Starting phenix.real_space_refine on Mon Apr 6 06:49:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eno_28275/04_2026/8eno_28275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eno_28275/04_2026/8eno_28275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eno_28275/04_2026/8eno_28275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eno_28275/04_2026/8eno_28275.map" model { file = "/net/cci-nas-00/data/ceres_data/8eno_28275/04_2026/8eno_28275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eno_28275/04_2026/8eno_28275.cif" } resolution = 2.71 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= 0.022 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 143 5.16 5 C 10496 2.51 5 N 2781 2.21 5 O 3031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s 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: 16485 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3756 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 451} Chain breaks: 1 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: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3235 Classifications: {'peptide': 407} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 387} Chain breaks: 3 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: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 111} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'CIT': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2055 SG CYS A 275 51.347 36.265 124.754 1.00103.82 S ATOM 1136 SG CYS A 154 31.675 46.958 125.825 1.00 53.84 S ATOM 4515 SG CYS B 95 32.936 49.940 121.621 1.00 53.26 S ATOM 431 SG CYS A 62 37.141 44.993 122.886 1.00 68.36 S ATOM 618 SG CYS A 88 31.225 44.987 119.875 1.00 68.56 S ATOM 618 SG CYS A 88 31.225 44.987 119.875 1.00 68.56 S ATOM 4968 SG CYS B 153 28.489 48.252 122.620 1.00 65.54 S ATOM 4335 SG CYS B 70 30.009 49.971 115.706 1.00 60.21 S ATOM 4515 SG CYS B 95 32.936 49.940 121.621 1.00 53.26 S ATOM 9658 SG CYS C 275 34.962 35.504 49.456 1.00107.63 S ATOM 8739 SG CYS C 154 52.761 49.070 48.692 1.00 61.30 S ATOM 11924 SG CYS D 95 50.995 51.748 52.925 1.00 51.87 S ATOM 8034 SG CYS C 62 47.671 46.131 51.495 1.00 52.85 S ATOM 8221 SG CYS C 88 53.314 47.033 54.648 1.00 63.52 S ATOM 8221 SG CYS C 88 53.314 47.033 54.648 1.00 63.52 S ATOM 12377 SG CYS D 153 55.679 50.738 51.891 1.00 72.65 S ATOM 11744 SG CYS D 70 53.909 52.222 58.800 1.00 64.33 S ATOM 11924 SG CYS D 95 50.995 51.748 52.925 1.00 51.87 S Time building chain proxies: 3.88, per 1000 atoms: 0.24 Number of scatterers: 16485 At special positions: 0 Unit cell: (85.15, 96.2, 150.8, 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 143 16.00 O 3031 8.00 N 2781 7.00 C 10496 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: 1.51 Conformation dependent library (CDL) restraints added in 654.1 milliseconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3750 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 13 sheets defined 56.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 85 through 92 removed outlier: 4.669A 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 153 through 159 removed outlier: 3.937A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.813A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.171A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.460A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.833A 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 279 through 290 removed outlier: 3.720A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 343 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.659A pdb=" N TYR A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.123A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 435 removed outlier: 4.027A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.806A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.502A pdb=" N TRP A 472 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 474 " --> pdb=" O CYS A 471 " (cutoff:3.500A) 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: 3.941A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.040A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.791A pdb=" N VAL B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) 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: 3.620A pdb=" N ILE B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 241 " --> pdb=" O PHE B 237 " (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 298 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 358 Processing helix chain 'B' and resid 358 through 363 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: 3.928A 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 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.570A pdb=" N ARG B 481 " --> pdb=" O HIS B 478 " (cutoff:3.500A) 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 86 through 92 Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.026A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.510A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.260A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.956A 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 290 removed outlier: 5.752A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.550A pdb=" N VAL C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.571A pdb=" N TYR C 367 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 424 through 435 removed outlier: 3.632A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.864A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.988A 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 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 3.959A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.042A 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 removed outlier: 3.508A pdb=" N LYS D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.760A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 241 " --> pdb=" O PHE D 237 " (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 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 4.939A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.658A 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: 3.917A 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 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.529A pdb=" N ARG D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.517A pdb=" N ASN D 518 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 62 Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.710A pdb=" N ILE E 113 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.603A pdb=" N LEU A 399 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL A 351 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR A 377 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A 353 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR A 379 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.981A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.519A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (cutoff:3.500A) 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: 6.508A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.322A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE B 367 " --> pdb=" O HIS B 392 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU B 394 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 369 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.977A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE C 79 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN C 151 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 81 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 4.119A 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: 6.538A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.875A 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 removed outlier: 6.592A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) 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: 6.541A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.423A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 39 removed outlier: 9.866A pdb=" N GLY E 72 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 11.162A pdb=" N ALA E 91 " --> pdb=" O GLY E 72 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE E 74 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU E 89 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG E 4 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA E 90 " --> pdb=" O ARG E 4 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU E 6 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU E 92 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N CYS E 8 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 13.345A pdb=" N ILE E 5 " --> pdb=" O PRO E 22 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU E 7 " --> pdb=" O LEU E 20 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2211 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: 2.80 Time building geometry restraints manager: 1.95 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: 16523 1.54 - 1.89: 299 1.89 - 2.25: 32 2.25 - 2.60: 86 2.60 - 2.95: 18 Bond restraints: 16958 Sorted by residual: bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.955 -0.755 2.00e-02 2.50e+03 1.42e+03 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.950 -0.750 2.00e-02 2.50e+03 1.41e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.948 -0.748 2.00e-02 2.50e+03 1.40e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.940 -0.740 2.00e-02 2.50e+03 1.37e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.857 -0.657 2.00e-02 2.50e+03 1.08e+03 ... (remaining 16953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.82: 22886 6.82 - 13.65: 11 13.65 - 20.47: 4 20.47 - 27.30: 0 27.30 - 34.12: 4 Bond angle restraints: 22905 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 55.88 34.12 3.00e+00 1.11e-01 1.29e+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 55.89 34.11 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 57.11 32.89 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 57.11 32.89 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CA PRO E 86 " pdb=" N PRO E 86 " pdb=" CD PRO E 86 " ideal model delta sigma weight residual 112.00 100.49 11.51 1.40e+00 5.10e-01 6.75e+01 ... (remaining 22900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.42: 9241 20.42 - 40.83: 952 40.83 - 61.25: 229 61.25 - 81.67: 36 81.67 - 102.09: 9 Dihedral angle restraints: 10467 sinusoidal: 4605 harmonic: 5862 Sorted by residual: dihedral pdb=" CA MET E 85 " pdb=" C MET E 85 " pdb=" N PRO E 86 " pdb=" CA PRO E 86 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA VAL C 351 " pdb=" C VAL C 351 " pdb=" N MET C 352 " pdb=" CA MET C 352 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" C22 1N7 B 602 " pdb=" C23 1N7 B 602 " pdb=" C24 1N7 B 602 " pdb=" N1 1N7 B 602 " ideal model delta sinusoidal sigma weight residual -132.70 -30.61 -102.09 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 10464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.472: 2419 0.472 - 0.944: 0 0.944 - 1.416: 0 1.416 - 1.888: 0 1.888 - 2.360: 2 Chirality restraints: 2421 Sorted by residual: chirality pdb=" C31 1N7 B 602 " pdb=" C28 1N7 B 602 " pdb=" C32 1N7 B 602 " pdb=" O5 1N7 B 602 " both_signs ideal model delta sigma weight residual False -2.34 0.02 -2.36 2.00e-01 2.50e+01 1.39e+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 0.01 -2.35 2.00e-01 2.50e+01 1.39e+02 chirality pdb=" C2 1N7 B 602 " pdb=" C1 1N7 B 602 " pdb=" C15 1N7 B 602 " pdb=" C19 1N7 B 602 " both_signs ideal model delta sigma weight residual False -2.81 -2.53 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2418 not shown) Planarity restraints: 2917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 85 " 0.115 5.00e-02 4.00e+02 1.65e-01 4.38e+01 pdb=" N PRO E 86 " -0.286 5.00e-02 4.00e+02 pdb=" CA PRO E 86 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO E 86 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 85 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C MET E 85 " -0.045 2.00e-02 2.50e+03 pdb=" O MET E 85 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO E 86 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 343 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO A 344 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.029 5.00e-02 4.00e+02 ... (remaining 2914 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 153 2.61 - 3.18: 13944 3.18 - 3.76: 28091 3.76 - 4.33: 41112 4.33 - 4.90: 66484 Nonbonded interactions: 149784 Sorted by model distance: nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 603 " model vdw 2.038 2.260 nonbonded pdb=" OD2 ASP B 357 " pdb="FE FE B 603 " model vdw 2.058 2.260 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.110 2.260 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.114 2.260 nonbonded pdb=" OG SER C 423 " pdb=" OE2 GLU C 427 " model vdw 2.153 3.040 ... (remaining 149779 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 375 or resid 384 through 389 or resid 399 throu \ gh 401 or resid 410 through 600)) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } 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: 12.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 16.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 0.024 0.755 16974 Z= 1.235 Angle : 0.765 34.123 22905 Z= 0.337 Chirality : 0.081 2.360 2421 Planarity : 0.005 0.165 2917 Dihedral : 16.954 102.087 6717 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.65 % Allowed : 21.14 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.64 (0.19), residues: 2027 helix: 1.34 (0.17), residues: 965 sheet: -0.49 (0.35), residues: 214 loop : -0.30 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 206 TYR 0.014 0.001 TYR A 229 PHE 0.017 0.001 PHE C 412 TRP 0.013 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.02368 (16958) covalent geometry : angle 0.76467 (22905) hydrogen bonds : bond 0.14921 ( 766) hydrogen bonds : angle 6.48189 ( 2211) Misc. bond : bond 0.16027 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: D 118 MET cc_start: 0.9300 (mtp) cc_final: 0.9059 (mtp) outliers start: 29 outliers final: 20 residues processed: 154 average time/residue: 0.7653 time to fit residues: 129.3884 Evaluate side-chains 147 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 96 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 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 29 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.075950 restraints weight = 20951.425| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.68 r_work: 0.2776 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 16974 Z= 0.159 Angle : 0.674 28.891 22905 Z= 0.306 Chirality : 0.043 0.198 2421 Planarity : 0.005 0.102 2917 Dihedral : 6.308 77.166 2743 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.27 % Allowed : 20.00 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.73 (0.19), residues: 2027 helix: 1.35 (0.17), residues: 989 sheet: -0.23 (0.35), residues: 224 loop : -0.28 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 359 TYR 0.015 0.001 TYR A 229 PHE 0.013 0.001 PHE A 409 TRP 0.014 0.001 TRP A 253 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00349 (16958) covalent geometry : angle 0.67361 (22905) hydrogen bonds : bond 0.04076 ( 766) hydrogen bonds : angle 5.41278 ( 2211) Misc. bond : bond 0.07184 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6217 (mt-10) REVERT: A 288 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8372 (tm-30) REVERT: A 318 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: C 334 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8068 (mt-10) outliers start: 40 outliers final: 16 residues processed: 155 average time/residue: 0.7246 time to fit residues: 123.2664 Evaluate side-chains 149 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 99 optimal weight: 0.4980 chunk 189 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.074184 restraints weight = 20721.449| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.69 r_work: 0.2733 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 16974 Z= 0.186 Angle : 0.674 28.987 22905 Z= 0.306 Chirality : 0.045 0.185 2421 Planarity : 0.005 0.083 2917 Dihedral : 5.744 69.144 2722 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.44 % Allowed : 19.94 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.65 (0.19), residues: 2027 helix: 1.27 (0.17), residues: 996 sheet: -0.21 (0.35), residues: 224 loop : -0.33 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 359 TYR 0.017 0.001 TYR C 354 PHE 0.019 0.001 PHE A 409 TRP 0.013 0.001 TRP A 253 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00424 (16958) covalent geometry : angle 0.67402 (22905) hydrogen bonds : bond 0.04169 ( 766) hydrogen bonds : angle 5.25345 ( 2211) Misc. bond : bond 0.07111 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6202 (mt-10) REVERT: A 288 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: A 318 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: A 359 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.5483 (mtt180) REVERT: A 465 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8390 (ttm) REVERT: B 4 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7219 (mm-40) REVERT: C 120 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: C 334 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: C 476 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: D 211 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8912 (mppt) outliers start: 43 outliers final: 15 residues processed: 154 average time/residue: 0.7924 time to fit residues: 133.5561 Evaluate side-chains 147 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 123 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 151 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.076575 restraints weight = 20663.185| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.68 r_work: 0.2778 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 16974 Z= 0.117 Angle : 0.642 29.040 22905 Z= 0.286 Chirality : 0.042 0.175 2421 Planarity : 0.004 0.071 2917 Dihedral : 5.452 65.042 2718 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.44 % Allowed : 20.45 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.81 (0.19), residues: 2027 helix: 1.45 (0.17), residues: 996 sheet: -0.19 (0.35), residues: 224 loop : -0.32 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 523 TYR 0.013 0.001 TYR A 229 PHE 0.028 0.001 PHE A 409 TRP 0.013 0.001 TRP A 253 HIS 0.006 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00249 (16958) covalent geometry : angle 0.64177 (22905) hydrogen bonds : bond 0.03425 ( 766) hydrogen bonds : angle 5.07984 ( 2211) Misc. bond : bond 0.05082 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.566 Fit side-chains REVERT: A 277 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7781 (tpm170) REVERT: A 288 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: A 345 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7175 (ptm160) REVERT: A 359 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.5393 (mtt180) REVERT: A 465 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8428 (ttm) REVERT: B 4 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7222 (mm-40) REVERT: B 118 MET cc_start: 0.9349 (mtp) cc_final: 0.9120 (mtp) REVERT: C 476 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: D 211 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8918 (mppt) REVERT: E 115 MET cc_start: 0.6600 (ttm) cc_final: 0.6361 (ttt) outliers start: 43 outliers final: 19 residues processed: 159 average time/residue: 0.7609 time to fit residues: 132.9105 Evaluate side-chains 150 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 148 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.075509 restraints weight = 20749.496| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.69 r_work: 0.2758 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 16974 Z= 0.145 Angle : 0.650 29.068 22905 Z= 0.291 Chirality : 0.043 0.193 2421 Planarity : 0.004 0.064 2917 Dihedral : 5.340 63.875 2716 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.67 % Allowed : 20.34 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.82 (0.19), residues: 2027 helix: 1.46 (0.17), residues: 996 sheet: -0.18 (0.35), residues: 226 loop : -0.31 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 523 TYR 0.013 0.001 TYR D 88 PHE 0.021 0.001 PHE A 409 TRP 0.012 0.001 TRP A 253 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00327 (16958) covalent geometry : angle 0.64983 (22905) hydrogen bonds : bond 0.03636 ( 766) hydrogen bonds : angle 5.05461 ( 2211) Misc. bond : bond 0.05630 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.627 Fit side-chains REVERT: A 288 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: A 345 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7031 (ptm160) REVERT: A 359 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.5421 (mtt180) REVERT: A 401 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8189 (p90) REVERT: A 465 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8418 (ttm) REVERT: B 4 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7203 (mm-40) REVERT: C 476 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: D 211 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8916 (mppt) outliers start: 47 outliers final: 18 residues processed: 158 average time/residue: 0.7411 time to fit residues: 128.6999 Evaluate side-chains 149 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.075326 restraints weight = 20736.372| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.68 r_work: 0.2755 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 16974 Z= 0.150 Angle : 0.656 29.063 22905 Z= 0.293 Chirality : 0.043 0.208 2421 Planarity : 0.004 0.060 2917 Dihedral : 5.311 63.045 2716 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.33 % Allowed : 20.28 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.82 (0.19), residues: 2027 helix: 1.46 (0.17), residues: 996 sheet: -0.18 (0.35), residues: 224 loop : -0.32 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 523 TYR 0.014 0.001 TYR D 88 PHE 0.022 0.001 PHE A 409 TRP 0.012 0.001 TRP A 253 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00340 (16958) covalent geometry : angle 0.65606 (22905) hydrogen bonds : bond 0.03654 ( 766) hydrogen bonds : angle 5.04714 ( 2211) Misc. bond : bond 0.05650 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 345 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7147 (ptm160) REVERT: A 359 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5481 (mtt180) REVERT: A 401 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8228 (p90) REVERT: A 465 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8441 (ttm) REVERT: B 4 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7196 (mm-40) REVERT: C 476 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: D 211 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8921 (mppt) outliers start: 41 outliers final: 21 residues processed: 153 average time/residue: 0.7532 time to fit residues: 126.6649 Evaluate side-chains 152 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 157 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** C 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.075981 restraints weight = 20741.427| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.69 r_work: 0.2767 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 16974 Z= 0.131 Angle : 0.649 29.059 22905 Z= 0.290 Chirality : 0.043 0.207 2421 Planarity : 0.004 0.058 2917 Dihedral : 5.222 61.269 2716 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.39 % Allowed : 20.11 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.84 (0.19), residues: 2027 helix: 1.50 (0.17), residues: 996 sheet: -0.21 (0.34), residues: 232 loop : -0.33 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 523 TYR 0.013 0.001 TYR A 229 PHE 0.022 0.001 PHE A 409 TRP 0.013 0.001 TRP A 253 HIS 0.006 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00291 (16958) covalent geometry : angle 0.64923 (22905) hydrogen bonds : bond 0.03462 ( 766) hydrogen bonds : angle 5.00244 ( 2211) Misc. bond : bond 0.05145 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.682 Fit side-chains REVERT: A 345 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7177 (ptm160) REVERT: A 394 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7649 (mmm) REVERT: A 401 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8253 (p90) REVERT: A 465 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8429 (ttm) REVERT: B 4 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7198 (mm-40) REVERT: C 476 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: D 211 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8916 (mppt) outliers start: 42 outliers final: 21 residues processed: 157 average time/residue: 0.7192 time to fit residues: 124.3813 Evaluate side-chains 153 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 151 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** C 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.075764 restraints weight = 20899.353| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.69 r_work: 0.2767 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 16974 Z= 0.140 Angle : 0.659 29.063 22905 Z= 0.294 Chirality : 0.043 0.234 2421 Planarity : 0.004 0.058 2917 Dihedral : 5.207 60.248 2716 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.93 % Allowed : 20.62 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.83 (0.19), residues: 2027 helix: 1.49 (0.17), residues: 996 sheet: -0.19 (0.34), residues: 233 loop : -0.33 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 523 TYR 0.013 0.001 TYR D 88 PHE 0.025 0.001 PHE A 409 TRP 0.012 0.001 TRP A 253 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00316 (16958) covalent geometry : angle 0.65922 (22905) hydrogen bonds : bond 0.03536 ( 766) hydrogen bonds : angle 5.00069 ( 2211) Misc. bond : bond 0.05301 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.661 Fit side-chains REVERT: A 345 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7178 (ptm160) REVERT: A 359 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.5443 (mtt180) REVERT: A 394 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7702 (mmm) REVERT: A 401 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8290 (p90) REVERT: A 465 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8462 (ttm) REVERT: B 4 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7213 (mm-40) REVERT: C 476 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: D 211 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8907 (mppt) outliers start: 34 outliers final: 22 residues processed: 152 average time/residue: 0.7150 time to fit residues: 120.0625 Evaluate side-chains 154 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 121 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.075282 restraints weight = 20850.697| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.69 r_work: 0.2753 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 16974 Z= 0.154 Angle : 0.666 29.064 22905 Z= 0.298 Chirality : 0.044 0.241 2421 Planarity : 0.004 0.063 2917 Dihedral : 5.213 59.944 2716 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.10 % Allowed : 20.40 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.81 (0.19), residues: 2027 helix: 1.46 (0.17), residues: 996 sheet: -0.17 (0.34), residues: 233 loop : -0.34 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 523 TYR 0.014 0.001 TYR D 88 PHE 0.028 0.001 PHE A 409 TRP 0.012 0.001 TRP A 253 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00352 (16958) covalent geometry : angle 0.66591 (22905) hydrogen bonds : bond 0.03652 ( 766) hydrogen bonds : angle 5.01307 ( 2211) Misc. bond : bond 0.05531 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.668 Fit side-chains REVERT: A 359 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.5438 (mtt180) REVERT: A 394 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7645 (mmm) REVERT: A 401 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8211 (p90) REVERT: A 465 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8459 (ttm) REVERT: B 4 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7202 (mm-40) REVERT: C 345 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8096 (ptp-170) REVERT: C 476 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: D 211 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8923 (mppt) outliers start: 37 outliers final: 21 residues processed: 152 average time/residue: 0.7415 time to fit residues: 124.1289 Evaluate side-chains 152 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 94 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 198 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.075200 restraints weight = 20844.587| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.69 r_work: 0.2757 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 16974 Z= 0.153 Angle : 0.668 29.064 22905 Z= 0.299 Chirality : 0.044 0.243 2421 Planarity : 0.004 0.063 2917 Dihedral : 5.089 58.922 2712 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.93 % Allowed : 20.45 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.78 (0.19), residues: 2027 helix: 1.44 (0.17), residues: 996 sheet: -0.17 (0.33), residues: 249 loop : -0.36 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 523 TYR 0.014 0.001 TYR B 88 PHE 0.030 0.001 PHE A 409 TRP 0.012 0.001 TRP A 253 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00348 (16958) covalent geometry : angle 0.66806 (22905) hydrogen bonds : bond 0.03665 ( 766) hydrogen bonds : angle 5.02283 ( 2211) Misc. bond : bond 0.05547 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 359 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.5455 (mtt180) REVERT: A 394 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7665 (mmm) REVERT: A 401 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8199 (p90) REVERT: A 465 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8464 (ttm) REVERT: B 4 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7197 (mm-40) REVERT: C 345 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8105 (ptp-170) REVERT: C 476 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: D 211 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8930 (mppt) outliers start: 34 outliers final: 23 residues processed: 148 average time/residue: 0.7631 time to fit residues: 123.9696 Evaluate side-chains 153 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 172 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 170 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.076229 restraints weight = 20816.257| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.69 r_work: 0.2769 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 16974 Z= 0.122 Angle : 0.657 29.055 22905 Z= 0.292 Chirality : 0.043 0.230 2421 Planarity : 0.004 0.062 2917 Dihedral : 5.034 57.770 2712 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.88 % Allowed : 20.57 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.93 % Cis-general : 0.10 % 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: 0.84 (0.19), residues: 2027 helix: 1.50 (0.17), residues: 996 sheet: -0.14 (0.33), residues: 250 loop : -0.34 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.013 0.001 TYR B 88 PHE 0.028 0.001 PHE A 409 TRP 0.013 0.001 TRP A 253 HIS 0.006 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00268 (16958) covalent geometry : angle 0.65661 (22905) hydrogen bonds : bond 0.03405 ( 766) hydrogen bonds : angle 4.97898 ( 2211) Misc. bond : bond 0.04983 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5838.10 seconds wall clock time: 100 minutes 31.96 seconds (6031.96 seconds total)