Starting phenix.real_space_refine on Mon Apr 6 16:16:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut8_26760/04_2026/7ut8_26760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut8_26760/04_2026/7ut8_26760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ut8_26760/04_2026/7ut8_26760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut8_26760/04_2026/7ut8_26760.map" model { file = "/net/cci-nas-00/data/ceres_data/7ut8_26760/04_2026/7ut8_26760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut8_26760/04_2026/7ut8_26760.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 8 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 36 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 180 5.16 5 C 12748 2.51 5 N 3411 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 20221 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3782 Classifications: {'peptide': 476} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 454} Chain: "B" Number of atoms: 4180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Conformer: "B" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} bond proxies already assigned to first conformer: 4273 Chain: "C" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3782 Classifications: {'peptide': 476} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 454} 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: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2053 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "F" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2053 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'ATP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2081 SG CYS A 275 33.388 60.631 65.167 1.00 19.66 S ATOM 1162 SG CYS A 154 53.648 59.586 54.829 1.00 10.26 S ATOM 4547 SG CYS B 95 51.765 63.160 51.069 1.00 8.81 S ATOM 457 SG CYS A 62 47.820 61.848 56.257 1.00 20.03 S ATOM 644 SG CYS A 88 53.457 65.754 56.495 1.00 20.47 S ATOM 644 SG CYS A 88 53.457 65.754 56.495 1.00 20.47 S ATOM 5000 SG CYS B 153 57.019 62.664 52.916 1.00 19.89 S ATOM 4367 SG CYS B 70 55.011 69.039 50.844 1.00 16.40 S ATOM 4547 SG CYS B 95 51.765 63.160 51.069 1.00 8.81 S ATOM 10043 SG CYS C 275 47.661 136.996 58.795 1.00 20.63 S ATOM 9124 SG CYS C 154 29.413 135.702 45.210 1.00 30.58 S ATOM 12503 SG CYS D 95 31.839 131.376 42.643 1.00 11.82 S ATOM 8419 SG CYS C 62 34.883 133.640 48.263 1.00 15.18 S ATOM 8606 SG CYS C 88 29.401 129.685 47.992 1.00 23.03 S ATOM 8606 SG CYS C 88 29.401 129.685 47.992 1.00 23.03 S ATOM 12956 SG CYS D 153 26.172 132.102 43.449 1.00 29.98 S ATOM 12323 SG CYS D 70 28.439 125.560 42.955 1.00 8.08 S ATOM 12503 SG CYS D 95 31.839 131.376 42.643 1.00 11.82 S ATOM 16607 SG CYS E 97 61.860 50.927 53.799 1.00 21.46 S ATOM 16878 SG CYS E 132 67.052 49.986 57.077 1.00 21.41 S ATOM 18660 SG CYS F 97 66.776 55.571 53.876 1.00 19.39 S ATOM 18931 SG CYS F 132 67.533 50.600 50.428 1.00 35.26 S Time building chain proxies: 5.54, per 1000 atoms: 0.27 Number of scatterers: 20221 At special positions: 0 Unit cell: (116.065, 163.66, 102.705, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 2 41.97 Fe 36 26.01 S 180 16.00 P 6 15.00 Mg 2 11.99 O 3836 8.00 N 3411 7.00 C 12748 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: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 E 301 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 132 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS F 97 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 97 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS F 132 " Number of angles added : 12 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4642 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 14 sheets defined 56.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 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 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.577A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.218A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 removed outlier: 4.493A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.780A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.593A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 6.000A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.540A pdb=" N TYR A 387 " --> pdb=" O HIS A 383 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.737A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.698A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.605A 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 32 removed outlier: 3.713A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.071A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.891A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.596A pdb=" N ILE B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.818A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.194A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.580A pdb=" N SER B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 417 removed outlier: 3.739A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 417' Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.507A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 removed outlier: 3.571A pdb=" N GLU B 463 " --> pdb=" O LYS B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.598A pdb=" N ASN B 518 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.874A pdb=" N LYS C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.569A pdb=" N LYS C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.025A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 4.266A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 233 through 244 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: 5.757A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 4.098A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 357 through 363 removed outlier: 4.563A pdb=" N ARG C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.023A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 removed outlier: 3.573A pdb=" N ARG C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 433 removed outlier: 4.456A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.692A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.505A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.644A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.046A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.246A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.811A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 3.578A pdb=" N THR D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.526A pdb=" N GLY D 416 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 413 through 417' Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.484A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.545A 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 Processing helix chain 'E' and resid 14 through 30 Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 97 through 112 Processing helix chain 'E' and resid 133 through 140 Proline residue: E 138 - end of helix Processing helix chain 'E' and resid 154 through 175 removed outlier: 4.264A pdb=" N LYS E 170 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 214 through 223 removed outlier: 4.460A pdb=" N GLN E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 249 Processing helix chain 'E' and resid 260 through 269 Processing helix chain 'F' and resid 14 through 30 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 56 through 64 Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.919A pdb=" N VAL F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 97 through 113 removed outlier: 3.654A pdb=" N GLY F 101 " --> pdb=" O CYS F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 117 removed outlier: 3.992A pdb=" N ASP F 117 " --> pdb=" O ALA F 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 114 through 117' Processing helix chain 'F' and resid 132 through 140 Proline residue: F 138 - end of helix Processing helix chain 'F' and resid 154 through 173 removed outlier: 4.194A pdb=" N LYS F 170 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 removed outlier: 3.644A pdb=" N LEU F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 221 removed outlier: 4.419A pdb=" N GLN F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 238 through 249 Processing helix chain 'F' and resid 260 through 271 removed outlier: 3.906A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.585A pdb=" N LEU A 399 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.399A 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: 6.793A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.108A 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: 7.267A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 removed outlier: 8.781A pdb=" N VAL B 114 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.454A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.534A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 10.771A pdb=" N LEU C 399 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL C 375 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N TYR C 401 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.939A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 7.453A pdb=" N ILE C 225 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN C 252 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY C 227 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER C 254 " --> pdb=" O GLY C 227 " (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: 6.488A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.392A 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: 8.658A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78 removed outlier: 6.443A pdb=" N MET E 34 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP E 125 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL E 36 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN E 4 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR E 148 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA E 6 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL E 150 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR E 8 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE E 147 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY E 181 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 208 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU E 182 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE E 210 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N CYS E 184 " --> pdb=" O PHE E 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.768A pdb=" N VAL F 33 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL F 86 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE F 35 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL F 126 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLY F 9 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN F 4 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TYR F 148 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA F 6 " --> pdb=" O TYR F 148 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL F 150 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR F 8 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE F 149 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU F 182 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET F 207 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU F 182 " --> pdb=" O MET F 207 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N HIS F 209 " --> pdb=" O LEU F 182 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.55: 20297 1.55 - 1.90: 256 1.90 - 2.25: 37 2.25 - 2.60: 93 2.60 - 2.95: 18 Bond restraints: 20701 Sorted by residual: bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.947 -0.747 2.00e-02 2.50e+03 1.39e+03 bond pdb="FE2 CLF D 602 " pdb="FE8 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="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.930 -0.730 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.922 -0.722 2.00e-02 2.50e+03 1.30e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.848 -0.648 2.00e-02 2.50e+03 1.05e+03 ... (remaining 20696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.87: 27931 6.87 - 13.74: 10 13.74 - 20.61: 2 20.61 - 27.48: 0 27.48 - 34.35: 4 Bond angle restraints: 27947 Sorted by residual: angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.65 34.35 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.93 34.07 3.00e+00 1.11e-01 1.29e+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 57.19 32.81 3.00e+00 1.11e-01 1.20e+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 57.70 32.30 3.00e+00 1.11e-01 1.16e+02 angle pdb=" PB ATP F 302 " pdb=" O3B ATP F 302 " pdb=" PG ATP F 302 " ideal model delta sigma weight residual 139.87 131.38 8.49 1.00e+00 1.00e+00 7.20e+01 ... (remaining 27942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10752 17.83 - 35.66: 1379 35.66 - 53.48: 423 53.48 - 71.31: 116 71.31 - 89.14: 43 Dihedral angle restraints: 12713 sinusoidal: 5443 harmonic: 7270 Sorted by residual: dihedral pdb=" CG ARG D 238 " pdb=" CD ARG D 238 " pdb=" NE ARG D 238 " pdb=" CZ ARG D 238 " ideal model delta sinusoidal sigma weight residual -90.00 -38.65 -51.35 2 1.50e+01 4.44e-03 1.30e+01 dihedral pdb=" CA MET E 29 " pdb=" C MET E 29 " pdb=" N GLY E 30 " pdb=" CA GLY E 30 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CG ARG A 284 " pdb=" CD ARG A 284 " pdb=" NE ARG A 284 " pdb=" CZ ARG A 284 " ideal model delta sinusoidal sigma weight residual 90.00 41.01 48.99 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 12710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2152 0.045 - 0.090: 621 0.090 - 0.136: 198 0.136 - 0.181: 10 0.181 - 0.226: 4 Chirality restraints: 2985 Sorted by residual: chirality pdb=" CG LEU D 24 " pdb=" CB LEU D 24 " pdb=" CD1 LEU D 24 " pdb=" CD2 LEU D 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA CYS D 153 " pdb=" N CYS D 153 " pdb=" C CYS D 153 " pdb=" CB CYS D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA CYS E 97 " pdb=" N CYS E 97 " pdb=" C CYS E 97 " pdb=" CB CYS E 97 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 2982 not shown) Planarity restraints: 3594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 359 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A 360 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 442 " 0.020 2.00e-02 2.50e+03 1.96e-02 5.75e+00 pdb=" CG HIS A 442 " -0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS A 442 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS A 442 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS A 442 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 442 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 152 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C SER C 152 " 0.034 2.00e-02 2.50e+03 pdb=" O SER C 152 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU C 153 " -0.012 2.00e-02 2.50e+03 ... (remaining 3591 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 344 2.66 - 3.22: 18836 3.22 - 3.78: 33864 3.78 - 4.34: 48026 4.34 - 4.90: 76632 Nonbonded interactions: 177702 Sorted by model distance: nonbonded pdb=" O1 HCA A 501 " pdb=" O7 HCA A 501 " model vdw 2.099 3.040 nonbonded pdb=" ND1 HIS D 90 " pdb=" OD2 ASP D 116 " model vdw 2.217 3.120 nonbonded pdb=" OH TYR A 221 " pdb=" OD2 ASP A 317 " model vdw 2.222 3.040 nonbonded pdb=" OG SER A 42 " pdb=" OD1 ASP A 388 " model vdw 2.233 3.040 nonbonded pdb=" O ALA B 205 " pdb=" OG1 THR B 209 " model vdw 2.234 3.040 ... (remaining 177697 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 2 through 44 or resid 46 through 523)) selection = (chain 'D' and (resid 2 through 44 or resid 46 through 523)) } ncs_group { reference = (chain 'E' and resid 1 through 271) selection = (chain 'F' and resid 1 through 271) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.650 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.022 0.747 20721 Z= 1.105 Angle : 0.777 34.350 27959 Z= 0.390 Chirality : 0.045 0.226 2985 Planarity : 0.004 0.062 3594 Dihedral : 18.373 89.138 8071 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 3.66 % Allowed : 26.24 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.19 (0.17), residues: 2527 helix: 1.02 (0.15), residues: 1209 sheet: -0.12 (0.34), residues: 216 loop : -0.78 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 187 TYR 0.017 0.001 TYR B 88 PHE 0.013 0.001 PHE B 31 TRP 0.016 0.002 TRP C 335 HIS 0.019 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.02129 (20701) covalent geometry : angle 0.76935 (27947) hydrogen bonds : bond 0.15070 ( 953) hydrogen bonds : angle 6.64632 ( 2753) metal coordination : bond 0.04909 ( 4) metal coordination : angle 5.32006 ( 12) Misc. bond : bond 0.11577 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 642 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 442 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.5668 (m-70) REVERT: E 135 PHE cc_start: 0.8595 (m-80) cc_final: 0.8267 (m-80) outliers start: 78 outliers final: 65 residues processed: 700 average time/residue: 0.7264 time to fit residues: 563.5455 Evaluate side-chains 704 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 638 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 442 HIS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 264 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 297 HIS B 338 GLN C 98 ASN C 298 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 137 ASN D 167 ASN D 168 ASN E 4 GLN E 21 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121163 restraints weight = 27465.229| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.27 r_work: 0.3465 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 20721 Z= 0.194 Angle : 0.710 28.989 27959 Z= 0.335 Chirality : 0.046 0.152 2985 Planarity : 0.005 0.054 3594 Dihedral : 9.244 89.614 3296 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 5.33 % Allowed : 22.30 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.30 (0.17), residues: 2527 helix: 1.05 (0.15), residues: 1229 sheet: -0.10 (0.35), residues: 216 loop : -0.67 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 46 TYR 0.026 0.002 TYR E 230 PHE 0.016 0.002 PHE B 31 TRP 0.017 0.002 TRP C 335 HIS 0.011 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00424 (20701) covalent geometry : angle 0.70069 (27947) hydrogen bonds : bond 0.05093 ( 953) hydrogen bonds : angle 5.41685 ( 2753) metal coordination : bond 0.01443 ( 4) metal coordination : angle 5.65377 ( 12) Misc. bond : bond 0.11294 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 648 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8075 (pttt) REVERT: C 166 VAL cc_start: 0.8238 (m) cc_final: 0.8038 (t) REVERT: C 411 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5583 (mt-10) REVERT: E 28 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: E 261 MET cc_start: 0.6803 (tpt) cc_final: 0.6301 (tpt) outliers start: 114 outliers final: 63 residues processed: 712 average time/residue: 0.7429 time to fit residues: 585.1703 Evaluate side-chains 698 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 632 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 264 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 93 optimal weight: 0.0670 chunk 227 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 44 optimal weight: 0.0030 chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 145 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 338 GLN C 98 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 137 ASN D 167 ASN D 168 ASN D 518 ASN E 4 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122187 restraints weight = 27755.365| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.30 r_work: 0.3480 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 20721 Z= 0.143 Angle : 0.677 29.068 27959 Z= 0.314 Chirality : 0.044 0.152 2985 Planarity : 0.004 0.043 3594 Dihedral : 8.245 88.538 3237 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 4.78 % Allowed : 22.67 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.43 (0.17), residues: 2527 helix: 1.20 (0.15), residues: 1229 sheet: -0.02 (0.35), residues: 212 loop : -0.67 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 284 TYR 0.015 0.001 TYR B 88 PHE 0.013 0.001 PHE B 375 TRP 0.016 0.001 TRP C 335 HIS 0.010 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00305 (20701) covalent geometry : angle 0.66614 (27947) hydrogen bonds : bond 0.04304 ( 953) hydrogen bonds : angle 5.19197 ( 2753) metal coordination : bond 0.00824 ( 4) metal coordination : angle 5.80437 ( 12) Misc. bond : bond 0.08472 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 629 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8089 (pttt) REVERT: C 411 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5405 (mp0) REVERT: C 414 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7373 (mtmt) REVERT: C 462 ASP cc_start: 0.7901 (m-30) cc_final: 0.7680 (m-30) REVERT: E 168 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7719 (mt) REVERT: E 261 MET cc_start: 0.6794 (tpt) cc_final: 0.6263 (tpt) outliers start: 102 outliers final: 61 residues processed: 680 average time/residue: 0.7529 time to fit residues: 564.6003 Evaluate side-chains 679 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 615 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 170 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 140 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 338 GLN C 298 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 137 ASN D 167 ASN D 225 ASN E 4 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119340 restraints weight = 36852.655| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.55 r_work: 0.3427 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 20721 Z= 0.180 Angle : 0.693 29.064 27959 Z= 0.324 Chirality : 0.045 0.205 2985 Planarity : 0.004 0.049 3594 Dihedral : 7.818 86.604 3222 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 4.68 % Allowed : 23.09 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.39 (0.17), residues: 2527 helix: 1.23 (0.15), residues: 1217 sheet: -0.15 (0.32), residues: 246 loop : -0.74 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 238 TYR 0.018 0.002 TYR B 88 PHE 0.014 0.001 PHE F 121 TRP 0.017 0.002 TRP C 335 HIS 0.011 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00407 (20701) covalent geometry : angle 0.68310 (27947) hydrogen bonds : bond 0.04637 ( 953) hydrogen bonds : angle 5.16761 ( 2753) metal coordination : bond 0.01272 ( 4) metal coordination : angle 5.65756 ( 12) Misc. bond : bond 0.08854 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 626 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8077 (pttt) REVERT: C 166 VAL cc_start: 0.8285 (m) cc_final: 0.8080 (t) REVERT: C 411 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5710 (mp0) REVERT: E 261 MET cc_start: 0.6920 (tpt) cc_final: 0.6366 (tpt) outliers start: 100 outliers final: 67 residues processed: 680 average time/residue: 0.7494 time to fit residues: 563.4274 Evaluate side-chains 686 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 617 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 231 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 145 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN B 297 HIS B 338 GLN C 98 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 128 GLN D 137 ASN D 167 ASN E 4 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119709 restraints weight = 32122.287| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.41 r_work: 0.3438 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 20721 Z= 0.185 Angle : 0.702 29.072 27959 Z= 0.329 Chirality : 0.046 0.201 2985 Planarity : 0.005 0.065 3594 Dihedral : 7.701 85.105 3220 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 5.05 % Allowed : 22.76 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.35 (0.17), residues: 2527 helix: 1.23 (0.15), residues: 1215 sheet: -0.18 (0.32), residues: 246 loop : -0.78 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 401 TYR 0.020 0.002 TYR B 88 PHE 0.014 0.001 PHE B 375 TRP 0.017 0.002 TRP C 335 HIS 0.011 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00418 (20701) covalent geometry : angle 0.69296 (27947) hydrogen bonds : bond 0.04741 ( 953) hydrogen bonds : angle 5.15299 ( 2753) metal coordination : bond 0.01306 ( 4) metal coordination : angle 5.58677 ( 12) Misc. bond : bond 0.08998 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 622 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: B 12 TYR cc_start: 0.8210 (t80) cc_final: 0.7926 (t80) REVERT: B 68 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8079 (pttt) REVERT: C 43 LYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5520 (mmmt) REVERT: C 411 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5455 (mp0) REVERT: C 414 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7367 (mtmt) REVERT: E 168 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7764 (mt) REVERT: E 261 MET cc_start: 0.6902 (tpt) cc_final: 0.6301 (tpt) REVERT: F 207 MET cc_start: 0.6706 (tmm) cc_final: 0.5900 (tmm) outliers start: 108 outliers final: 74 residues processed: 679 average time/residue: 0.7565 time to fit residues: 567.1194 Evaluate side-chains 702 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 624 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 182 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 164 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 205 optimal weight: 0.0980 chunk 213 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 338 GLN C 98 ASN C 298 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 137 ASN D 167 ASN E 4 GLN E 206 GLN E 250 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121662 restraints weight = 25468.507| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.22 r_work: 0.3478 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 20721 Z= 0.149 Angle : 0.686 29.078 27959 Z= 0.318 Chirality : 0.044 0.177 2985 Planarity : 0.004 0.047 3594 Dihedral : 7.505 83.841 3217 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 4.91 % Allowed : 23.46 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.38 (0.17), residues: 2527 helix: 1.25 (0.15), residues: 1227 sheet: -0.29 (0.31), residues: 258 loop : -0.76 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 401 TYR 0.017 0.001 TYR B 88 PHE 0.015 0.001 PHE A 409 TRP 0.016 0.001 TRP C 335 HIS 0.010 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00325 (20701) covalent geometry : angle 0.67511 (27947) hydrogen bonds : bond 0.04244 ( 953) hydrogen bonds : angle 5.07647 ( 2753) metal coordination : bond 0.00923 ( 4) metal coordination : angle 5.88323 ( 12) Misc. bond : bond 0.08070 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 624 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8033 (pttt) REVERT: C 43 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5595 (mmmt) REVERT: C 76 LYS cc_start: 0.8088 (pttt) cc_final: 0.7783 (pttt) REVERT: C 256 ASP cc_start: 0.7884 (t0) cc_final: 0.7660 (t70) REVERT: C 411 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5380 (mp0) REVERT: C 414 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7325 (mtmt) REVERT: C 462 ASP cc_start: 0.7957 (m-30) cc_final: 0.7721 (m-30) REVERT: D 32 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7250 (mt-10) REVERT: E 75 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8093 (m) REVERT: E 168 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7736 (mt) REVERT: E 261 MET cc_start: 0.6776 (tpt) cc_final: 0.6172 (tpt) outliers start: 105 outliers final: 71 residues processed: 672 average time/residue: 0.7383 time to fit residues: 548.1807 Evaluate side-chains 684 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 608 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 93 optimal weight: 0.0070 chunk 147 optimal weight: 0.0670 chunk 153 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 231 optimal weight: 0.6980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 145 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 338 GLN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 137 ASN D 167 ASN E 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122372 restraints weight = 28099.242| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.30 r_work: 0.3484 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 20721 Z= 0.128 Angle : 0.672 29.048 27959 Z= 0.310 Chirality : 0.043 0.207 2985 Planarity : 0.004 0.040 3594 Dihedral : 7.291 85.361 3217 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.82 % Allowed : 24.15 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.47 (0.17), residues: 2527 helix: 1.34 (0.15), residues: 1229 sheet: -0.27 (0.31), residues: 258 loop : -0.74 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 238 TYR 0.016 0.001 TYR B 88 PHE 0.013 0.001 PHE B 375 TRP 0.016 0.001 TRP C 335 HIS 0.010 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00273 (20701) covalent geometry : angle 0.66095 (27947) hydrogen bonds : bond 0.03807 ( 953) hydrogen bonds : angle 4.98436 ( 2753) metal coordination : bond 0.00710 ( 4) metal coordination : angle 5.89533 ( 12) Misc. bond : bond 0.07119 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 614 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.8149 (mppt) cc_final: 0.7928 (mppt) REVERT: B 12 TYR cc_start: 0.8146 (t80) cc_final: 0.7874 (t80) REVERT: B 68 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8021 (pttt) REVERT: C 76 LYS cc_start: 0.8059 (pttt) cc_final: 0.7621 (pttt) REVERT: C 411 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5648 (mp0) REVERT: D 32 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7109 (mt-10) REVERT: D 242 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8123 (ttp-170) REVERT: E 140 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7935 (mtm180) REVERT: E 165 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8322 (p) REVERT: E 168 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7723 (mt) REVERT: E 261 MET cc_start: 0.6823 (tpt) cc_final: 0.6148 (tpt) REVERT: F 3 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7581 (mtm180) outliers start: 104 outliers final: 62 residues processed: 666 average time/residue: 0.7584 time to fit residues: 558.0418 Evaluate side-chains 673 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 606 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 3 ARG Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 55 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 338 GLN C 98 ASN C 298 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 137 ASN D 167 ASN E 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.137535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119437 restraints weight = 27098.826| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.27 r_work: 0.3442 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.198 20721 Z= 0.254 Angle : 0.751 29.084 27959 Z= 0.357 Chirality : 0.049 0.264 2985 Planarity : 0.005 0.061 3594 Dihedral : 7.477 83.290 3211 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.45 % Allowed : 24.43 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.19 (0.17), residues: 2527 helix: 1.06 (0.15), residues: 1235 sheet: -0.41 (0.31), residues: 272 loop : -0.81 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 238 TYR 0.023 0.002 TYR B 88 PHE 0.019 0.002 PHE F 121 TRP 0.018 0.002 TRP C 335 HIS 0.011 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00592 (20701) covalent geometry : angle 0.74240 (27947) hydrogen bonds : bond 0.05361 ( 953) hydrogen bonds : angle 5.22000 ( 2753) metal coordination : bond 0.01851 ( 4) metal coordination : angle 5.45228 ( 12) Misc. bond : bond 0.09705 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 621 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: B 7 LYS cc_start: 0.8120 (mppt) cc_final: 0.7905 (mppt) REVERT: B 68 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8110 (pttt) REVERT: C 76 LYS cc_start: 0.8202 (pttt) cc_final: 0.7862 (pttt) REVERT: C 411 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5759 (mp0) REVERT: D 32 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7250 (mt-10) REVERT: E 168 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7797 (mt) REVERT: E 207 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7128 (tmm) REVERT: E 261 MET cc_start: 0.6831 (tpt) cc_final: 0.6189 (tpt) REVERT: F 207 MET cc_start: 0.6779 (tmm) cc_final: 0.5998 (tmm) outliers start: 96 outliers final: 73 residues processed: 664 average time/residue: 0.7487 time to fit residues: 548.8123 Evaluate side-chains 699 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 622 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 265 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 125 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS C 98 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 137 ASN D 167 ASN E 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.138465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120436 restraints weight = 27409.047| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.28 r_work: 0.3458 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 20721 Z= 0.189 Angle : 0.728 29.035 27959 Z= 0.343 Chirality : 0.047 0.268 2985 Planarity : 0.005 0.066 3594 Dihedral : 7.342 83.743 3209 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.36 % Allowed : 25.22 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.25 (0.17), residues: 2527 helix: 1.17 (0.15), residues: 1217 sheet: -0.31 (0.31), residues: 258 loop : -0.85 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 187 TYR 0.020 0.002 TYR B 88 PHE 0.016 0.002 PHE A 409 TRP 0.017 0.002 TRP C 335 HIS 0.010 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00429 (20701) covalent geometry : angle 0.71791 (27947) hydrogen bonds : bond 0.04742 ( 953) hydrogen bonds : angle 5.17051 ( 2753) metal coordination : bond 0.01316 ( 4) metal coordination : angle 5.76925 ( 12) Misc. bond : bond 0.08820 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 620 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: B 7 LYS cc_start: 0.8118 (mppt) cc_final: 0.7901 (mppt) REVERT: B 12 TYR cc_start: 0.8214 (t80) cc_final: 0.7941 (t80) REVERT: B 68 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8080 (pttt) REVERT: C 76 LYS cc_start: 0.8181 (pttt) cc_final: 0.7789 (pttt) REVERT: C 256 ASP cc_start: 0.7917 (t0) cc_final: 0.7684 (t70) REVERT: C 411 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5864 (mp0) REVERT: C 462 ASP cc_start: 0.7958 (m-30) cc_final: 0.7735 (m-30) REVERT: D 32 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7175 (mt-10) REVERT: E 135 PHE cc_start: 0.8547 (m-80) cc_final: 0.8216 (m-80) REVERT: E 168 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7781 (mt) REVERT: E 261 MET cc_start: 0.6820 (tpt) cc_final: 0.6183 (tpt) REVERT: F 207 MET cc_start: 0.6726 (tmm) cc_final: 0.5961 (tmm) outliers start: 94 outliers final: 77 residues processed: 663 average time/residue: 0.7552 time to fit residues: 552.9324 Evaluate side-chains 690 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 610 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 469 ASN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 265 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 142 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 220 optimal weight: 0.0670 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 0.0040 overall best weight: 0.4930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 338 GLN C 98 ASN C 298 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 137 ASN D 167 ASN E 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121404 restraints weight = 27736.144| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.29 r_work: 0.3472 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 20721 Z= 0.152 Angle : 0.711 29.049 27959 Z= 0.332 Chirality : 0.045 0.195 2985 Planarity : 0.005 0.084 3594 Dihedral : 7.195 85.616 3209 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.89 % Allowed : 25.64 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.33 (0.17), residues: 2527 helix: 1.26 (0.15), residues: 1217 sheet: -0.32 (0.31), residues: 258 loop : -0.83 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 46 TYR 0.017 0.001 TYR B 88 PHE 0.017 0.001 PHE A 409 TRP 0.017 0.001 TRP C 335 HIS 0.011 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00337 (20701) covalent geometry : angle 0.70057 (27947) hydrogen bonds : bond 0.04238 ( 953) hydrogen bonds : angle 5.10659 ( 2753) metal coordination : bond 0.00947 ( 4) metal coordination : angle 5.85590 ( 12) Misc. bond : bond 0.07890 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 606 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: B 7 LYS cc_start: 0.8119 (mppt) cc_final: 0.7890 (mppt) REVERT: B 68 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8020 (pttt) REVERT: C 76 LYS cc_start: 0.8125 (pttt) cc_final: 0.7784 (pttt) REVERT: D 32 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7324 (mt-10) REVERT: E 75 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8111 (m) REVERT: E 165 SER cc_start: 0.8639 (t) cc_final: 0.8277 (p) REVERT: E 261 MET cc_start: 0.6814 (tpt) cc_final: 0.6185 (tpt) REVERT: F 207 MET cc_start: 0.6670 (tmm) cc_final: 0.5899 (tmm) outliers start: 84 outliers final: 69 residues processed: 644 average time/residue: 0.7612 time to fit residues: 540.8176 Evaluate side-chains 674 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 603 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 469 ASN Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 265 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 82 optimal weight: 0.7980 chunk 227 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 5 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 338 GLN C 98 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 128 GLN D 137 ASN D 167 ASN E 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121078 restraints weight = 31080.004| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.39 r_work: 0.3462 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 20721 Z= 0.151 Angle : 0.716 29.028 27959 Z= 0.334 Chirality : 0.045 0.208 2985 Planarity : 0.004 0.064 3594 Dihedral : 7.133 86.827 3209 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.80 % Allowed : 25.78 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.35 (0.17), residues: 2527 helix: 1.27 (0.15), residues: 1217 sheet: -0.32 (0.32), residues: 258 loop : -0.81 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 46 TYR 0.018 0.001 TYR B 88 PHE 0.018 0.001 PHE A 409 TRP 0.017 0.001 TRP C 335 HIS 0.011 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00334 (20701) covalent geometry : angle 0.70561 (27947) hydrogen bonds : bond 0.04222 ( 953) hydrogen bonds : angle 5.08771 ( 2753) metal coordination : bond 0.01012 ( 4) metal coordination : angle 5.85677 ( 12) Misc. bond : bond 0.07760 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11973.40 seconds wall clock time: 203 minutes 20.32 seconds (12200.32 seconds total)