Starting phenix.real_space_refine on Wed May 21 09:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2c_17360/05_2025/8p2c_17360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2c_17360/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p2c_17360/05_2025/8p2c_17360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2c_17360/05_2025/8p2c_17360.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2c_17360/05_2025/8p2c_17360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2c_17360/05_2025/8p2c_17360.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.41, per 1000 atoms: 0.78 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: 5.15 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.54 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: 7.15 Time building geometry restraints manager: 5.97 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 674 or \ resid 801 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 674 or resid 801 through 804)) selection = (chain 'C' and (resid 1 through 305 or resid 311 through 674 or resid 801 throug \ h 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 674 or resid 801 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: 6.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 50.990 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.540 ------------------------------------------------------------------------------- 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 : 5.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP A 409 HIS 0.003 0.001 HIS D 279 PHE 0.015 0.001 PHE D 438 TYR 0.015 0.001 TYR B 163 ARG 0.003 0.000 ARG C 330 Details of bonding type rmsd hydrogen bonds : bond 0.17239 ( 878) hydrogen bonds : angle 5.89374 ( 2544) covalent geometry : bond 0.00294 (21605) covalent geometry : angle 0.49444 (29197) *********************** 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 : 2.141 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: 1.3003 time to fit residues: 908.4393 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 : 2.318 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 0.0070 overall best weight: 0.3254 ------------------------------------------------------------------------------- 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 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 B 541 HIS C 42 GLN C 54 GLN C 88 ASN C 154 ASN C 181 ASN C 219 GLN C 237 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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.138675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.125884 restraints weight = 30417.503| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.72 r_work: 0.3659 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1854 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= 0.116 Angle : 0.530 10.735 29197 Z= 0.282 Chirality : 0.043 0.180 3134 Planarity : 0.004 0.038 3718 Dihedral : 11.159 87.470 3223 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 3.71 % Allowed : 13.53 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2556 helix: 0.85 (0.16), residues: 1264 sheet: 1.12 (0.37), residues: 212 loop : -2.04 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 409 HIS 0.006 0.001 HIS B 297 PHE 0.024 0.001 PHE B 641 TYR 0.019 0.001 TYR D 337 ARG 0.009 0.000 ARG D 400 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 878) hydrogen bonds : angle 4.29396 ( 2544) covalent geometry : bond 0.00256 (21605) covalent geometry : angle 0.52955 (29197) *********************** 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 568 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 485 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7582 (mtm) cc_final: 0.7260 (mmm) REVERT: A 489 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7397 (mtp) REVERT: A 549 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: A 594 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: A 645 ILE cc_start: 0.8514 (tt) cc_final: 0.8296 (pt) REVERT: B 96 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7605 (mtp180) REVERT: B 397 GLU cc_start: 0.7720 (pp20) cc_final: 0.7503 (pp20) REVERT: C 39 LEU cc_start: 0.8466 (tp) cc_final: 0.8141 (tt) REVERT: C 66 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7770 (tpt) REVERT: C 301 THR cc_start: 0.8066 (t) cc_final: 0.7829 (p) REVERT: C 489 MET cc_start: 0.7441 (mtp) cc_final: 0.7113 (mtp) REVERT: D 41 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: D 148 ARG cc_start: 0.6835 (ttt-90) cc_final: 0.6543 (ttt-90) REVERT: D 152 MET cc_start: 0.6611 (ttm) cc_final: 0.6388 (ttm) REVERT: D 397 GLU cc_start: 0.7354 (pm20) cc_final: 0.7152 (pm20) REVERT: D 548 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.6098 (tt0) REVERT: D 587 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7188 (m-80) outliers start: 83 outliers final: 22 residues processed: 528 average time/residue: 1.4069 time to fit residues: 832.8961 Evaluate side-chains 483 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 454 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET 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 66 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 311 VAL 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 22 optimal weight: 0.9980 chunk 253 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 96 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 208 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN B 46 HIS B 78 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS C 237 GLN C 253 ASN C 609 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125686 restraints weight = 29768.711| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.72 r_work: 0.3621 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21605 Z= 0.167 Angle : 0.559 7.731 29197 Z= 0.299 Chirality : 0.045 0.178 3134 Planarity : 0.004 0.039 3718 Dihedral : 11.084 85.868 3210 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 3.89 % Allowed : 15.36 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2556 helix: 0.82 (0.15), residues: 1266 sheet: 0.57 (0.35), residues: 234 loop : -2.09 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 409 HIS 0.005 0.001 HIS B 541 PHE 0.024 0.002 PHE D 184 TYR 0.021 0.002 TYR C 631 ARG 0.009 0.001 ARG D 400 Details of bonding type rmsd hydrogen bonds : bond 0.05277 ( 878) hydrogen bonds : angle 4.22500 ( 2544) covalent geometry : bond 0.00389 (21605) covalent geometry : angle 0.55865 (29197) *********************** 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 561 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 474 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7753 (mp0) REVERT: A 195 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.6925 (mtpp) REVERT: A 487 THR cc_start: 0.7801 (p) cc_final: 0.7567 (p) REVERT: A 508 LYS cc_start: 0.8432 (mppt) cc_final: 0.8177 (mmtt) REVERT: B 397 GLU cc_start: 0.7833 (pp20) cc_final: 0.7548 (pp20) REVERT: C 39 LEU cc_start: 0.8453 (tp) cc_final: 0.8184 (tt) REVERT: C 49 TYR cc_start: 0.7537 (t80) cc_final: 0.7147 (t80) REVERT: C 66 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7872 (tpt) REVERT: C 301 THR cc_start: 0.8166 (t) cc_final: 0.7832 (m) REVERT: D 41 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: D 148 ARG cc_start: 0.6745 (ttt-90) cc_final: 0.6450 (ttt-90) REVERT: D 152 MET cc_start: 0.6534 (ttm) cc_final: 0.6277 (ttm) REVERT: D 449 GLU cc_start: 0.7569 (tt0) cc_final: 0.7227 (tm-30) REVERT: D 468 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6392 (t0) REVERT: D 587 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7388 (m-80) outliers start: 87 outliers final: 33 residues processed: 518 average time/residue: 1.4444 time to fit residues: 839.2596 Evaluate side-chains 499 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 461 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 66 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 319 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 576 LEU 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 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 462 MET 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 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 265 LYS 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 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 392 THR Chi-restraints excluded: chain D residue 468 ASP 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 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 193 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 138 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 242 ASN B 289 HIS B 297 HIS B 342 ASN C 289 HIS C 338 GLN C 609 ASN D 242 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127017 restraints weight = 30028.518| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.72 r_work: 0.3643 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21605 Z= 0.136 Angle : 0.540 6.837 29197 Z= 0.287 Chirality : 0.043 0.176 3134 Planarity : 0.004 0.041 3718 Dihedral : 10.643 85.546 3208 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 3.80 % Allowed : 16.30 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2556 helix: 0.93 (0.15), residues: 1264 sheet: 0.95 (0.37), residues: 212 loop : -2.04 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 409 HIS 0.004 0.001 HIS B 297 PHE 0.023 0.002 PHE D 184 TYR 0.026 0.001 TYR B 371 ARG 0.009 0.000 ARG B 50 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 878) hydrogen bonds : angle 4.10721 ( 2544) covalent geometry : bond 0.00314 (21605) covalent geometry : angle 0.53952 (29197) *********************** 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 560 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 475 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8328 (mtm) cc_final: 0.8118 (mtm) REVERT: A 195 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6903 (mtpp) REVERT: A 301 THR cc_start: 0.8351 (t) cc_final: 0.8110 (t) REVERT: A 398 LYS cc_start: 0.8382 (mtpm) cc_final: 0.8152 (ttmt) REVERT: A 487 THR cc_start: 0.7645 (p) cc_final: 0.7402 (p) REVERT: A 508 LYS cc_start: 0.8449 (mppt) cc_final: 0.8186 (mmtt) REVERT: A 603 ASP cc_start: 0.6989 (m-30) cc_final: 0.6752 (m-30) REVERT: B 96 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7541 (mtp180) REVERT: B 344 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 397 GLU cc_start: 0.7896 (pp20) cc_final: 0.7557 (pp20) REVERT: C 39 LEU cc_start: 0.8290 (tp) cc_final: 0.7853 (tt) REVERT: C 41 GLU cc_start: 0.6925 (mp0) cc_final: 0.6633 (mp0) REVERT: C 49 TYR cc_start: 0.7502 (t80) cc_final: 0.7100 (t80) REVERT: C 66 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7840 (tpt) REVERT: C 100 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7325 (mpp) REVERT: C 301 THR cc_start: 0.8204 (t) cc_final: 0.7889 (m) REVERT: C 410 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7486 (mt-10) REVERT: C 628 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7965 (mt-10) REVERT: D 11 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7763 (mtp-110) REVERT: D 41 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: D 468 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6407 (t0) outliers start: 85 outliers final: 29 residues processed: 516 average time/residue: 1.4506 time to fit residues: 838.4660 Evaluate side-chains 497 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 463 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 319 THR Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 MET 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 37 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 100 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 643 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 101 SER 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 537 ILE 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 110 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 248 optimal weight: 0.0770 chunk 158 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN C 609 ASN 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 = 0.3866 r_free = 0.3866 target = 0.134780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.122237 restraints weight = 30089.183| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.68 r_work: 0.3606 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2831 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= 0.215 Angle : 0.606 8.896 29197 Z= 0.322 Chirality : 0.047 0.177 3134 Planarity : 0.005 0.046 3718 Dihedral : 10.960 86.771 3204 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.28 % Favored : 92.64 % Rotamer: Outliers : 3.80 % Allowed : 16.79 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2556 helix: 0.84 (0.15), residues: 1254 sheet: 0.41 (0.35), residues: 234 loop : -2.13 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 501 HIS 0.005 0.001 HIS A 541 PHE 0.027 0.002 PHE D 184 TYR 0.024 0.002 TYR C 631 ARG 0.013 0.001 ARG D 400 Details of bonding type rmsd hydrogen bonds : bond 0.05725 ( 878) hydrogen bonds : angle 4.23278 ( 2544) covalent geometry : bond 0.00513 (21605) covalent geometry : angle 0.60646 (29197) *********************** 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 567 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 482 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7011 (tp30) cc_final: 0.6693 (mm-30) REVERT: A 195 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6904 (mtpp) REVERT: A 237 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: A 301 THR cc_start: 0.8388 (t) cc_final: 0.8075 (m) REVERT: A 508 LYS cc_start: 0.8497 (mppt) cc_final: 0.8239 (mmtt) REVERT: A 576 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8266 (tp) REVERT: B 96 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7526 (mtp180) REVERT: B 344 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 382 PHE cc_start: 0.7021 (m-80) cc_final: 0.6782 (m-80) REVERT: B 397 GLU cc_start: 0.7911 (pp20) cc_final: 0.7637 (pp20) REVERT: C 39 LEU cc_start: 0.8355 (tp) cc_final: 0.8017 (tt) REVERT: C 41 GLU cc_start: 0.7048 (mp0) cc_final: 0.6818 (mp0) REVERT: C 47 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6920 (mm) REVERT: C 49 TYR cc_start: 0.7513 (t80) cc_final: 0.7140 (t80) REVERT: C 66 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7925 (tpt) REVERT: C 301 THR cc_start: 0.8264 (t) cc_final: 0.7955 (m) REVERT: C 414 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7946 (ttp) REVERT: C 628 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8022 (mt-10) REVERT: D 41 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: D 370 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5808 (mt) REVERT: D 449 GLU cc_start: 0.7685 (tt0) cc_final: 0.7381 (tm-30) REVERT: D 468 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6394 (t0) outliers start: 85 outliers final: 36 residues processed: 528 average time/residue: 1.3888 time to fit residues: 821.8430 Evaluate side-chains 520 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 475 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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 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 319 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 502 VAL 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 101 SER Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 251 LEU 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 17 GLU Chi-restraints excluded: chain C residue 37 THR 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 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 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 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 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 186 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 252 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 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 = 0.3873 r_free = 0.3873 target = 0.135194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122787 restraints weight = 29877.395| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.66 r_work: 0.3617 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21605 Z= 0.181 Angle : 0.584 8.292 29197 Z= 0.311 Chirality : 0.045 0.171 3134 Planarity : 0.004 0.043 3718 Dihedral : 10.757 87.606 3200 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.85 % Favored : 93.08 % Rotamer: Outliers : 3.84 % Allowed : 16.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2556 helix: 0.88 (0.15), residues: 1258 sheet: 0.42 (0.35), residues: 232 loop : -2.13 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 409 HIS 0.005 0.001 HIS A 541 PHE 0.027 0.002 PHE D 184 TYR 0.023 0.002 TYR D 337 ARG 0.008 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 878) hydrogen bonds : angle 4.17439 ( 2544) covalent geometry : bond 0.00429 (21605) covalent geometry : angle 0.58395 (29197) *********************** 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 560 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 474 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.6996 (tp30) cc_final: 0.6723 (mm-30) REVERT: A 195 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.6878 (mtpp) REVERT: A 301 THR cc_start: 0.8383 (t) cc_final: 0.8177 (t) REVERT: A 508 LYS cc_start: 0.8485 (mppt) cc_final: 0.8235 (mmtt) REVERT: A 576 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8274 (tp) REVERT: A 603 ASP cc_start: 0.7113 (m-30) cc_final: 0.6881 (m-30) REVERT: B 96 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7559 (mtp180) REVERT: B 270 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6371 (tt) REVERT: B 344 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 382 PHE cc_start: 0.7003 (m-80) cc_final: 0.6772 (m-80) REVERT: B 397 GLU cc_start: 0.7880 (pp20) cc_final: 0.7556 (pp20) REVERT: C 39 LEU cc_start: 0.8320 (tp) cc_final: 0.7981 (tt) REVERT: C 47 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6905 (mm) REVERT: C 49 TYR cc_start: 0.7446 (t80) cc_final: 0.7095 (t80) REVERT: C 66 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7905 (tpt) REVERT: C 67 GLU cc_start: 0.7680 (tp30) cc_final: 0.7433 (tp30) REVERT: C 301 THR cc_start: 0.8255 (t) cc_final: 0.7949 (m) REVERT: C 380 ARG cc_start: 0.8060 (tpt-90) cc_final: 0.7644 (tpt-90) REVERT: C 414 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.8002 (ttp) REVERT: C 628 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8022 (mt-10) REVERT: D 370 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5797 (mt) REVERT: D 449 GLU cc_start: 0.7682 (tt0) cc_final: 0.7382 (tm-30) REVERT: D 468 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6372 (t0) outliers start: 86 outliers final: 38 residues processed: 518 average time/residue: 1.4327 time to fit residues: 832.7948 Evaluate side-chains 516 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 470 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 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 319 THR Chi-restraints excluded: chain A residue 451 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 101 SER 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 460 ILE 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 37 THR 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 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 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 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 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 173 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.120596 restraints weight = 29960.745| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.67 r_work: 0.3587 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 21605 Z= 0.283 Angle : 0.675 8.775 29197 Z= 0.360 Chirality : 0.050 0.221 3134 Planarity : 0.005 0.049 3718 Dihedral : 11.288 89.716 3200 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.75 % Favored : 92.18 % Rotamer: Outliers : 3.48 % Allowed : 18.22 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2556 helix: 0.68 (0.15), residues: 1252 sheet: 0.28 (0.35), residues: 234 loop : -2.26 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 501 HIS 0.007 0.001 HIS A 541 PHE 0.031 0.003 PHE D 184 TYR 0.028 0.002 TYR C 631 ARG 0.010 0.001 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.06554 ( 878) hydrogen bonds : angle 4.38423 ( 2544) covalent geometry : bond 0.00682 (21605) covalent geometry : angle 0.67470 (29197) *********************** 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 562 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 484 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7876 (mp) REVERT: A 195 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6904 (mtpp) REVERT: A 233 ARG cc_start: 0.7347 (tpt-90) cc_final: 0.7130 (mtp85) REVERT: A 237 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: A 301 THR cc_start: 0.8416 (t) cc_final: 0.8113 (m) REVERT: A 508 LYS cc_start: 0.8511 (mppt) cc_final: 0.8285 (mmtt) REVERT: A 543 GLU cc_start: 0.7505 (tt0) cc_final: 0.7303 (mt-10) REVERT: A 576 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 594 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: B 96 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7564 (mtp180) REVERT: B 270 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6335 (tt) REVERT: B 344 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 382 PHE cc_start: 0.7039 (m-80) cc_final: 0.6783 (m-80) REVERT: B 397 GLU cc_start: 0.7909 (pp20) cc_final: 0.7532 (pp20) REVERT: B 462 MET cc_start: 0.5239 (ptt) cc_final: 0.4818 (pp-130) REVERT: C 39 LEU cc_start: 0.8342 (tp) cc_final: 0.8005 (tt) REVERT: C 47 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7021 (mm) REVERT: C 49 TYR cc_start: 0.7479 (t80) cc_final: 0.7154 (t80) REVERT: C 66 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7817 (tpt) REVERT: C 67 GLU cc_start: 0.7754 (tp30) cc_final: 0.7418 (tp30) REVERT: C 198 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: C 301 THR cc_start: 0.8302 (t) cc_final: 0.8004 (m) REVERT: C 380 ARG cc_start: 0.8134 (tpt-90) cc_final: 0.7719 (tpt-90) REVERT: C 414 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7997 (ttp) REVERT: C 628 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8095 (mt-10) REVERT: D 41 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: D 163 TYR cc_start: 0.8529 (m-80) cc_final: 0.8323 (m-80) REVERT: D 449 GLU cc_start: 0.7757 (tt0) cc_final: 0.7457 (tm-30) outliers start: 78 outliers final: 39 residues processed: 525 average time/residue: 1.4382 time to fit residues: 844.2316 Evaluate side-chains 523 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 473 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 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 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 451 MET 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 29 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 162 ASP 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 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 37 THR 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 198 GLU 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 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 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 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: 0.9990 chunk 235 optimal weight: 0.0010 chunk 228 optimal weight: 0.5980 chunk 237 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN B 242 ASN B 342 ASN C 42 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN D 18 GLN 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 = 0.3881 r_free = 0.3881 target = 0.135780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.123367 restraints weight = 30087.882| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.68 r_work: 0.3626 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21605 Z= 0.151 Angle : 0.592 9.441 29197 Z= 0.314 Chirality : 0.044 0.169 3134 Planarity : 0.004 0.045 3718 Dihedral : 10.616 88.248 3200 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 2.95 % Allowed : 19.65 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2556 helix: 1.00 (0.15), residues: 1246 sheet: 0.34 (0.34), residues: 244 loop : -2.23 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 409 HIS 0.004 0.001 HIS A 541 PHE 0.029 0.002 PHE D 184 TYR 0.024 0.001 TYR D 337 ARG 0.011 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 878) hydrogen bonds : angle 4.16239 ( 2544) covalent geometry : bond 0.00352 (21605) covalent geometry : angle 0.59196 (29197) *********************** 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 536 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 470 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6848 (mtpp) REVERT: A 301 THR cc_start: 0.8373 (t) cc_final: 0.8171 (t) REVERT: A 508 LYS cc_start: 0.8449 (mppt) cc_final: 0.8195 (mmtt) REVERT: A 576 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8262 (tp) REVERT: B 96 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7519 (mtp180) REVERT: B 270 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6307 (tt) REVERT: B 344 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 382 PHE cc_start: 0.6978 (m-80) cc_final: 0.6740 (m-80) REVERT: B 397 GLU cc_start: 0.7844 (pp20) cc_final: 0.7520 (pp20) REVERT: C 39 LEU cc_start: 0.8275 (tp) cc_final: 0.7949 (tt) REVERT: C 47 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6922 (mm) REVERT: C 49 TYR cc_start: 0.7397 (t80) cc_final: 0.7059 (t80) REVERT: C 66 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.8017 (tpt) REVERT: C 67 GLU cc_start: 0.7822 (tp30) cc_final: 0.7428 (tp30) REVERT: C 301 THR cc_start: 0.8254 (t) cc_final: 0.7966 (m) REVERT: C 380 ARG cc_start: 0.8036 (tpt-90) cc_final: 0.7614 (tpt-90) REVERT: D 370 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5738 (mt) REVERT: D 468 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6262 (t0) outliers start: 66 outliers final: 35 residues processed: 499 average time/residue: 1.4939 time to fit residues: 846.0875 Evaluate side-chains 501 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 459 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 451 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 101 SER Chi-restraints excluded: chain B residue 162 ASP 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 460 ILE 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 37 THR 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 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 578 THR 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 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 620 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 166 optimal weight: 0.4980 chunk 183 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 95 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 101 optimal weight: 0.0980 chunk 246 optimal weight: 0.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN B 242 ASN B 342 ASN C 181 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN C 609 ASN D 18 GLN D 54 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.124681 restraints weight = 30013.424| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.68 r_work: 0.3644 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.003 0.043 21605 Z= 0.129 Angle : 0.570 9.971 29197 Z= 0.301 Chirality : 0.043 0.163 3134 Planarity : 0.004 0.045 3718 Dihedral : 10.257 88.508 3200 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.69 % Favored : 93.27 % Rotamer: Outliers : 2.32 % Allowed : 20.59 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2556 helix: 1.20 (0.15), residues: 1250 sheet: 0.59 (0.35), residues: 232 loop : -2.12 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 409 HIS 0.003 0.001 HIS A 216 PHE 0.028 0.001 PHE D 184 TYR 0.024 0.001 TYR D 337 ARG 0.011 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 878) hydrogen bonds : angle 4.04802 ( 2544) covalent geometry : bond 0.00293 (21605) covalent geometry : angle 0.57031 (29197) *********************** 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 513 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 461 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8248 (t) cc_final: 0.8041 (t) REVERT: A 17 GLU cc_start: 0.6978 (tp30) cc_final: 0.6690 (mm-30) REVERT: A 39 LEU cc_start: 0.8224 (tp) cc_final: 0.7929 (tm) REVERT: A 41 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 132 GLU cc_start: 0.7546 (mp0) cc_final: 0.7343 (mp0) REVERT: A 195 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6781 (mtpp) REVERT: A 508 LYS cc_start: 0.8439 (mppt) cc_final: 0.8202 (mmtt) REVERT: A 539 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7230 (mtpp) REVERT: A 576 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8250 (tp) REVERT: A 586 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8404 (mttm) REVERT: B 96 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7529 (mtp180) REVERT: B 270 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6261 (tt) REVERT: B 342 ASN cc_start: 0.7951 (m-40) cc_final: 0.7682 (m110) REVERT: B 344 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 382 PHE cc_start: 0.6949 (m-80) cc_final: 0.6735 (m-80) REVERT: B 397 GLU cc_start: 0.7860 (pp20) cc_final: 0.7550 (pp20) REVERT: C 47 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6851 (mm) REVERT: C 49 TYR cc_start: 0.7412 (t80) cc_final: 0.7088 (t80) REVERT: C 66 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.8009 (tpt) REVERT: C 67 GLU cc_start: 0.7749 (tp30) cc_final: 0.7363 (tp30) REVERT: C 87 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7771 (mmm160) REVERT: C 301 THR cc_start: 0.8239 (t) cc_final: 0.7942 (m) REVERT: D 41 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: D 370 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5760 (mt) REVERT: D 468 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6255 (t0) outliers start: 52 outliers final: 28 residues processed: 488 average time/residue: 1.4518 time to fit residues: 793.6392 Evaluate side-chains 489 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 453 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 451 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 66 MET Chi-restraints excluded: chain B residue 162 ASP 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 377 VAL Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 633 ASP 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 292 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 643 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 152 MET 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 620 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 194 optimal weight: 1.9990 chunk 201 optimal weight: 0.0470 chunk 254 optimal weight: 0.0070 chunk 246 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 216 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.124067 restraints weight = 29957.464| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.67 r_work: 0.3634 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21605 Z= 0.149 Angle : 0.598 10.367 29197 Z= 0.314 Chirality : 0.044 0.176 3134 Planarity : 0.004 0.045 3718 Dihedral : 10.326 89.523 3200 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.83 % Allowed : 21.17 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2556 helix: 1.19 (0.15), residues: 1254 sheet: 0.52 (0.35), residues: 234 loop : -2.10 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 409 HIS 0.004 0.001 HIS A 289 PHE 0.029 0.002 PHE D 184 TYR 0.024 0.001 TYR D 337 ARG 0.011 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 878) hydrogen bonds : angle 4.07166 ( 2544) covalent geometry : bond 0.00348 (21605) covalent geometry : angle 0.59775 (29197) ********************** 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 494 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 453 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.6988 (tp30) cc_final: 0.6688 (mm-30) REVERT: A 21 MET cc_start: 0.7652 (mmm) cc_final: 0.7448 (mmm) REVERT: A 41 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7178 (mm-30) REVERT: A 195 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6792 (mtpp) REVERT: A 508 LYS cc_start: 0.8452 (mppt) cc_final: 0.8232 (mmtt) REVERT: A 539 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7480 (mtpp) REVERT: A 576 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8273 (tp) REVERT: A 586 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8424 (mttm) REVERT: B 96 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7519 (mtp180) REVERT: B 270 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6295 (tt) REVERT: B 342 ASN cc_start: 0.7965 (m-40) cc_final: 0.7706 (m110) REVERT: B 344 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 382 PHE cc_start: 0.6950 (m-80) cc_final: 0.6742 (m-80) REVERT: B 397 GLU cc_start: 0.7876 (pp20) cc_final: 0.7568 (pp20) REVERT: C 47 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6859 (mm) REVERT: C 49 TYR cc_start: 0.7410 (t80) cc_final: 0.7097 (t80) REVERT: C 66 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7996 (tpt) REVERT: C 87 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7796 (mmm160) REVERT: C 301 THR cc_start: 0.8235 (t) cc_final: 0.7951 (m) REVERT: C 380 ARG cc_start: 0.8055 (tpt-90) cc_final: 0.7637 (tpt-90) REVERT: D 41 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: D 370 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5775 (mt) outliers start: 41 outliers final: 27 residues processed: 471 average time/residue: 1.4830 time to fit residues: 781.5091 Evaluate side-chains 486 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 452 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 134 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 451 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 162 ASP Chi-restraints excluded: chain B residue 246 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 606 TYR Chi-restraints excluded: chain B residue 633 ASP 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 292 MET Chi-restraints excluded: chain C residue 451 MET 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 147 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 245 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 220 optimal weight: 0.0980 chunk 47 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 242 ASN B 334 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN C 609 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 = 0.3892 r_free = 0.3892 target = 0.136766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124313 restraints weight = 30144.911| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.68 r_work: 0.3637 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21605 Z= 0.142 Angle : 0.589 10.951 29197 Z= 0.309 Chirality : 0.044 0.179 3134 Planarity : 0.004 0.045 3718 Dihedral : 10.253 89.750 3200 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.88 % Allowed : 21.13 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2556 helix: 1.24 (0.15), residues: 1254 sheet: 0.48 (0.35), residues: 234 loop : -2.06 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 425 HIS 0.007 0.001 HIS A 540 PHE 0.029 0.002 PHE D 184 TYR 0.023 0.001 TYR D 337 ARG 0.010 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 878) hydrogen bonds : angle 4.04285 ( 2544) covalent geometry : bond 0.00331 (21605) covalent geometry : angle 0.58937 (29197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18355.25 seconds wall clock time: 315 minutes 30.30 seconds (18930.30 seconds total)