Starting phenix.real_space_refine on Sun Aug 24 16:21:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2c_17360/08_2025/8p2c_17360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2c_17360/08_2025/8p2c_17360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p2c_17360/08_2025/8p2c_17360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2c_17360/08_2025/8p2c_17360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p2c_17360/08_2025/8p2c_17360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2c_17360/08_2025/8p2c_17360.map" } resolution = 2.59 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 4 5.21 5 S 136 5.16 5 C 13258 2.51 5 N 3694 2.21 5 O 4045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21173 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5203 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "B" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "C" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.76, per 1000 atoms: 0.18 Number of scatterers: 21173 At special positions: 0 Unit cell: (168.434, 104.107, 129.499, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 36 15.00 Mg 4 11.99 O 4045 8.00 N 3694 7.00 C 13258 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=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 880.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4864 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 14 sheets defined 54.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.575A pdb=" N ALA A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 4.207A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.614A pdb=" N GLN A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 92 removed outlier: 3.854A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 121 through 142 removed outlier: 3.699A pdb=" N ALA A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 175 through 182 removed outlier: 4.064A pdb=" N ILE A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.949A pdb=" N VAL A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 247 Proline residue: A 230 - end of helix removed outlier: 4.160A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 301 removed outlier: 3.626A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.699A pdb=" N LYS A 408 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 455 through 486 removed outlier: 3.534A pdb=" N ASN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.548A pdb=" N ILE A 517 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 518 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS A 519 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 544 through 570 removed outlier: 3.728A pdb=" N GLN A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 596 removed outlier: 3.815A pdb=" N LYS A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.382A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'B' and resid 17 through 29 removed outlier: 3.550A pdb=" N MET B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 4.027A pdb=" N GLN B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.619A pdb=" N ALA B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 93 removed outlier: 4.081A pdb=" N ALA B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.922A pdb=" N SER B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 103' Processing helix chain 'B' and resid 121 through 142 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 175 through 182 removed outlier: 4.156A pdb=" N ILE B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.717A pdb=" N LEU B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 229 through 247 removed outlier: 4.020A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 277 through 305 removed outlier: 3.845A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 3.512A pdb=" N CYS B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 331 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.953A pdb=" N CYS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.588A pdb=" N LYS B 408 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'B' and resid 462 through 486 removed outlier: 3.731A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 512 through 520 removed outlier: 4.554A pdb=" N SER B 515 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 517 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN B 518 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS B 519 " --> pdb=" O VAL B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 535 removed outlier: 3.549A pdb=" N CYS B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 570 removed outlier: 4.058A pdb=" N GLN B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU B 549 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 596 removed outlier: 3.883A pdb=" N GLN B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 630 through 633 removed outlier: 3.691A pdb=" N ASP B 633 " --> pdb=" O PRO B 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 633' Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.508A pdb=" N VAL B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 29 removed outlier: 3.728A pdb=" N MET C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 removed outlier: 3.935A pdb=" N ILE C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 70 removed outlier: 3.718A pdb=" N LYS C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 92 removed outlier: 3.860A pdb=" N GLN C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS C 79 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 101 Processing helix chain 'C' and resid 121 through 142 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 175 through 182 removed outlier: 4.208A pdb=" N ILE C 179 " --> pdb=" O PRO C 175 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.975A pdb=" N ALA C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 231 through 247 removed outlier: 3.702A pdb=" N GLU C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 301 removed outlier: 3.605A pdb=" N GLN C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 290 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 339 removed outlier: 3.529A pdb=" N ARG C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.648A pdb=" N TYR C 371 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.754A pdb=" N LYS C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 457 through 486 removed outlier: 3.651A pdb=" N ASP C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.539A pdb=" N GLN C 492 " --> pdb=" O MET C 489 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 493 " --> pdb=" O ALA C 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 493' Processing helix chain 'C' and resid 513 through 518 removed outlier: 4.403A pdb=" N ASN C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 537 Processing helix chain 'C' and resid 544 through 570 removed outlier: 3.525A pdb=" N GLN C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 596 removed outlier: 3.857A pdb=" N LYS C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 629 Processing helix chain 'C' and resid 653 through 666 Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.537A pdb=" N LYS D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 4.570A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 69 removed outlier: 3.645A pdb=" N ALA D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 93 removed outlier: 3.969A pdb=" N ALA D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 121 through 142 Proline residue: D 136 - end of helix Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 175 through 183 removed outlier: 4.174A pdb=" N ILE D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 213 removed outlier: 3.636A pdb=" N ALA D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.543A pdb=" N LEU D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 removed outlier: 4.008A pdb=" N ARG D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.883A pdb=" N TYR D 255 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 304 removed outlier: 3.534A pdb=" N HIS D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS D 303 " --> pdb=" O MET D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 removed outlier: 3.546A pdb=" N GLN D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.694A pdb=" N LYS D 408 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 Processing helix chain 'D' and resid 455 through 486 removed outlier: 3.506A pdb=" N ASN D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 493 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 512 through 516 removed outlier: 4.420A pdb=" N SER D 515 " --> pdb=" O THR D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 537 Processing helix chain 'D' and resid 544 through 570 Processing helix chain 'D' and resid 588 through 596 removed outlier: 3.967A pdb=" N GLN D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 630 through 635 removed outlier: 4.391A pdb=" N ASP D 633 " --> pdb=" O PRO D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 666 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.455A pdb=" N THR A 4 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 removed outlier: 5.119A pdb=" N ASN A 435 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLY A 523 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 437 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLY A 525 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 527 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 441 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 526 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.525A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN A 219 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN A 316 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 221 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 641 " --> pdb=" O SER A 672 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.883A pdb=" N GLY B 523 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B 438 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY B 525 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR B 440 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE B 527 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN B 442 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 526 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 173 removed outlier: 6.497A pdb=" N VAL B 172 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER B 313 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE B 352 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 315 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS B 354 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B 317 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN B 351 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU B 387 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP B 353 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 186 removed outlier: 3.575A pdb=" N GLY B 189 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.352A pdb=" N THR C 4 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 156 through 158 removed outlier: 5.139A pdb=" N ASN C 435 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLY C 523 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 437 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY C 525 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER C 439 " --> pdb=" O GLY C 525 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE C 527 " --> pdb=" O SER C 439 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE C 441 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C 522 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 576 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE C 524 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 173 removed outlier: 6.609A pdb=" N VAL C 172 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN C 219 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASN C 316 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 221 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 313 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE C 352 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 315 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LYS C 354 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR C 317 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.644A pdb=" N SER D 53 " --> pdb=" O ILE D 2 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 156 through 158 removed outlier: 5.021A pdb=" N ASN D 435 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY D 523 " --> pdb=" O ASN D 435 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER D 437 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLY D 525 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER D 439 " --> pdb=" O GLY D 525 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE D 527 " --> pdb=" O SER D 439 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE D 441 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE D 526 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 172 through 173 removed outlier: 6.463A pdb=" N VAL D 172 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER D 313 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE D 352 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 315 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LYS D 354 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR D 317 " --> pdb=" O LYS D 354 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN D 351 " --> pdb=" O ASN D 385 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU D 387 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP D 353 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 184 through 186 removed outlier: 3.557A pdb=" N GLY D 189 " --> pdb=" O ALA D 186 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2544 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: 4.02 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6968 1.34 - 1.46: 3841 1.46 - 1.58: 10502 1.58 - 1.69: 58 1.69 - 1.81: 236 Bond restraints: 21605 Sorted by residual: bond pdb=" CA TYR B 607 " pdb=" C TYR B 607 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.08e-02 8.57e+03 9.40e-01 bond pdb=" CA LYS C 135 " pdb=" C LYS C 135 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.23e-02 6.61e+03 8.82e-01 bond pdb=" CA GLY C 325 " pdb=" C GLY C 325 " ideal model delta sigma weight residual 1.515 1.509 0.006 6.20e-03 2.60e+04 8.79e-01 bond pdb=" CA LYS A 135 " pdb=" C LYS A 135 " ideal model delta sigma weight residual 1.520 1.532 -0.011 1.23e-02 6.61e+03 8.33e-01 bond pdb=" CG PRO D 384 " pdb=" CD PRO D 384 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.87e-01 ... (remaining 21600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 28665 1.47 - 2.94: 453 2.94 - 4.40: 59 4.40 - 5.87: 16 5.87 - 7.34: 4 Bond angle restraints: 29197 Sorted by residual: angle pdb=" C ARG D 604 " pdb=" N ASP D 605 " pdb=" CA ASP D 605 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ILE B 443 " pdb=" CA ILE B 443 " pdb=" C ILE B 443 " ideal model delta sigma weight residual 113.71 110.22 3.49 9.50e-01 1.11e+00 1.35e+01 angle pdb=" C SER C 48 " pdb=" N TYR C 49 " pdb=" CA TYR C 49 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.64e+00 angle pdb=" N VAL B 377 " pdb=" CA VAL B 377 " pdb=" C VAL B 377 " ideal model delta sigma weight residual 111.81 109.58 2.23 8.60e-01 1.35e+00 6.72e+00 angle pdb=" C ALA C 504 " pdb=" N GLU C 505 " pdb=" CA GLU C 505 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.32e+00 ... (remaining 29192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 12218 17.65 - 35.30: 723 35.30 - 52.95: 207 52.95 - 70.59: 50 70.59 - 88.24: 23 Dihedral angle restraints: 13221 sinusoidal: 5665 harmonic: 7556 Sorted by residual: dihedral pdb=" CA ILE B 460 " pdb=" C ILE B 460 " pdb=" N ASP B 461 " pdb=" CA ASP B 461 " ideal model delta harmonic sigma weight residual 180.00 149.51 30.49 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA GLY B 34 " pdb=" C GLY B 34 " pdb=" N GLU B 35 " pdb=" CA GLU B 35 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA SER D 71 " pdb=" C SER D 71 " pdb=" N ALA D 72 " pdb=" CA ALA D 72 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 13218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1642 0.027 - 0.053: 901 0.053 - 0.080: 391 0.080 - 0.106: 131 0.106 - 0.133: 69 Chirality restraints: 3134 Sorted by residual: chirality pdb=" CA ILE D 598 " pdb=" N ILE D 598 " pdb=" C ILE D 598 " pdb=" CB ILE D 598 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL D 613 " pdb=" N VAL D 613 " pdb=" C VAL D 613 " pdb=" CB VAL D 613 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 3131 not shown) Planarity restraints: 3718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 298 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C ASN B 298 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN B 298 " -0.011 2.00e-02 2.50e+03 pdb=" N MET B 299 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 121 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 122 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 121 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO C 122 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " -0.022 5.00e-02 4.00e+02 ... (remaining 3715 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 101 2.53 - 3.12: 15481 3.12 - 3.71: 31294 3.71 - 4.31: 45268 4.31 - 4.90: 77305 Nonbonded interactions: 169449 Sorted by model distance: nonbonded pdb=" O3B DTP C 801 " pdb="MG MG D 804 " model vdw 1.935 2.170 nonbonded pdb=" O2A DTP A 801 " pdb="MG MG B 804 " model vdw 2.009 2.170 nonbonded pdb="MG MG C 804 " pdb=" O3G DTP D 801 " model vdw 2.025 2.170 nonbonded pdb=" O3B DTP A 801 " pdb="MG MG B 804 " model vdw 2.037 2.170 nonbonded pdb=" O2A DTP C 801 " pdb="MG MG D 804 " model vdw 2.038 2.170 ... (remaining 169444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 305 or resid 311 through 804)) selection = (chain 'B' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 804)) selection = (chain 'C' and (resid 1 through 305 or resid 311 through 804)) selection = (chain 'D' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 804)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.070 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.350 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.003 0.036 21605 Z= 0.134 Angle : 0.494 7.340 29197 Z= 0.277 Chirality : 0.042 0.133 3134 Planarity : 0.004 0.042 3718 Dihedral : 13.175 88.243 8357 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.04 % Rotamer: Outliers : 2.68 % Allowed : 5.81 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.17), residues: 2556 helix: 0.71 (0.16), residues: 1230 sheet: 0.72 (0.37), residues: 224 loop : -2.17 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 330 TYR 0.015 0.001 TYR B 163 PHE 0.015 0.001 PHE D 438 TRP 0.009 0.001 TRP A 409 HIS 0.003 0.001 HIS D 279 Details of bonding type rmsd covalent geometry : bond 0.00294 (21605) covalent geometry : angle 0.49444 (29197) hydrogen bonds : bond 0.17239 ( 878) hydrogen bonds : angle 5.89374 ( 2544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 572 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6747 (mm-30) REVERT: A 604 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.8037 (mtt-85) REVERT: A 628 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 645 ILE cc_start: 0.8613 (tt) cc_final: 0.8325 (pt) REVERT: B 96 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7725 (mtp180) REVERT: B 497 MET cc_start: 0.8725 (mmt) cc_final: 0.8185 (mmt) REVERT: C 206 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8084 (mm) REVERT: D 17 GLU cc_start: 0.7272 (tp30) cc_final: 0.7041 (tp30) REVERT: D 152 MET cc_start: 0.6358 (ttm) cc_final: 0.6065 (ttm) REVERT: D 160 ASP cc_start: 0.6753 (p0) cc_final: 0.6385 (p0) REVERT: D 273 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7431 (ttt-90) REVERT: D 405 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7137 (pp20) REVERT: D 587 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7206 (m-80) outliers start: 60 outliers final: 10 residues processed: 618 average time/residue: 0.5632 time to fit residues: 393.9265 Evaluate side-chains 503 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 490 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 338 GLN A 435 ASN A 455 ASN A 477 GLN A 518 ASN A 639 HIS A 667 ASN B 85 ASN B 88 ASN B 219 GLN B 271 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 342 ASN B 385 ASN B 388 ASN C 42 GLN C 54 GLN C 154 ASN C 181 ASN C 219 GLN C 242 ASN C 253 ASN C 338 GLN C 455 ASN C 458 GLN C 477 GLN C 492 GLN C 541 HIS C 609 ASN C 626 GLN D 30 HIS D 54 GLN D 78 GLN D 85 ASN D 213 ASN D 237 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122557 restraints weight = 30348.378| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.71 r_work: 0.3613 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21605 Z= 0.205 Angle : 0.609 10.944 29197 Z= 0.325 Chirality : 0.046 0.209 3134 Planarity : 0.005 0.041 3718 Dihedral : 11.760 91.039 3223 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.04 % Favored : 92.84 % Rotamer: Outliers : 4.38 % Allowed : 13.62 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.17), residues: 2556 helix: 0.62 (0.15), residues: 1252 sheet: 0.62 (0.36), residues: 234 loop : -2.23 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 400 TYR 0.023 0.002 TYR C 631 PHE 0.028 0.002 PHE D 184 TRP 0.011 0.002 TRP A 409 HIS 0.005 0.001 HIS C 541 Details of bonding type rmsd covalent geometry : bond 0.00484 (21605) covalent geometry : angle 0.60866 (29197) hydrogen bonds : bond 0.05850 ( 878) hydrogen bonds : angle 4.45060 ( 2544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 506 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (mpt) REVERT: A 357 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7762 (mtt180) REVERT: A 487 THR cc_start: 0.7808 (p) cc_final: 0.7403 (p) REVERT: A 508 LYS cc_start: 0.8411 (mppt) cc_final: 0.8162 (mmtt) REVERT: A 543 GLU cc_start: 0.7513 (tt0) cc_final: 0.7297 (mt-10) REVERT: A 549 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6462 (mp0) REVERT: A 594 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: B 397 GLU cc_start: 0.7791 (pp20) cc_final: 0.7568 (pp20) REVERT: B 449 GLU cc_start: 0.7489 (tt0) cc_final: 0.7163 (tm-30) REVERT: C 39 LEU cc_start: 0.8504 (tp) cc_final: 0.8195 (tt) REVERT: C 66 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7749 (tpt) REVERT: C 100 MET cc_start: 0.7572 (mpp) cc_final: 0.7281 (mpp) REVERT: C 301 THR cc_start: 0.8221 (t) cc_final: 0.7864 (m) REVERT: C 489 MET cc_start: 0.7726 (mtp) cc_final: 0.7442 (mtp) REVERT: D 41 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: D 148 ARG cc_start: 0.6859 (ttt-90) cc_final: 0.6566 (ttt-90) REVERT: D 152 MET cc_start: 0.6608 (ttm) cc_final: 0.6398 (ttm) REVERT: D 283 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7559 (mtpp) REVERT: D 548 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6189 (tt0) REVERT: D 587 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7233 (m-80) outliers start: 98 outliers final: 36 residues processed: 557 average time/residue: 0.6956 time to fit residues: 432.7723 Evaluate side-chains 512 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 469 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 1 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 105 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 88 ASN B 289 HIS ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN C 253 ASN C 541 HIS D 54 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.136534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123960 restraints weight = 30549.323| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.71 r_work: 0.3633 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21605 Z= 0.138 Angle : 0.539 7.192 29197 Z= 0.288 Chirality : 0.043 0.180 3134 Planarity : 0.004 0.042 3718 Dihedral : 11.147 86.816 3219 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 3.97 % Allowed : 15.45 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.17), residues: 2556 helix: 0.80 (0.15), residues: 1266 sheet: 0.96 (0.37), residues: 212 loop : -2.12 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 419 TYR 0.026 0.001 TYR B 371 PHE 0.023 0.002 PHE D 184 TRP 0.009 0.001 TRP A 409 HIS 0.005 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00318 (21605) covalent geometry : angle 0.53859 (29197) hydrogen bonds : bond 0.04708 ( 878) hydrogen bonds : angle 4.19587 ( 2544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 469 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8090 (mtt) cc_final: 0.7855 (mtm) REVERT: A 100 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7591 (mpt) REVERT: A 357 ARG cc_start: 0.7954 (mtp85) cc_final: 0.7711 (mtt180) REVERT: A 487 THR cc_start: 0.7702 (p) cc_final: 0.7409 (p) REVERT: A 508 LYS cc_start: 0.8450 (mppt) cc_final: 0.8183 (mmtt) REVERT: B 96 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7516 (mtp180) REVERT: B 397 GLU cc_start: 0.7805 (pp20) cc_final: 0.7441 (pp20) REVERT: B 449 GLU cc_start: 0.7481 (tt0) cc_final: 0.7128 (tm-30) REVERT: C 39 LEU cc_start: 0.8456 (tp) cc_final: 0.8202 (tt) REVERT: C 49 TYR cc_start: 0.7476 (t80) cc_final: 0.7076 (t80) REVERT: C 52 LYS cc_start: 0.7227 (mmmm) cc_final: 0.6992 (mmmm) REVERT: C 66 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7904 (tpt) REVERT: C 301 THR cc_start: 0.8181 (t) cc_final: 0.7850 (m) REVERT: D 41 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: D 254 LEU cc_start: 0.7259 (mt) cc_final: 0.7003 (mp) REVERT: D 449 GLU cc_start: 0.7590 (tt0) cc_final: 0.7281 (tm-30) REVERT: D 468 ASP cc_start: 0.6603 (OUTLIER) cc_final: 0.6327 (t0) REVERT: D 587 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7387 (m-80) outliers start: 89 outliers final: 32 residues processed: 517 average time/residue: 0.6448 time to fit residues: 372.7876 Evaluate side-chains 492 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 455 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 198 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 219 optimal weight: 0.9980 chunk 246 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 199 optimal weight: 0.0770 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN C 289 HIS C 338 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN D 626 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.135321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.122763 restraints weight = 29968.695| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.67 r_work: 0.3615 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21605 Z= 0.184 Angle : 0.574 7.511 29197 Z= 0.307 Chirality : 0.045 0.166 3134 Planarity : 0.004 0.043 3718 Dihedral : 11.146 86.970 3213 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 4.20 % Allowed : 16.03 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.17), residues: 2556 helix: 0.83 (0.15), residues: 1254 sheet: 0.39 (0.35), residues: 236 loop : -2.15 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 400 TYR 0.022 0.002 TYR B 371 PHE 0.025 0.002 PHE D 184 TRP 0.008 0.001 TRP C 425 HIS 0.006 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00436 (21605) covalent geometry : angle 0.57385 (29197) hydrogen bonds : bond 0.05379 ( 878) hydrogen bonds : angle 4.19542 ( 2544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 483 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8055 (mt) cc_final: 0.7840 (mp) REVERT: A 100 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7676 (mpt) REVERT: A 132 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 301 THR cc_start: 0.8315 (t) cc_final: 0.7991 (m) REVERT: A 508 LYS cc_start: 0.8468 (mppt) cc_final: 0.8203 (mmtt) REVERT: A 576 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8270 (tp) REVERT: B 96 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7526 (mtp180) REVERT: B 342 ASN cc_start: 0.7959 (m-40) cc_final: 0.7758 (m110) REVERT: B 344 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 382 PHE cc_start: 0.7012 (m-80) cc_final: 0.6763 (m-80) REVERT: B 397 GLU cc_start: 0.7878 (pp20) cc_final: 0.7564 (pp20) REVERT: B 449 GLU cc_start: 0.7475 (tt0) cc_final: 0.7125 (tm-30) REVERT: B 663 MET cc_start: 0.5380 (mmm) cc_final: 0.5097 (mmm) REVERT: C 39 LEU cc_start: 0.8427 (tp) cc_final: 0.8008 (tt) REVERT: C 49 TYR cc_start: 0.7485 (t80) cc_final: 0.7109 (t80) REVERT: C 52 LYS cc_start: 0.7248 (mmmm) cc_final: 0.6999 (mmmm) REVERT: C 66 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7844 (tpt) REVERT: C 301 THR cc_start: 0.8231 (t) cc_final: 0.7910 (m) REVERT: C 628 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7974 (mt-10) REVERT: D 449 GLU cc_start: 0.7661 (tt0) cc_final: 0.7340 (tm-30) REVERT: D 587 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7467 (m-80) outliers start: 94 outliers final: 42 residues processed: 530 average time/residue: 0.6393 time to fit residues: 379.2147 Evaluate side-chains 523 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 476 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 82 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN C 338 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.137846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125153 restraints weight = 29737.981| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.70 r_work: 0.3615 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21605 Z= 0.174 Angle : 0.573 7.340 29197 Z= 0.306 Chirality : 0.045 0.168 3134 Planarity : 0.004 0.044 3718 Dihedral : 10.958 86.925 3209 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.04 % Rotamer: Outliers : 4.15 % Allowed : 16.61 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.17), residues: 2556 helix: 0.88 (0.15), residues: 1252 sheet: 0.34 (0.35), residues: 236 loop : -2.13 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 148 TYR 0.022 0.002 TYR D 337 PHE 0.026 0.002 PHE D 184 TRP 0.009 0.001 TRP A 409 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00411 (21605) covalent geometry : angle 0.57279 (29197) hydrogen bonds : bond 0.05160 ( 878) hydrogen bonds : angle 4.15582 ( 2544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 483 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8077 (mt) cc_final: 0.7820 (mp) REVERT: A 70 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8461 (mtmp) REVERT: A 100 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7624 (mpt) REVERT: A 195 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6869 (mtpp) REVERT: A 301 THR cc_start: 0.8380 (t) cc_final: 0.8062 (m) REVERT: A 398 LYS cc_start: 0.8402 (mtpm) cc_final: 0.8158 (ttmt) REVERT: A 508 LYS cc_start: 0.8478 (mppt) cc_final: 0.8215 (mmtt) REVERT: A 576 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8272 (tp) REVERT: B 96 ARG cc_start: 0.7802 (mtp180) cc_final: 0.7533 (mtp180) REVERT: B 342 ASN cc_start: 0.7976 (m-40) cc_final: 0.7761 (m110) REVERT: B 344 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 397 GLU cc_start: 0.7901 (pp20) cc_final: 0.7578 (pp20) REVERT: B 449 GLU cc_start: 0.7460 (tt0) cc_final: 0.7099 (tm-30) REVERT: B 663 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.4981 (mmm) REVERT: C 39 LEU cc_start: 0.8438 (tp) cc_final: 0.8173 (tt) REVERT: C 47 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6793 (mm) REVERT: C 49 TYR cc_start: 0.7463 (t80) cc_final: 0.7097 (t80) REVERT: C 52 LYS cc_start: 0.7286 (mmmm) cc_final: 0.7023 (mmmm) REVERT: C 66 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7927 (tpt) REVERT: C 301 THR cc_start: 0.8250 (t) cc_final: 0.7931 (m) REVERT: C 380 ARG cc_start: 0.8059 (tpt-90) cc_final: 0.7632 (tpt-90) REVERT: C 414 MET cc_start: 0.8407 (ttp) cc_final: 0.8115 (ttp) REVERT: C 628 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 41 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: D 370 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5831 (mt) REVERT: D 449 GLU cc_start: 0.7654 (tt0) cc_final: 0.7367 (tm-30) REVERT: D 468 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6376 (t0) REVERT: D 587 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7522 (m-80) outliers start: 93 outliers final: 48 residues processed: 532 average time/residue: 0.6488 time to fit residues: 386.6398 Evaluate side-chains 533 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 475 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 121 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 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 278 GLN C 667 ASN D 54 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.125931 restraints weight = 29830.418| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.67 r_work: 0.3617 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21605 Z= 0.175 Angle : 0.581 7.640 29197 Z= 0.309 Chirality : 0.045 0.165 3134 Planarity : 0.004 0.044 3718 Dihedral : 10.912 87.564 3209 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.04 % Favored : 92.88 % Rotamer: Outliers : 4.15 % Allowed : 17.11 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.17), residues: 2556 helix: 0.95 (0.15), residues: 1246 sheet: 0.30 (0.35), residues: 236 loop : -2.13 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 148 TYR 0.023 0.002 TYR D 337 PHE 0.028 0.002 PHE D 184 TRP 0.008 0.001 TRP C 425 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00413 (21605) covalent geometry : angle 0.58073 (29197) hydrogen bonds : bond 0.05180 ( 878) hydrogen bonds : angle 4.13685 ( 2544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 479 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8066 (mt) cc_final: 0.7781 (mp) REVERT: A 100 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7656 (mpt) REVERT: A 195 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6879 (mtpp) REVERT: A 301 THR cc_start: 0.8380 (t) cc_final: 0.8171 (t) REVERT: A 508 LYS cc_start: 0.8476 (mppt) cc_final: 0.8226 (mmtt) REVERT: A 576 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8275 (tp) REVERT: A 586 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8389 (mttm) REVERT: A 603 ASP cc_start: 0.7050 (m-30) cc_final: 0.6796 (m-30) REVERT: B 96 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7555 (mtp180) REVERT: B 342 ASN cc_start: 0.7983 (m-40) cc_final: 0.7775 (m110) REVERT: B 344 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 382 PHE cc_start: 0.6990 (m-80) cc_final: 0.6755 (m-80) REVERT: B 397 GLU cc_start: 0.7903 (pp20) cc_final: 0.7586 (pp20) REVERT: B 449 GLU cc_start: 0.7447 (tt0) cc_final: 0.7101 (tm-30) REVERT: C 39 LEU cc_start: 0.8427 (tp) cc_final: 0.8155 (tt) REVERT: C 47 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6797 (mm) REVERT: C 49 TYR cc_start: 0.7454 (t80) cc_final: 0.7101 (t80) REVERT: C 52 LYS cc_start: 0.7303 (mmmm) cc_final: 0.7031 (mmmm) REVERT: C 66 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7980 (tpt) REVERT: C 301 THR cc_start: 0.8255 (t) cc_final: 0.7952 (m) REVERT: C 380 ARG cc_start: 0.8058 (tpt-90) cc_final: 0.7629 (tpt-90) REVERT: C 414 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7970 (ttp) REVERT: C 628 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8025 (mt-10) REVERT: D 41 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: D 370 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5843 (mt) REVERT: D 449 GLU cc_start: 0.7640 (tt0) cc_final: 0.7327 (tm-30) REVERT: D 468 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6274 (t0) REVERT: D 587 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7546 (m-80) outliers start: 93 outliers final: 53 residues processed: 526 average time/residue: 0.6442 time to fit residues: 378.8244 Evaluate side-chains 539 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 476 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 220 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 154 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN C 181 ASN D 54 GLN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.135447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123003 restraints weight = 29918.825| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.67 r_work: 0.3622 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21605 Z= 0.165 Angle : 0.579 7.263 29197 Z= 0.308 Chirality : 0.045 0.160 3134 Planarity : 0.004 0.044 3718 Dihedral : 10.838 87.613 3209 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 3.80 % Allowed : 18.18 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.17), residues: 2556 helix: 1.00 (0.15), residues: 1246 sheet: 0.30 (0.35), residues: 236 loop : -2.11 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 148 TYR 0.021 0.001 TYR D 337 PHE 0.028 0.002 PHE D 184 TRP 0.008 0.001 TRP A 409 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00388 (21605) covalent geometry : angle 0.57888 (29197) hydrogen bonds : bond 0.05018 ( 878) hydrogen bonds : angle 4.10841 ( 2544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 474 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8531 (mtmp) cc_final: 0.7951 (mtmt) REVERT: A 100 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7634 (mpt) REVERT: A 195 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6874 (mtpp) REVERT: A 301 THR cc_start: 0.8378 (t) cc_final: 0.8172 (t) REVERT: A 508 LYS cc_start: 0.8490 (mppt) cc_final: 0.8237 (mmtt) REVERT: A 576 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8263 (tp) REVERT: B 96 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7536 (mtp180) REVERT: B 342 ASN cc_start: 0.7992 (m-40) cc_final: 0.7789 (m110) REVERT: B 344 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 382 PHE cc_start: 0.6970 (m-80) cc_final: 0.6738 (m-80) REVERT: B 397 GLU cc_start: 0.7901 (pp20) cc_final: 0.7609 (OUTLIER) REVERT: C 39 LEU cc_start: 0.8448 (tp) cc_final: 0.8075 (tt) REVERT: C 47 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6780 (mm) REVERT: C 49 TYR cc_start: 0.7457 (t80) cc_final: 0.7121 (t80) REVERT: C 66 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7961 (tpt) REVERT: C 275 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6644 (ptp-170) REVERT: C 301 THR cc_start: 0.8236 (t) cc_final: 0.7935 (m) REVERT: C 380 ARG cc_start: 0.8080 (tpt-90) cc_final: 0.7650 (tpt-90) REVERT: C 628 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 41 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: D 163 TYR cc_start: 0.8530 (m-80) cc_final: 0.8304 (m-80) REVERT: D 468 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6265 (t0) outliers start: 85 outliers final: 53 residues processed: 515 average time/residue: 0.6550 time to fit residues: 377.4156 Evaluate side-chains 526 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 466 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 201 optimal weight: 0.0270 chunk 150 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 175 optimal weight: 0.0570 chunk 105 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124560 restraints weight = 29946.170| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.67 r_work: 0.3642 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21605 Z= 0.127 Angle : 0.552 6.900 29197 Z= 0.293 Chirality : 0.043 0.159 3134 Planarity : 0.004 0.044 3718 Dihedral : 10.511 89.858 3209 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 3.17 % Allowed : 19.16 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.17), residues: 2556 helix: 1.14 (0.15), residues: 1246 sheet: 0.55 (0.36), residues: 234 loop : -2.12 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 148 TYR 0.024 0.001 TYR D 337 PHE 0.028 0.001 PHE D 184 TRP 0.009 0.001 TRP A 409 HIS 0.005 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00288 (21605) covalent geometry : angle 0.55192 (29197) hydrogen bonds : bond 0.04332 ( 878) hydrogen bonds : angle 4.01776 ( 2544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 460 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7802 (mtm) cc_final: 0.7502 (mmm) REVERT: A 67 GLU cc_start: 0.7854 (tp30) cc_final: 0.7625 (tp30) REVERT: A 70 LYS cc_start: 0.8500 (mtmp) cc_final: 0.8034 (mtmt) REVERT: A 100 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7589 (mpt) REVERT: A 195 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6808 (mtpp) REVERT: A 237 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: A 301 THR cc_start: 0.8348 (t) cc_final: 0.8146 (t) REVERT: A 489 MET cc_start: 0.7658 (mtp) cc_final: 0.7349 (mtp) REVERT: A 508 LYS cc_start: 0.8449 (mppt) cc_final: 0.8205 (mmtt) REVERT: A 576 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8253 (tp) REVERT: A 586 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8407 (mttm) REVERT: A 603 ASP cc_start: 0.6980 (m-30) cc_final: 0.6749 (m-30) REVERT: B 96 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7537 (mtp180) REVERT: B 342 ASN cc_start: 0.7995 (m-40) cc_final: 0.7773 (m110) REVERT: B 344 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 382 PHE cc_start: 0.6957 (m-80) cc_final: 0.6736 (m-80) REVERT: B 397 GLU cc_start: 0.7893 (pp20) cc_final: 0.7560 (pp20) REVERT: C 39 LEU cc_start: 0.8376 (tp) cc_final: 0.7996 (tt) REVERT: C 47 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6745 (mm) REVERT: C 49 TYR cc_start: 0.7407 (t80) cc_final: 0.7080 (t80) REVERT: C 66 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7999 (tpt) REVERT: C 301 THR cc_start: 0.8221 (t) cc_final: 0.7928 (m) REVERT: C 380 ARG cc_start: 0.8048 (tpt-90) cc_final: 0.7627 (tpt-90) REVERT: C 628 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8027 (mt-10) REVERT: D 3 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: D 41 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: D 283 LYS cc_start: 0.7613 (mtpp) cc_final: 0.7391 (mtpp) REVERT: D 468 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6237 (t0) outliers start: 71 outliers final: 38 residues processed: 497 average time/residue: 0.5846 time to fit residues: 326.4528 Evaluate side-chains 502 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 455 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 185 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 52 optimal weight: 0.0570 chunk 70 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN B 541 HIS C 338 GLN D 18 GLN D 88 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.136486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124045 restraints weight = 29767.700| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.67 r_work: 0.3636 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21605 Z= 0.144 Angle : 0.570 9.099 29197 Z= 0.303 Chirality : 0.044 0.158 3134 Planarity : 0.004 0.044 3718 Dihedral : 10.485 86.618 3207 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.13 % Allowed : 19.25 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.17), residues: 2556 helix: 1.13 (0.15), residues: 1244 sheet: 0.40 (0.34), residues: 244 loop : -2.10 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 148 TYR 0.024 0.001 TYR D 337 PHE 0.028 0.002 PHE D 184 TRP 0.009 0.001 TRP A 409 HIS 0.004 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00337 (21605) covalent geometry : angle 0.57040 (29197) hydrogen bonds : bond 0.04605 ( 878) hydrogen bonds : angle 4.05037 ( 2544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 458 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7754 (mtm) cc_final: 0.7425 (mmm) REVERT: A 70 LYS cc_start: 0.8496 (mtmp) cc_final: 0.8100 (mtmt) REVERT: A 100 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7611 (mpt) REVERT: A 195 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6791 (mtpp) REVERT: A 237 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: A 508 LYS cc_start: 0.8466 (mppt) cc_final: 0.8229 (mmtt) REVERT: A 576 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 594 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: A 603 ASP cc_start: 0.6974 (m-30) cc_final: 0.6735 (m-30) REVERT: B 96 ARG cc_start: 0.7777 (mtp180) cc_final: 0.7505 (mtp180) REVERT: B 342 ASN cc_start: 0.8007 (m-40) cc_final: 0.7807 (m110) REVERT: B 344 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7635 (mm-30) REVERT: B 397 GLU cc_start: 0.7890 (pp20) cc_final: 0.7558 (pp20) REVERT: C 39 LEU cc_start: 0.8350 (tp) cc_final: 0.8052 (tt) REVERT: C 47 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6765 (mm) REVERT: C 49 TYR cc_start: 0.7437 (t80) cc_final: 0.7115 (t80) REVERT: C 275 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6514 (ptp-170) REVERT: C 301 THR cc_start: 0.8246 (t) cc_final: 0.7952 (m) REVERT: C 380 ARG cc_start: 0.8057 (tpt-90) cc_final: 0.7636 (tpt-90) REVERT: C 628 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8037 (mt-10) REVERT: D 3 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: D 41 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: D 468 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6355 (t0) REVERT: D 487 THR cc_start: 0.8387 (p) cc_final: 0.8181 (p) outliers start: 70 outliers final: 42 residues processed: 492 average time/residue: 0.6017 time to fit residues: 332.0588 Evaluate side-chains 508 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 456 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 134 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 250 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN B 334 GLN C 338 GLN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.138654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126023 restraints weight = 29776.793| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.70 r_work: 0.3626 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21605 Z= 0.157 Angle : 0.586 9.739 29197 Z= 0.311 Chirality : 0.045 0.172 3134 Planarity : 0.004 0.044 3718 Dihedral : 10.539 87.837 3207 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.64 % Allowed : 20.10 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.17), residues: 2556 helix: 1.10 (0.15), residues: 1244 sheet: 0.46 (0.34), residues: 242 loop : -2.09 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 148 TYR 0.024 0.001 TYR D 337 PHE 0.030 0.002 PHE D 184 TRP 0.008 0.001 TRP A 409 HIS 0.004 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00370 (21605) covalent geometry : angle 0.58647 (29197) hydrogen bonds : bond 0.04816 ( 878) hydrogen bonds : angle 4.09694 ( 2544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 460 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7706 (mtm) cc_final: 0.7421 (mmm) REVERT: A 70 LYS cc_start: 0.8521 (mtmp) cc_final: 0.8161 (mtmt) REVERT: A 100 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7610 (mpt) REVERT: A 195 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6816 (mtpp) REVERT: A 237 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: A 508 LYS cc_start: 0.8471 (mppt) cc_final: 0.8237 (mmtt) REVERT: A 576 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8270 (tp) REVERT: A 594 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: A 603 ASP cc_start: 0.7014 (m-30) cc_final: 0.6788 (m-30) REVERT: B 96 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7532 (mtp180) REVERT: B 342 ASN cc_start: 0.8008 (m-40) cc_final: 0.7744 (m110) REVERT: B 344 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 397 GLU cc_start: 0.7906 (pp20) cc_final: 0.7587 (pp20) REVERT: C 39 LEU cc_start: 0.8286 (tp) cc_final: 0.7828 (tt) REVERT: C 47 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6790 (mm) REVERT: C 49 TYR cc_start: 0.7450 (t80) cc_final: 0.7138 (t80) REVERT: C 275 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6533 (ptp-170) REVERT: C 301 THR cc_start: 0.8259 (t) cc_final: 0.7974 (m) REVERT: C 380 ARG cc_start: 0.8085 (tpt-90) cc_final: 0.7655 (tpt-90) REVERT: D 3 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: D 41 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: D 283 LYS cc_start: 0.7557 (mtpp) cc_final: 0.7351 (mtpp) REVERT: D 468 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6382 (t0) outliers start: 59 outliers final: 43 residues processed: 489 average time/residue: 0.6521 time to fit residues: 356.6427 Evaluate side-chains 509 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 456 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 620 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 43 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 210 optimal weight: 0.4980 chunk 184 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 278 GLN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.122696 restraints weight = 29975.084| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.67 r_work: 0.3617 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21605 Z= 0.188 Angle : 0.621 13.544 29197 Z= 0.329 Chirality : 0.046 0.180 3134 Planarity : 0.004 0.043 3718 Dihedral : 10.731 88.983 3207 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.77 % Allowed : 20.01 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.17), residues: 2556 helix: 0.99 (0.15), residues: 1244 sheet: 0.23 (0.34), residues: 252 loop : -2.14 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 148 TYR 0.024 0.002 TYR D 337 PHE 0.031 0.002 PHE D 184 TRP 0.008 0.001 TRP C 425 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00448 (21605) covalent geometry : angle 0.62104 (29197) hydrogen bonds : bond 0.05280 ( 878) hydrogen bonds : angle 4.16634 ( 2544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8552.37 seconds wall clock time: 145 minutes 59.23 seconds (8759.23 seconds total)