 removed outlier: 3.691A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 316 " --> pdb=" O ILE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.731A pdb=" N TYR C 367 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 435 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.641A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 80 removed outlier: 3.882A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.953A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.714A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 4.964A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.910A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.333A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 116 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 7.013A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.471A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 373 through 375 removed outlier: 6.907A pdb=" N VAL A 351 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.324A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.376A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 369 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE B 393 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.980A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.461A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 373 through 374 Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.401A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.539A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 68 through 80 removed outlier: 4.606A pdb=" N LEU E 89 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N GLU E 73 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N ILE E 87 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N ARG E 75 " --> pdb=" O MET E 85 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N MET E 85 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN E 77 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N GLN E 83 " --> pdb=" O ASN E 77 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS E 10 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU E 7 " --> pdb=" O LEU E 20 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2106 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: 2.83 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 15396 1.54 - 1.90: 218 1.90 - 2.26: 38 2.26 - 2.62: 80 2.62 - 2.97: 18 Bond restraints: 15750 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.974 -0.774 2.00e-02 2.50e+03 1.50e+03 bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.970 -0.770 2.00e-02 2.50e+03 1.48e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.933 -0.733 2.00e-02 2.50e+03 1.34e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.928 -0.728 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.862 -0.662 2.00e-02 2.50e+03 1.09e+03 ... (remaining 15745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.83: 21262 6.83 - 13.66: 9 13.66 - 20.50: 3 20.50 - 27.33: 0 27.33 - 34.16: 4 Bond angle restraints: 21278 Sorted by residual: angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.84 34.16 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.87 34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 57.10 32.90 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE1 CLF B 601 " ideal model delta sigma weight residual 90.00 57.12 32.88 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE3 CLF B 601 " ideal model delta sigma weight residual 90.00 107.22 -17.22 3.00e+00 1.11e-01 3.29e+01 ... (remaining 21273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.75: 8564 18.75 - 37.51: 866 37.51 - 56.26: 230 56.26 - 75.01: 51 75.01 - 93.76: 16 Dihedral angle restraints: 9727 sinusoidal: 4288 harmonic: 5439 Sorted by residual: dihedral pdb=" CA SER B 11 " pdb=" C SER B 11 " pdb=" N TYR B 12 " pdb=" CA TYR B 12 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" C22 1N7 D 603 " pdb=" C23 1N7 D 603 " pdb=" C24 1N7 D 603 " pdb=" N1 1N7 D 603 " ideal model delta sinusoidal sigma weight residual 227.30 133.54 93.76 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CA ASP C 419 " pdb=" CB ASP C 419 " pdb=" CG ASP C 419 " pdb=" OD1 ASP C 419 " ideal model delta sinusoidal sigma weight residual -30.00 -87.21 57.21 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 9724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.461: 2252 0.461 - 0.922: 0 0.922 - 1.382: 0 1.382 - 1.843: 0 1.843 - 2.304: 2 Chirality restraints: 2254 Sorted by residual: chirality pdb=" C31 1N7 B 603 " pdb=" C28 1N7 B 603 " pdb=" C32 1N7 B 603 " pdb=" O5 1N7 B 603 " both_signs ideal model delta sigma weight residual False -2.34 -0.04 -2.30 2.00e-01 2.50e+01 1.33e+02 chirality pdb=" C31 1N7 D 603 " pdb=" C28 1N7 D 603 " pdb=" C32 1N7 D 603 " pdb=" O5 1N7 D 603 " both_signs ideal model delta sigma weight residual False -2.34 -0.06 -2.28 2.00e-01 2.50e+01 1.31e+02 chirality pdb=" C2 1N7 B 603 " pdb=" C1 1N7 B 603 " pdb=" C15 1N7 B 603 " pdb=" C19 1N7 B 603 " both_signs ideal model delta sigma weight residual False -2.81 -2.55 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2251 not shown) Planarity restraints: 2701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 115 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO E 116 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 116 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 116 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO C 74 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 74 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.020 5.00e-02 4.00e+02 ... (remaining 2698 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 338 2.61 - 3.18: 13839 3.18 - 3.75: 29974 3.75 - 4.33: 43604 4.33 - 4.90: 66051 Nonbonded interactions: 153806 Sorted by model distance: nonbonded pdb="FE FE B 602 " pdb=" O HOH D 738 " model vdw 2.031 2.260 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.067 2.260 nonbonded pdb="FE FE D 601 " pdb=" O HOH B 802 " model vdw 2.082 2.260 nonbonded pdb="FE FE D 601 " pdb=" O HOH D 735 " model vdw 2.115 2.260 nonbonded pdb="FE FE B 602 " pdb=" O HOH D 791 " model vdw 2.116 2.260 ... (remaining 153801 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 49 through 353 or resid 362 through 422 or resid 427 throu \ gh 439 or resid 443 through 600)) selection = (chain 'C' and (resid 49 through 375 or resid 418 through 600)) } ncs_group { reference = (chain 'B' and (resid 2 through 523 or resid 603)) selection = (chain 'D' and (resid 2 through 523 or resid 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.820 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.230 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.025 0.774 15766 Z= 1.331 Angle : 0.736 34.162 21278 Z= 0.314 Chirality : 0.081 2.304 2254 Planarity : 0.004 0.042 2701 Dihedral : 16.451 93.764 6245 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.10 % Allowed : 16.82 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 1.02 (0.19), residues: 1877 helix: 1.51 (0.17), residues: 901 sheet: -0.28 (0.33), residues: 221 loop : 0.08 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 350 TYR 0.014 0.001 TYR D 88 PHE 0.009 0.001 PHE D 237 TRP 0.016 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.02464 (15750) covalent geometry : angle 0.73612 (21278) hydrogen bonds : bond 0.13355 ( 739) hydrogen bonds : angle 6.54477 ( 2106) Misc. bond : bond 0.16031 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.635 Fit side-chains REVERT: C 191 GLN cc_start: 0.8142 (mt0) cc_final: 0.7672 (mp-120) REVERT: C 322 LYS cc_start: 0.7906 (ttmt) cc_final: 0.6924 (ttpt) REVERT: C 334 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8138 (mt-10) REVERT: D 279 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7206 (mp0) outliers start: 18 outliers final: 15 residues processed: 186 average time/residue: 0.8302 time to fit residues: 166.9397 Evaluate side-chains 178 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 476 GLN D 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103808 restraints weight = 13754.799| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 0.92 r_work: 0.3102 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 15766 Z= 0.177 Angle : 0.690 29.022 21278 Z= 0.319 Chirality : 0.044 0.146 2254 Planarity : 0.004 0.053 2701 Dihedral : 6.587 89.711 2557 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.39 % Allowed : 15.17 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 0.96 (0.19), residues: 1877 helix: 1.45 (0.17), residues: 916 sheet: -0.36 (0.33), residues: 237 loop : 0.09 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 182 TYR 0.018 0.002 TYR D 88 PHE 0.012 0.001 PHE B 15 TRP 0.015 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00364 (15750) covalent geometry : angle 0.68961 (21278) hydrogen bonds : bond 0.04494 ( 739) hydrogen bonds : angle 5.69668 ( 2106) Misc. bond : bond 0.10642 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.611 Fit side-chains REVERT: A 57 MET cc_start: 0.8217 (mtt) cc_final: 0.7961 (mtt) REVERT: A 434 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8112 (mtt) REVERT: B 54 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: C 191 GLN cc_start: 0.8076 (mt0) cc_final: 0.7706 (mp-120) REVERT: C 322 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7316 (ttpt) REVERT: C 334 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 54 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: D 279 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7540 (mp0) outliers start: 39 outliers final: 16 residues processed: 199 average time/residue: 0.8129 time to fit residues: 175.0852 Evaluate side-chains 186 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 0.0020 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105586 restraints weight = 13935.747| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 0.92 r_work: 0.3127 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 15766 Z= 0.137 Angle : 0.657 29.124 21278 Z= 0.299 Chirality : 0.043 0.141 2254 Planarity : 0.004 0.049 2701 Dihedral : 6.125 92.646 2546 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.02 % Allowed : 15.84 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 1.03 (0.20), residues: 1877 helix: 1.53 (0.17), residues: 916 sheet: -0.34 (0.33), residues: 237 loop : 0.07 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 350 TYR 0.016 0.001 TYR E 127 PHE 0.009 0.001 PHE B 15 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00280 (15750) covalent geometry : angle 0.65722 (21278) hydrogen bonds : bond 0.03957 ( 739) hydrogen bonds : angle 5.49916 ( 2106) Misc. bond : bond 0.07772 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.624 Fit side-chains REVERT: A 57 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7528 (mtm) REVERT: A 133 LYS cc_start: 0.8602 (tptm) cc_final: 0.8376 (tptm) REVERT: A 321 GLN cc_start: 0.8371 (mt0) cc_final: 0.8058 (mt0) REVERT: A 434 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8051 (mtt) REVERT: B 54 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: C 191 GLN cc_start: 0.8012 (mt0) cc_final: 0.7653 (mp10) REVERT: C 287 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: C 322 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7261 (ttpt) REVERT: C 334 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8005 (mt-10) REVERT: D 39 LYS cc_start: 0.8045 (tptt) cc_final: 0.7669 (tppt) REVERT: D 54 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: D 279 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7571 (mp0) REVERT: E 78 MET cc_start: 0.5751 (mpp) cc_final: 0.5310 (mmm) outliers start: 33 outliers final: 16 residues processed: 197 average time/residue: 0.8624 time to fit residues: 183.3964 Evaluate side-chains 189 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 148 optimal weight: 0.0040 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101922 restraints weight = 14005.030| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.00 r_work: 0.3060 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 15766 Z= 0.129 Angle : 0.649 29.081 21278 Z= 0.294 Chirality : 0.042 0.142 2254 Planarity : 0.004 0.049 2701 Dihedral : 5.985 91.911 2545 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.14 % Allowed : 15.66 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 1.07 (0.20), residues: 1877 helix: 1.54 (0.17), residues: 928 sheet: -0.33 (0.33), residues: 237 loop : 0.11 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 350 TYR 0.015 0.001 TYR D 88 PHE 0.009 0.001 PHE B 15 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00265 (15750) covalent geometry : angle 0.64908 (21278) hydrogen bonds : bond 0.03781 ( 739) hydrogen bonds : angle 5.40001 ( 2106) Misc. bond : bond 0.06896 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.598 Fit side-chains REVERT: A 168 LYS cc_start: 0.8216 (mttm) cc_final: 0.7713 (mtmt) REVERT: A 321 GLN cc_start: 0.8350 (mt0) cc_final: 0.8038 (mt0) REVERT: A 434 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8006 (mtt) REVERT: B 54 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: B 172 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: C 182 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7997 (mpt90) REVERT: C 191 GLN cc_start: 0.8037 (mt0) cc_final: 0.7596 (mp-120) REVERT: C 287 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: C 322 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7177 (ttpt) REVERT: C 334 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7997 (mt-10) REVERT: D 39 LYS cc_start: 0.8057 (tptt) cc_final: 0.7756 (tppt) REVERT: D 54 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: D 279 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7490 (mp0) REVERT: E 78 MET cc_start: 0.5704 (mpp) cc_final: 0.5238 (mmm) outliers start: 35 outliers final: 16 residues processed: 192 average time/residue: 0.8052 time to fit residues: 167.4554 Evaluate side-chains 187 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 77 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 111 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101668 restraints weight = 14070.056| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.01 r_work: 0.3057 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 15766 Z= 0.133 Angle : 0.651 29.101 21278 Z= 0.295 Chirality : 0.042 0.142 2254 Planarity : 0.004 0.048 2701 Dihedral : 5.781 88.740 2539 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.77 % Allowed : 16.21 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 1.07 (0.20), residues: 1877 helix: 1.55 (0.17), residues: 928 sheet: -0.36 (0.33), residues: 237 loop : 0.10 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 350 TYR 0.020 0.001 TYR E 127 PHE 0.010 0.001 PHE B 15 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00274 (15750) covalent geometry : angle 0.65086 (21278) hydrogen bonds : bond 0.03797 ( 739) hydrogen bonds : angle 5.37889 ( 2106) Misc. bond : bond 0.07004 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.635 Fit side-chains REVERT: A 133 LYS cc_start: 0.8554 (tptm) cc_final: 0.8215 (tptm) REVERT: A 168 LYS cc_start: 0.8209 (mttm) cc_final: 0.7695 (mtmt) REVERT: A 321 GLN cc_start: 0.8334 (mt0) cc_final: 0.8037 (mt0) REVERT: A 350 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.6965 (ttp-110) REVERT: A 434 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8003 (mtt) REVERT: B 54 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: B 172 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: C 182 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8019 (mpt90) REVERT: C 191 GLN cc_start: 0.8051 (mt0) cc_final: 0.7592 (mp-120) REVERT: C 287 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6522 (tt0) REVERT: C 322 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7180 (ttpt) REVERT: C 334 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7996 (mt-10) REVERT: D 39 LYS cc_start: 0.8094 (tptt) cc_final: 0.7851 (tppt) REVERT: D 54 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: D 279 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7502 (mp0) REVERT: E 78 MET cc_start: 0.5732 (mpp) cc_final: 0.5287 (mmm) outliers start: 29 outliers final: 18 residues processed: 193 average time/residue: 0.8166 time to fit residues: 170.6398 Evaluate side-chains 190 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 163 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 154 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099878 restraints weight = 13983.447| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 0.99 r_work: 0.3023 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 15766 Z= 0.160 Angle : 0.672 29.137 21278 Z= 0.309 Chirality : 0.044 0.144 2254 Planarity : 0.004 0.047 2701 Dihedral : 5.848 85.749 2539 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.45 % Allowed : 15.47 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 1.00 (0.20), residues: 1877 helix: 1.53 (0.17), residues: 916 sheet: -0.40 (0.33), residues: 237 loop : 0.04 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.019 0.002 TYR D 88 PHE 0.012 0.001 PHE B 201 TRP 0.014 0.002 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00340 (15750) covalent geometry : angle 0.67201 (21278) hydrogen bonds : bond 0.04157 ( 739) hydrogen bonds : angle 5.44191 ( 2106) Misc. bond : bond 0.07974 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.649 Fit side-chains REVERT: A 168 LYS cc_start: 0.8211 (mttm) cc_final: 0.7684 (mtmt) REVERT: A 321 GLN cc_start: 0.8355 (mt0) cc_final: 0.8067 (mt0) REVERT: A 350 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.6975 (ttp-110) REVERT: A 434 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: A 445 ASP cc_start: 0.5243 (OUTLIER) cc_final: 0.5002 (m-30) REVERT: B 54 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: B 172 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: C 182 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8101 (mpt90) REVERT: C 191 GLN cc_start: 0.8124 (mt0) cc_final: 0.7632 (mp-120) REVERT: C 287 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: C 322 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7207 (ttpt) REVERT: C 334 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 54 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: D 279 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7473 (mp0) REVERT: E 78 MET cc_start: 0.5835 (mpp) cc_final: 0.5349 (mmm) outliers start: 40 outliers final: 20 residues processed: 196 average time/residue: 0.8172 time to fit residues: 173.6094 Evaluate side-chains 194 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 156 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100619 restraints weight = 14056.816| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.01 r_work: 0.3039 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 15766 Z= 0.142 Angle : 0.660 29.105 21278 Z= 0.301 Chirality : 0.043 0.142 2254 Planarity : 0.004 0.047 2701 Dihedral : 5.740 86.160 2539 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.02 % Allowed : 15.96 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 0.99 (0.20), residues: 1877 helix: 1.55 (0.17), residues: 918 sheet: -0.40 (0.33), residues: 237 loop : -0.02 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 182 TYR 0.016 0.001 TYR D 88 PHE 0.010 0.001 PHE B 201 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00298 (15750) covalent geometry : angle 0.66001 (21278) hydrogen bonds : bond 0.03941 ( 739) hydrogen bonds : angle 5.40421 ( 2106) Misc. bond : bond 0.07266 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.628 Fit side-chains REVERT: A 168 LYS cc_start: 0.8203 (mttm) cc_final: 0.7712 (mtmt) REVERT: A 321 GLN cc_start: 0.8343 (mt0) cc_final: 0.8052 (mt0) REVERT: A 350 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.6954 (ttp-110) REVERT: A 434 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7993 (mtt) REVERT: A 445 ASP cc_start: 0.5249 (OUTLIER) cc_final: 0.5008 (m-30) REVERT: B 54 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: B 172 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: C 191 GLN cc_start: 0.8094 (mt0) cc_final: 0.7614 (mp-120) REVERT: C 287 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: C 322 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7243 (ttpt) REVERT: C 334 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8016 (mt-10) REVERT: D 54 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: D 279 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7482 (mp0) REVERT: E 78 MET cc_start: 0.5929 (mpp) cc_final: 0.5474 (mmm) outliers start: 33 outliers final: 17 residues processed: 195 average time/residue: 0.8215 time to fit residues: 173.2570 Evaluate side-chains 188 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 158 optimal weight: 0.0010 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.100999 restraints weight = 14186.325| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.02 r_work: 0.3044 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 15766 Z= 0.139 Angle : 0.659 29.102 21278 Z= 0.300 Chirality : 0.043 0.142 2254 Planarity : 0.004 0.048 2701 Dihedral : 5.666 85.918 2539 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.65 % Allowed : 16.45 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 1.01 (0.20), residues: 1877 helix: 1.57 (0.17), residues: 918 sheet: -0.41 (0.33), residues: 237 loop : -0.01 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 182 TYR 0.016 0.001 TYR D 88 PHE 0.010 0.001 PHE B 201 TRP 0.014 0.001 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00290 (15750) covalent geometry : angle 0.65950 (21278) hydrogen bonds : bond 0.03879 ( 739) hydrogen bonds : angle 5.38463 ( 2106) Misc. bond : bond 0.07112 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.626 Fit side-chains REVERT: A 168 LYS cc_start: 0.8191 (mttm) cc_final: 0.7707 (mtmt) REVERT: A 321 GLN cc_start: 0.8342 (mt0) cc_final: 0.8054 (mt0) REVERT: A 350 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.6955 (ttp-110) REVERT: A 434 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8005 (mtt) REVERT: B 54 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: B 172 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: C 182 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7083 (mpt90) REVERT: C 191 GLN cc_start: 0.8087 (mt0) cc_final: 0.7606 (mp-120) REVERT: C 287 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: C 322 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7242 (ttpt) REVERT: C 334 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8007 (mt-10) REVERT: D 54 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: D 279 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7491 (mp0) REVERT: E 78 MET cc_start: 0.5899 (mpp) cc_final: 0.5462 (mmm) outliers start: 27 outliers final: 18 residues processed: 186 average time/residue: 0.8307 time to fit residues: 167.1179 Evaluate side-chains 188 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 27 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.100122 restraints weight = 14141.838| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.01 r_work: 0.3030 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 15766 Z= 0.154 Angle : 0.672 29.118 21278 Z= 0.308 Chirality : 0.044 0.143 2254 Planarity : 0.004 0.046 2701 Dihedral : 5.664 85.034 2539 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.59 % Allowed : 16.70 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 0.96 (0.20), residues: 1877 helix: 1.53 (0.17), residues: 918 sheet: -0.43 (0.33), residues: 237 loop : -0.02 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 182 TYR 0.017 0.002 TYR D 88 PHE 0.011 0.001 PHE B 201 TRP 0.014 0.001 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00326 (15750) covalent geometry : angle 0.67159 (21278) hydrogen bonds : bond 0.04076 ( 739) hydrogen bonds : angle 5.42123 ( 2106) Misc. bond : bond 0.07633 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.612 Fit side-chains REVERT: A 168 LYS cc_start: 0.8200 (mttm) cc_final: 0.7701 (mtmt) REVERT: A 321 GLN cc_start: 0.8355 (mt0) cc_final: 0.8071 (mt0) REVERT: A 347 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: A 350 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.7168 (ttp-110) REVERT: A 434 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8019 (mtt) REVERT: B 54 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: C 59 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.6993 (mm) REVERT: C 191 GLN cc_start: 0.8124 (mt0) cc_final: 0.7635 (mp-120) REVERT: C 277 ARG cc_start: 0.8203 (ttt-90) cc_final: 0.7981 (ttt-90) REVERT: C 322 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7255 (ttpt) REVERT: C 334 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8042 (mt-10) REVERT: D 54 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: D 279 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7494 (mp0) REVERT: E 78 MET cc_start: 0.5976 (mpp) cc_final: 0.5527 (mmm) outliers start: 26 outliers final: 16 residues processed: 186 average time/residue: 0.7984 time to fit residues: 160.9560 Evaluate side-chains 186 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 14 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 168 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 187 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 518 ASN C 476 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101598 restraints weight = 14199.815| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.02 r_work: 0.3057 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 15766 Z= 0.131 Angle : 0.655 29.095 21278 Z= 0.297 Chirality : 0.042 0.142 2254 Planarity : 0.004 0.046 2701 Dihedral : 5.557 81.842 2539 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.47 % Allowed : 16.82 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 1.05 (0.20), residues: 1877 helix: 1.60 (0.17), residues: 916 sheet: -0.41 (0.33), residues: 237 loop : 0.04 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 182 TYR 0.015 0.001 TYR D 88 PHE 0.009 0.001 PHE B 15 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00272 (15750) covalent geometry : angle 0.65515 (21278) hydrogen bonds : bond 0.03778 ( 739) hydrogen bonds : angle 5.35841 ( 2106) Misc. bond : bond 0.06696 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.484 Fit side-chains REVERT: A 168 LYS cc_start: 0.8180 (mttm) cc_final: 0.7624 (mtmt) REVERT: A 321 GLN cc_start: 0.8323 (mt0) cc_final: 0.8048 (mt0) REVERT: A 347 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: A 350 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7136 (ttp-110) REVERT: A 434 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8014 (mtt) REVERT: B 54 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: C 59 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.6807 (tp) REVERT: C 191 GLN cc_start: 0.8078 (mt0) cc_final: 0.7588 (mp-120) REVERT: C 322 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7225 (ttpt) REVERT: C 334 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8003 (mt-10) REVERT: D 54 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: D 279 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7487 (mp0) REVERT: E 78 MET cc_start: 0.5918 (mpp) cc_final: 0.5441 (mmm) REVERT: E 85 MET cc_start: 0.5558 (ttp) cc_final: 0.3896 (tpt) outliers start: 24 outliers final: 16 residues processed: 185 average time/residue: 0.8119 time to fit residues: 162.6248 Evaluate side-chains 187 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098507 restraints weight = 13977.287| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 0.99 r_work: 0.3007 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 15766 Z= 0.199 Angle : 0.707 29.183 21278 Z= 0.329 Chirality : 0.045 0.145 2254 Planarity : 0.004 0.058 2701 Dihedral : 5.729 80.870 2539 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.47 % Allowed : 16.94 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.22 % Cis-general : 0.11 % 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: 0.88 (0.19), residues: 1877 helix: 1.43 (0.17), residues: 916 sheet: -0.47 (0.32), residues: 237 loop : -0.01 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 182 TYR 0.021 0.002 TYR D 88 PHE 0.014 0.002 PHE D 201 TRP 0.014 0.002 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00434 (15750) covalent geometry : angle 0.70741 (21278) hydrogen bonds : bond 0.04552 ( 739) hydrogen bonds : angle 5.52117 ( 2106) Misc. bond : bond 0.08762 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6465.40 seconds wall clock time: 111 minutes 10.48 seconds (6670.48 seconds total)