Starting phenix.real_space_refine on Tue May 13 23:04:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9z_39086/05_2025/8y9z_39086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9z_39086/05_2025/8y9z_39086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9z_39086/05_2025/8y9z_39086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9z_39086/05_2025/8y9z_39086.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9z_39086/05_2025/8y9z_39086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9z_39086/05_2025/8y9z_39086.cif" } resolution = 3.41 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= 0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 54 5.16 5 Be 1 3.05 5 C 7066 2.51 5 N 1894 2.21 5 O 2040 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11061 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6107 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 15, 'TRANS': 749} Chain: "Y" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3153 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 20, 'TRANS': 382} Chain breaks: 2 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "V" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.09, per 1000 atoms: 0.64 Number of scatterers: 11061 At special positions: 0 Unit cell: (94.16, 116.63, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 54 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2040 8.00 N 1894 7.00 C 7066 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 95 " distance=2.03 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 61.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 removed outlier: 3.586A pdb=" N ARG A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.071A pdb=" N ILE A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 55 " --> pdb=" O ARG A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 61 through 77 removed outlier: 3.851A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.527A pdb=" N LEU A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 130 through 149 removed outlier: 5.043A pdb=" N LYS A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 145 " --> pdb=" O MET A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.906A pdb=" N GLY A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.513A pdb=" N GLN A 195 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 196' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.662A pdb=" N ARG A 218 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 219 " --> pdb=" O GLU A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 219' Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.999A pdb=" N THR A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.685A pdb=" N ASP A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 305' Processing helix chain 'A' and resid 332 through 341 removed outlier: 3.706A pdb=" N ALA A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 377 through 384 Processing helix chain 'A' and resid 410 through 427 removed outlier: 3.892A pdb=" N MET A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.511A pdb=" N ILE A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 removed outlier: 4.143A pdb=" N GLY A 453 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 454 " --> pdb=" O ASN A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 454' Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 485 through 488 removed outlier: 3.658A pdb=" N GLY A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 515 through 524 removed outlier: 3.895A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 556 through 562 removed outlier: 4.412A pdb=" N ASP A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 562 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 619 removed outlier: 3.986A pdb=" N GLU A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 580 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 618 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 619 " --> pdb=" O PHE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.827A pdb=" N TYR A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 665 Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.540A pdb=" N ASP A 675 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 676 " --> pdb=" O LYS A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 672 through 676' Processing helix chain 'A' and resid 680 through 704 removed outlier: 3.727A pdb=" N ARG A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 735 removed outlier: 3.705A pdb=" N ARG A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 745 removed outlier: 4.224A pdb=" N HIS A 739 " --> pdb=" O GLN A 736 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 740 " --> pdb=" O GLY A 737 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 741 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 742 " --> pdb=" O HIS A 739 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 743 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 777 removed outlier: 4.197A pdb=" N GLU A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 9 removed outlier: 3.519A pdb=" N MET Y 9 " --> pdb=" O ILE Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 31 removed outlier: 3.634A pdb=" N GLY Y 31 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 34 No H-bonds generated for 'chain 'Y' and resid 32 through 34' Processing helix chain 'Y' and resid 74 through 88 removed outlier: 3.808A pdb=" N ILE Y 83 " --> pdb=" O THR Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 97 Processing helix chain 'Y' and resid 102 through 107 Processing helix chain 'Y' and resid 109 through 137 removed outlier: 3.737A pdb=" N LEU Y 126 " --> pdb=" O PHE Y 122 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 173 removed outlier: 3.936A pdb=" N TYR Y 149 " --> pdb=" O GLY Y 145 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU Y 150 " --> pdb=" O ILE Y 146 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU Y 151 " --> pdb=" O GLY Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 189 Processing helix chain 'Y' and resid 190 through 202 Processing helix chain 'Y' and resid 213 through 236 removed outlier: 3.614A pdb=" N VAL Y 220 " --> pdb=" O ARG Y 216 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL Y 225 " --> pdb=" O ALA Y 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 271 through 288 removed outlier: 4.280A pdb=" N ILE Y 275 " --> pdb=" O VAL Y 271 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE Y 276 " --> pdb=" O ILE Y 272 " (cutoff:3.500A) Proline residue: Y 284 - end of helix removed outlier: 3.755A pdb=" N ALA Y 288 " --> pdb=" O PRO Y 284 " (cutoff:3.500A) Processing helix chain 'Y' and resid 294 through 304 removed outlier: 3.733A pdb=" N ARG Y 302 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) Processing helix chain 'Y' and resid 308 through 332 removed outlier: 3.946A pdb=" N THR Y 313 " --> pdb=" O PRO Y 309 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE Y 314 " --> pdb=" O VAL Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 332 through 344 removed outlier: 3.538A pdb=" N MET Y 336 " --> pdb=" O ASN Y 332 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA Y 337 " --> pdb=" O PRO Y 333 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP Y 338 " --> pdb=" O GLU Y 334 " (cutoff:3.500A) Processing helix chain 'Y' and resid 353 through 390 removed outlier: 4.118A pdb=" N GLN Y 357 " --> pdb=" O GLY Y 353 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU Y 369 " --> pdb=" O TYR Y 365 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL Y 370 " --> pdb=" O ARG Y 366 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY Y 371 " --> pdb=" O LEU Y 367 " (cutoff:3.500A) Proline residue: Y 382 - end of helix removed outlier: 3.558A pdb=" N ASN Y 390 " --> pdb=" O VAL Y 386 " (cutoff:3.500A) Processing helix chain 'Y' and resid 399 through 419 removed outlier: 4.445A pdb=" N LEU Y 403 " --> pdb=" O GLY Y 399 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE Y 404 " --> pdb=" O THR Y 400 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL Y 405 " --> pdb=" O SER Y 401 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN Y 419 " --> pdb=" O GLN Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 424 Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 22 through 59 removed outlier: 3.673A pdb=" N LEU E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 removed outlier: 3.767A pdb=" N THR V 90 " --> pdb=" O PRO V 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 60 Processing helix chain 'B' and resid 73 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 154 removed outlier: 7.069A pdb=" N HIS A 125 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP A 207 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 127 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA A 204 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET A 370 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 206 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 371 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 97 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 224 removed outlier: 3.561A pdb=" N ALA A 353 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.641A pdb=" N GLN A 260 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 258 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 309 removed outlier: 4.062A pdb=" N ILE A 315 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.130A pdb=" N LEU A 406 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.158A pdb=" N LEU A 433 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 432 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA A 483 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL A 434 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN A 457 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 238 through 242 Processing sheet with id=AA8, first strand: chain 'Y' and resid 244 through 245 Processing sheet with id=AA9, first strand: chain 'V' and resid 5 through 7 removed outlier: 3.559A pdb=" N LEU V 18 " --> pdb=" O MET V 82 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET V 82 " --> pdb=" O LEU V 18 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU V 20 " --> pdb=" O LEU V 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'V' and resid 47 through 51 removed outlier: 3.593A pdb=" N ALA V 49 " --> pdb=" O TRP V 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA V 33 " --> pdb=" O GLN V 98 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY V 35 " --> pdb=" O TYR V 96 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR V 96 " --> pdb=" O GLY V 35 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 2.91 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: 3588 1.34 - 1.46: 2086 1.46 - 1.58: 5473 1.58 - 1.70: 3 1.70 - 1.81: 108 Bond restraints: 11258 Sorted by residual: bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" F1 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" F3 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C ILE Y 191 " pdb=" N PRO Y 192 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 2.97e+00 bond pdb=" C CYS V 22 " pdb=" N GLY V 23 " ideal model delta sigma weight residual 1.332 1.341 -0.008 5.00e-03 4.00e+04 2.76e+00 ... (remaining 11253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 14738 1.61 - 3.22: 391 3.22 - 4.84: 54 4.84 - 6.45: 20 6.45 - 8.06: 10 Bond angle restraints: 15213 Sorted by residual: angle pdb=" N ASP A 667 " pdb=" CA ASP A 667 " pdb=" C ASP A 667 " ideal model delta sigma weight residual 111.30 118.58 -7.28 1.36e+00 5.41e-01 2.86e+01 angle pdb=" C LEU A 666 " pdb=" N ASP A 667 " pdb=" CA ASP A 667 " ideal model delta sigma weight residual 122.46 129.92 -7.46 1.41e+00 5.03e-01 2.80e+01 angle pdb=" N PRO Y 284 " pdb=" CA PRO Y 284 " pdb=" C PRO Y 284 " ideal model delta sigma weight residual 110.70 115.31 -4.61 1.22e+00 6.72e-01 1.43e+01 angle pdb=" C TYR A 364 " pdb=" N GLU A 365 " pdb=" CA GLU A 365 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C MET Y 89 " pdb=" N ASP Y 90 " pdb=" CA ASP Y 90 " ideal model delta sigma weight residual 122.61 128.02 -5.41 1.56e+00 4.11e-01 1.20e+01 ... (remaining 15208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 6453 23.20 - 46.40: 286 46.40 - 69.61: 35 69.61 - 92.81: 3 92.81 - 116.01: 2 Dihedral angle restraints: 6779 sinusoidal: 2764 harmonic: 4015 Sorted by residual: dihedral pdb=" O1B ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PB ADP A1003 " pdb=" PA ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 -176.01 116.01 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" C5' ADP A1003 " pdb=" O5' ADP A1003 " pdb=" PA ADP A1003 " pdb=" O2A ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 -161.82 101.82 1 2.00e+01 2.50e-03 2.89e+01 dihedral pdb=" CA PRO V 41 " pdb=" C PRO V 41 " pdb=" N GLY V 42 " pdb=" CA GLY V 42 " ideal model delta harmonic sigma weight residual -180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 6776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1143 0.039 - 0.078: 422 0.078 - 0.117: 137 0.117 - 0.156: 25 0.156 - 0.196: 3 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CA ASP A 667 " pdb=" N ASP A 667 " pdb=" C ASP A 667 " pdb=" CB ASP A 667 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CA ALA Y 283 " pdb=" N ALA Y 283 " pdb=" C ALA Y 283 " pdb=" CB ALA Y 283 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA ILE Y 272 " pdb=" N ILE Y 272 " pdb=" C ILE Y 272 " pdb=" CB ILE Y 272 " both_signs ideal model delta sigma weight residual False 2.43 2.27 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 1727 not shown) Planarity restraints: 1942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Y 284 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO Y 285 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO Y 285 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO Y 285 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 39 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C VAL Y 39 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL Y 39 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN Y 40 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET Y 75 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO Y 76 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO Y 76 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO Y 76 " -0.031 5.00e-02 4.00e+02 ... (remaining 1939 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 57 2.58 - 3.16: 8380 3.16 - 3.74: 16621 3.74 - 4.32: 21783 4.32 - 4.90: 37806 Nonbonded interactions: 84647 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" F2 BEF A1002 " model vdw 2.003 2.120 nonbonded pdb="MG MG A1001 " pdb=" F3 BEF A1002 " model vdw 2.006 2.120 nonbonded pdb="MG MG A1001 " pdb="BE BEF A1002 " model vdw 2.171 1.550 nonbonded pdb=" F1 BEF A1002 " pdb=" O1B ADP A1003 " model vdw 2.283 2.990 nonbonded pdb=" O LEU Y 364 " pdb=" OG1 THR Y 368 " model vdw 2.306 3.040 ... (remaining 84642 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.006 0.289 11259 Z= 0.300 Angle : 0.670 8.062 15215 Z= 0.372 Chirality : 0.046 0.196 1730 Planarity : 0.006 0.060 1942 Dihedral : 12.844 116.009 4196 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.69 % Allowed : 8.19 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.93 (0.20), residues: 1372 helix: -0.88 (0.16), residues: 757 sheet: -0.73 (0.47), residues: 137 loop : -1.89 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 36 HIS 0.005 0.001 HIS A 288 PHE 0.016 0.001 PHE Y 428 TYR 0.013 0.001 TYR Y 359 ARG 0.005 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.15037 ( 572) hydrogen bonds : angle 5.94641 ( 1680) SS BOND : bond 0.00306 ( 1) SS BOND : angle 0.61402 ( 2) covalent geometry : bond 0.00607 (11258) covalent geometry : angle 0.66965 (15213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 277 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 79 MET cc_start: 0.7531 (mmt) cc_final: 0.7204 (mtt) REVERT: A 99 GLU cc_start: 0.7980 (tt0) cc_final: 0.7746 (tm-30) REVERT: A 137 ASP cc_start: 0.8824 (m-30) cc_final: 0.8513 (m-30) REVERT: A 324 MET cc_start: 0.8826 (mmm) cc_final: 0.8571 (mmt) REVERT: A 383 ASN cc_start: 0.7989 (m110) cc_final: 0.7757 (m110) REVERT: A 401 ASP cc_start: 0.8143 (t0) cc_final: 0.7941 (t0) REVERT: A 416 LYS cc_start: 0.8069 (tttm) cc_final: 0.7798 (ttpp) REVERT: A 544 GLU cc_start: 0.7566 (tp30) cc_final: 0.7264 (mp0) REVERT: A 572 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7704 (tppt) REVERT: A 600 ASP cc_start: 0.7742 (t70) cc_final: 0.7213 (t0) REVERT: A 629 ASN cc_start: 0.8298 (m-40) cc_final: 0.8071 (m-40) REVERT: A 636 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 679 LYS cc_start: 0.7464 (mmmm) cc_final: 0.7055 (mttm) REVERT: A 693 ILE cc_start: 0.8557 (mm) cc_final: 0.8346 (mm) REVERT: A 729 ASP cc_start: 0.7706 (t0) cc_final: 0.6869 (m-30) REVERT: A 731 MET cc_start: 0.8931 (mmm) cc_final: 0.8631 (mmm) REVERT: Y 72 MET cc_start: 0.8728 (tpt) cc_final: 0.8477 (tpt) REVERT: Y 98 TRP cc_start: 0.6991 (m-10) cc_final: 0.6755 (m-10) REVERT: Y 116 PHE cc_start: 0.7562 (t80) cc_final: 0.7359 (t80) REVERT: Y 299 TRP cc_start: 0.8261 (t60) cc_final: 0.7809 (t60) REVERT: Y 342 LYS cc_start: 0.8558 (tmmt) cc_final: 0.8101 (mptt) REVERT: Y 390 ASN cc_start: 0.7942 (t0) cc_final: 0.7660 (t0) REVERT: Y 413 MET cc_start: 0.8087 (tmm) cc_final: 0.7743 (tmm) REVERT: Y 422 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8614 (mttt) REVERT: V 58 MET cc_start: 0.7258 (ppp) cc_final: 0.6940 (ptt) outliers start: 20 outliers final: 9 residues processed: 292 average time/residue: 0.2498 time to fit residues: 99.3941 Evaluate side-chains 179 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain B residue 85 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 395 ASN A 430 GLN A 536 GLN A 697 ASN Y 169 GLN ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127938 restraints weight = 13685.725| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.37 r_work: 0.3187 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11259 Z= 0.122 Angle : 0.547 7.463 15215 Z= 0.289 Chirality : 0.041 0.154 1730 Planarity : 0.004 0.041 1942 Dihedral : 6.553 97.727 1545 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.03 % Allowed : 13.09 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1372 helix: 0.61 (0.18), residues: 766 sheet: -0.48 (0.45), residues: 144 loop : -1.58 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 20 HIS 0.003 0.001 HIS B 74 PHE 0.011 0.001 PHE A 590 TYR 0.017 0.001 TYR V 32 ARG 0.004 0.000 ARG Y 248 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 572) hydrogen bonds : angle 4.18686 ( 1680) SS BOND : bond 0.00613 ( 1) SS BOND : angle 0.49940 ( 2) covalent geometry : bond 0.00270 (11258) covalent geometry : angle 0.54682 (15213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.363 Fit side-chains REVERT: A 99 GLU cc_start: 0.8030 (tt0) cc_final: 0.7779 (tm-30) REVERT: A 137 ASP cc_start: 0.8644 (m-30) cc_final: 0.8313 (m-30) REVERT: A 310 ASP cc_start: 0.7824 (t0) cc_final: 0.7583 (t0) REVERT: A 350 MET cc_start: 0.7960 (ttp) cc_final: 0.7608 (ttt) REVERT: A 416 LYS cc_start: 0.8163 (tttm) cc_final: 0.7821 (ttpp) REVERT: A 544 GLU cc_start: 0.7624 (tp30) cc_final: 0.7218 (mp0) REVERT: A 572 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7633 (tppt) REVERT: A 604 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7902 (ttt-90) REVERT: A 629 ASN cc_start: 0.8206 (m-40) cc_final: 0.7952 (m-40) REVERT: A 679 LYS cc_start: 0.7361 (mmmm) cc_final: 0.6863 (mttm) REVERT: A 729 ASP cc_start: 0.7724 (t0) cc_final: 0.6862 (m-30) REVERT: A 731 MET cc_start: 0.8689 (mmm) cc_final: 0.8185 (mmm) REVERT: A 751 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7148 (mm-30) REVERT: Y 98 TRP cc_start: 0.6932 (m-10) cc_final: 0.6682 (m-10) REVERT: Y 165 TRP cc_start: 0.7588 (t60) cc_final: 0.7273 (t60) REVERT: Y 250 GLU cc_start: 0.5194 (OUTLIER) cc_final: 0.4870 (pm20) REVERT: Y 299 TRP cc_start: 0.8365 (t60) cc_final: 0.8023 (t60) REVERT: Y 342 LYS cc_start: 0.8584 (tmmt) cc_final: 0.8035 (mptt) REVERT: Y 390 ASN cc_start: 0.8199 (t0) cc_final: 0.7832 (t0) REVERT: Y 413 MET cc_start: 0.8044 (tmm) cc_final: 0.7677 (tmm) REVERT: Y 423 ARG cc_start: 0.8538 (mpt90) cc_final: 0.8300 (mpt-90) REVERT: V 31 MET cc_start: 0.7555 (tpp) cc_final: 0.7347 (tpt) outliers start: 24 outliers final: 13 residues processed: 196 average time/residue: 0.2572 time to fit residues: 69.9583 Evaluate side-chains 187 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 250 GLU Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 85 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN Y 88 GLN V 83 ASN ** V 109 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.171978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120696 restraints weight = 14113.469| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.66 r_work: 0.3122 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 11259 Z= 0.170 Angle : 0.567 7.370 15215 Z= 0.296 Chirality : 0.043 0.161 1730 Planarity : 0.004 0.062 1942 Dihedral : 6.267 89.769 1537 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.12 % Allowed : 12.16 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.23), residues: 1372 helix: 0.93 (0.19), residues: 770 sheet: -0.18 (0.50), residues: 118 loop : -1.61 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 78 HIS 0.003 0.001 HIS A 202 PHE 0.014 0.001 PHE A 711 TYR 0.017 0.001 TYR V 32 ARG 0.006 0.001 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 572) hydrogen bonds : angle 3.99731 ( 1680) SS BOND : bond 0.00587 ( 1) SS BOND : angle 0.35909 ( 2) covalent geometry : bond 0.00414 (11258) covalent geometry : angle 0.56683 (15213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 79 MET cc_start: 0.7880 (mtt) cc_final: 0.7668 (mtm) REVERT: A 137 ASP cc_start: 0.8559 (m-30) cc_final: 0.8322 (m-30) REVERT: A 310 ASP cc_start: 0.8201 (t0) cc_final: 0.7927 (t0) REVERT: A 424 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7890 (tm-30) REVERT: A 482 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8782 (mp) REVERT: A 544 GLU cc_start: 0.7798 (tp30) cc_final: 0.7416 (mp0) REVERT: A 629 ASN cc_start: 0.8288 (m-40) cc_final: 0.8047 (m-40) REVERT: A 653 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7899 (ttpp) REVERT: A 679 LYS cc_start: 0.7481 (mmmm) cc_final: 0.7103 (mttm) REVERT: A 725 MET cc_start: 0.7381 (mtt) cc_final: 0.6912 (mtp) REVERT: A 729 ASP cc_start: 0.7890 (t0) cc_final: 0.7091 (m-30) REVERT: A 761 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8373 (mm-30) REVERT: Y 75 MET cc_start: 0.7111 (mmm) cc_final: 0.6511 (tpt) REVERT: Y 98 TRP cc_start: 0.6915 (m-10) cc_final: 0.6663 (m-10) REVERT: Y 135 LEU cc_start: 0.8266 (tt) cc_final: 0.7804 (mm) REVERT: Y 299 TRP cc_start: 0.8366 (t60) cc_final: 0.8074 (t60) REVERT: Y 336 MET cc_start: 0.8319 (mtp) cc_final: 0.8087 (mtp) REVERT: Y 342 LYS cc_start: 0.8638 (tmmt) cc_final: 0.8109 (mptt) REVERT: Y 358 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: Y 390 ASN cc_start: 0.8232 (t0) cc_final: 0.7835 (t0) REVERT: Y 413 MET cc_start: 0.8128 (tmm) cc_final: 0.7788 (tmm) REVERT: Y 415 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7779 (tp40) REVERT: Y 423 ARG cc_start: 0.8599 (mpt90) cc_final: 0.8363 (mpt-90) REVERT: V 31 MET cc_start: 0.7769 (tpp) cc_final: 0.7569 (tpp) REVERT: B 58 MET cc_start: 0.5846 (tmm) cc_final: 0.5494 (ttp) outliers start: 37 outliers final: 22 residues processed: 206 average time/residue: 0.2416 time to fit residues: 69.9892 Evaluate side-chains 186 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 250 GLU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 358 GLU Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 2.9990 chunk 112 optimal weight: 0.0070 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.173611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126240 restraints weight = 13874.107| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.64 r_work: 0.3143 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11259 Z= 0.117 Angle : 0.515 7.176 15215 Z= 0.267 Chirality : 0.041 0.143 1730 Planarity : 0.003 0.046 1942 Dihedral : 6.125 94.887 1537 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.20 % Allowed : 13.68 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.23), residues: 1372 helix: 1.32 (0.19), residues: 766 sheet: -0.06 (0.50), residues: 118 loop : -1.58 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 78 HIS 0.002 0.000 HIS A 464 PHE 0.009 0.001 PHE Y 428 TYR 0.017 0.001 TYR V 32 ARG 0.004 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 572) hydrogen bonds : angle 3.78241 ( 1680) SS BOND : bond 0.00678 ( 1) SS BOND : angle 0.36216 ( 2) covalent geometry : bond 0.00268 (11258) covalent geometry : angle 0.51468 (15213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 79 MET cc_start: 0.7772 (mtt) cc_final: 0.7569 (mtm) REVERT: A 140 GLN cc_start: 0.7459 (mt0) cc_final: 0.7217 (tt0) REVERT: A 151 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.7894 (p) REVERT: A 310 ASP cc_start: 0.8238 (t0) cc_final: 0.7935 (t0) REVERT: A 424 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 544 GLU cc_start: 0.7689 (tp30) cc_final: 0.7247 (mp0) REVERT: A 629 ASN cc_start: 0.8194 (m-40) cc_final: 0.7963 (m-40) REVERT: A 653 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7744 (ttpp) REVERT: A 679 LYS cc_start: 0.7545 (mmmm) cc_final: 0.7128 (mttm) REVERT: A 689 MET cc_start: 0.7535 (tpt) cc_final: 0.7318 (tpt) REVERT: A 725 MET cc_start: 0.7246 (mtt) cc_final: 0.6704 (mtp) REVERT: A 729 ASP cc_start: 0.7801 (t0) cc_final: 0.6977 (m-30) REVERT: A 761 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8237 (mm-30) REVERT: Y 75 MET cc_start: 0.6865 (mmm) cc_final: 0.6242 (tpt) REVERT: Y 98 TRP cc_start: 0.7061 (m-10) cc_final: 0.6812 (m-10) REVERT: Y 106 ARG cc_start: 0.8084 (tmm160) cc_final: 0.7492 (ttm110) REVERT: Y 299 TRP cc_start: 0.8348 (t60) cc_final: 0.8092 (t60) REVERT: Y 336 MET cc_start: 0.8183 (mtp) cc_final: 0.7975 (mtp) REVERT: Y 342 LYS cc_start: 0.8600 (tmmt) cc_final: 0.8027 (mptt) REVERT: Y 390 ASN cc_start: 0.8376 (t0) cc_final: 0.7944 (t0) REVERT: Y 413 MET cc_start: 0.8022 (tmm) cc_final: 0.7688 (tmm) REVERT: Y 415 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7698 (tp40) REVERT: Y 423 ARG cc_start: 0.8532 (mpt90) cc_final: 0.8299 (mpt-90) REVERT: V 32 TYR cc_start: 0.7327 (t80) cc_final: 0.7084 (t80) REVERT: B 58 MET cc_start: 0.5764 (tmm) cc_final: 0.5417 (ttp) outliers start: 26 outliers final: 19 residues processed: 188 average time/residue: 0.2447 time to fit residues: 64.2771 Evaluate side-chains 182 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain B residue 81 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.0270 chunk 57 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.0370 chunk 36 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 697 ASN ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126712 restraints weight = 13747.419| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.55 r_work: 0.3144 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11259 Z= 0.104 Angle : 0.498 7.120 15215 Z= 0.256 Chirality : 0.040 0.142 1730 Planarity : 0.003 0.038 1942 Dihedral : 5.855 98.549 1535 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.53 % Allowed : 13.68 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.23), residues: 1372 helix: 1.57 (0.19), residues: 765 sheet: -0.07 (0.48), residues: 132 loop : -1.50 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 78 HIS 0.003 0.000 HIS B 74 PHE 0.009 0.001 PHE Y 428 TYR 0.014 0.001 TYR V 32 ARG 0.009 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 572) hydrogen bonds : angle 3.65103 ( 1680) SS BOND : bond 0.00629 ( 1) SS BOND : angle 0.36403 ( 2) covalent geometry : bond 0.00231 (11258) covalent geometry : angle 0.49812 (15213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 140 GLN cc_start: 0.7389 (mt0) cc_final: 0.7189 (tt0) REVERT: A 151 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.7847 (p) REVERT: A 310 ASP cc_start: 0.8320 (t0) cc_final: 0.8024 (t0) REVERT: A 424 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 544 GLU cc_start: 0.7659 (tp30) cc_final: 0.7215 (mp0) REVERT: A 629 ASN cc_start: 0.8172 (m-40) cc_final: 0.7946 (m-40) REVERT: A 653 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7801 (ttpp) REVERT: A 679 LYS cc_start: 0.7601 (mmmm) cc_final: 0.7103 (mttm) REVERT: A 689 MET cc_start: 0.7478 (tpt) cc_final: 0.7240 (tpt) REVERT: A 725 MET cc_start: 0.7259 (mtt) cc_final: 0.6706 (mtp) REVERT: A 729 ASP cc_start: 0.7833 (t0) cc_final: 0.7005 (m-30) REVERT: A 731 MET cc_start: 0.8774 (mmm) cc_final: 0.8383 (mmm) REVERT: A 761 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8231 (mm-30) REVERT: Y 75 MET cc_start: 0.6452 (mmm) cc_final: 0.6169 (tpt) REVERT: Y 98 TRP cc_start: 0.7104 (m-10) cc_final: 0.6851 (m-10) REVERT: Y 106 ARG cc_start: 0.8119 (tmm160) cc_final: 0.7479 (ttm110) REVERT: Y 298 LEU cc_start: 0.8286 (mt) cc_final: 0.7975 (tp) REVERT: Y 299 TRP cc_start: 0.8299 (t60) cc_final: 0.8065 (t60) REVERT: Y 342 LYS cc_start: 0.8596 (tmmt) cc_final: 0.8027 (mptt) REVERT: Y 390 ASN cc_start: 0.8421 (t0) cc_final: 0.7985 (t0) REVERT: Y 413 MET cc_start: 0.7976 (tmm) cc_final: 0.7638 (tmm) REVERT: Y 415 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7743 (tp40) REVERT: Y 423 ARG cc_start: 0.8556 (mpt90) cc_final: 0.8335 (mpt-90) REVERT: V 32 TYR cc_start: 0.7343 (t80) cc_final: 0.7142 (t80) REVERT: B 58 MET cc_start: 0.5696 (tmm) cc_final: 0.5400 (ttp) outliers start: 30 outliers final: 20 residues processed: 194 average time/residue: 0.2407 time to fit residues: 65.8194 Evaluate side-chains 185 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain B residue 81 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 126 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.172555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120224 restraints weight = 13914.873| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.66 r_work: 0.3124 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11259 Z= 0.134 Angle : 0.536 9.697 15215 Z= 0.272 Chirality : 0.041 0.154 1730 Planarity : 0.003 0.039 1942 Dihedral : 5.737 102.781 1533 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.45 % Allowed : 14.61 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.23), residues: 1372 helix: 1.58 (0.19), residues: 766 sheet: -0.10 (0.48), residues: 132 loop : -1.46 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 78 HIS 0.002 0.001 HIS A 464 PHE 0.011 0.001 PHE A 711 TYR 0.013 0.001 TYR V 32 ARG 0.004 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 572) hydrogen bonds : angle 3.69062 ( 1680) SS BOND : bond 0.00570 ( 1) SS BOND : angle 0.43692 ( 2) covalent geometry : bond 0.00318 (11258) covalent geometry : angle 0.53601 (15213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.7519 (mt0) cc_final: 0.7265 (tt0) REVERT: A 151 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.7877 (p) REVERT: A 310 ASP cc_start: 0.8381 (t0) cc_final: 0.8110 (t0) REVERT: A 424 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 544 GLU cc_start: 0.7719 (tp30) cc_final: 0.7315 (mp0) REVERT: A 629 ASN cc_start: 0.8278 (m-40) cc_final: 0.8053 (m-40) REVERT: A 653 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7810 (ttpp) REVERT: A 679 LYS cc_start: 0.7697 (mmmm) cc_final: 0.7159 (mttm) REVERT: A 689 MET cc_start: 0.7667 (tpt) cc_final: 0.7404 (tpt) REVERT: A 729 ASP cc_start: 0.7867 (t0) cc_final: 0.7141 (m-30) REVERT: A 761 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8312 (mm-30) REVERT: Y 75 MET cc_start: 0.6681 (mmm) cc_final: 0.6263 (tpt) REVERT: Y 98 TRP cc_start: 0.7066 (m-10) cc_final: 0.6813 (m-10) REVERT: Y 298 LEU cc_start: 0.8277 (mt) cc_final: 0.7960 (tp) REVERT: Y 299 TRP cc_start: 0.8324 (t60) cc_final: 0.8108 (t60) REVERT: Y 342 LYS cc_start: 0.8626 (tmmt) cc_final: 0.8085 (mptt) REVERT: Y 390 ASN cc_start: 0.8411 (t0) cc_final: 0.7978 (t0) REVERT: Y 413 MET cc_start: 0.8023 (tmm) cc_final: 0.7716 (tmm) REVERT: Y 423 ARG cc_start: 0.8580 (mpt90) cc_final: 0.8380 (mpt-90) REVERT: E 17 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8372 (mtmm) REVERT: B 58 MET cc_start: 0.5782 (tmm) cc_final: 0.5514 (ttp) outliers start: 29 outliers final: 23 residues processed: 190 average time/residue: 0.2353 time to fit residues: 63.1066 Evaluate side-chains 191 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain B residue 81 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 115 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 93 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.172708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126204 restraints weight = 13869.693| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.60 r_work: 0.3125 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11259 Z= 0.120 Angle : 0.522 8.691 15215 Z= 0.266 Chirality : 0.041 0.154 1730 Planarity : 0.003 0.039 1942 Dihedral : 5.699 108.437 1533 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.62 % Allowed : 14.61 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.23), residues: 1372 helix: 1.66 (0.19), residues: 766 sheet: -0.11 (0.47), residues: 132 loop : -1.44 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 78 HIS 0.002 0.001 HIS A 464 PHE 0.033 0.001 PHE A 549 TYR 0.012 0.001 TYR Y 359 ARG 0.009 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 572) hydrogen bonds : angle 3.64719 ( 1680) SS BOND : bond 0.00574 ( 1) SS BOND : angle 0.39528 ( 2) covalent geometry : bond 0.00280 (11258) covalent geometry : angle 0.52205 (15213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 151 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.7832 (p) REVERT: A 310 ASP cc_start: 0.8459 (t0) cc_final: 0.8204 (t0) REVERT: A 424 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 482 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8768 (mt) REVERT: A 544 GLU cc_start: 0.7665 (tp30) cc_final: 0.7249 (mp0) REVERT: A 653 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7846 (ttpp) REVERT: A 689 MET cc_start: 0.7636 (tpt) cc_final: 0.7360 (tpt) REVERT: A 725 MET cc_start: 0.7159 (mtt) cc_final: 0.6499 (mtp) REVERT: A 729 ASP cc_start: 0.7849 (t0) cc_final: 0.7104 (m-30) REVERT: A 761 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8276 (mm-30) REVERT: Y 75 MET cc_start: 0.6618 (mmm) cc_final: 0.6176 (tpt) REVERT: Y 98 TRP cc_start: 0.7040 (m-10) cc_final: 0.6806 (m-10) REVERT: Y 298 LEU cc_start: 0.8218 (mt) cc_final: 0.7914 (tp) REVERT: Y 299 TRP cc_start: 0.8294 (t60) cc_final: 0.8087 (t60) REVERT: Y 342 LYS cc_start: 0.8603 (tmmt) cc_final: 0.8056 (mptt) REVERT: Y 358 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: Y 390 ASN cc_start: 0.8473 (t0) cc_final: 0.8012 (t0) REVERT: Y 413 MET cc_start: 0.7992 (tmm) cc_final: 0.7694 (tmm) REVERT: E 17 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8349 (mtmm) outliers start: 31 outliers final: 23 residues processed: 191 average time/residue: 0.2309 time to fit residues: 62.5089 Evaluate side-chains 191 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 358 GLU Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain B residue 81 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 383 ASN A 395 ASN ** V 109 GLN ** 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 = 0.3949 r_free = 0.3949 target = 0.172345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116383 restraints weight = 13953.153| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.34 r_work: 0.3112 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11259 Z= 0.132 Angle : 0.546 10.183 15215 Z= 0.275 Chirality : 0.041 0.153 1730 Planarity : 0.004 0.041 1942 Dihedral : 5.734 113.870 1533 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.45 % Allowed : 15.54 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.23), residues: 1372 helix: 1.67 (0.19), residues: 765 sheet: 0.13 (0.51), residues: 117 loop : -1.49 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 78 HIS 0.002 0.001 HIS A 464 PHE 0.015 0.001 PHE A 549 TYR 0.017 0.001 TYR V 32 ARG 0.008 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 572) hydrogen bonds : angle 3.67064 ( 1680) SS BOND : bond 0.00561 ( 1) SS BOND : angle 0.40180 ( 2) covalent geometry : bond 0.00314 (11258) covalent geometry : angle 0.54591 (15213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.280 Fit side-chains REVERT: A 151 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.7849 (p) REVERT: A 310 ASP cc_start: 0.8513 (t0) cc_final: 0.8269 (t0) REVERT: A 424 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 544 GLU cc_start: 0.7717 (tp30) cc_final: 0.7318 (mp0) REVERT: A 552 GLU cc_start: 0.7757 (tp30) cc_final: 0.7524 (tp30) REVERT: A 653 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7808 (ttpp) REVERT: A 689 MET cc_start: 0.7673 (tpt) cc_final: 0.7387 (tpt) REVERT: A 729 ASP cc_start: 0.7925 (t0) cc_final: 0.7176 (m-30) REVERT: A 761 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8314 (mm-30) REVERT: Y 75 MET cc_start: 0.6568 (mmm) cc_final: 0.6216 (tpt) REVERT: Y 98 TRP cc_start: 0.7041 (m-10) cc_final: 0.6812 (m-10) REVERT: Y 135 LEU cc_start: 0.8293 (tt) cc_final: 0.8034 (tp) REVERT: Y 298 LEU cc_start: 0.8170 (mt) cc_final: 0.7853 (tp) REVERT: Y 299 TRP cc_start: 0.8327 (t60) cc_final: 0.8116 (t60) REVERT: Y 342 LYS cc_start: 0.8622 (tmmt) cc_final: 0.8099 (mptt) REVERT: Y 358 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: Y 390 ASN cc_start: 0.8464 (t0) cc_final: 0.7995 (t0) REVERT: Y 413 MET cc_start: 0.8074 (tmm) cc_final: 0.7787 (tmm) REVERT: E 17 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8324 (mtmm) REVERT: V 107 TRP cc_start: 0.8559 (m-10) cc_final: 0.8044 (m-10) outliers start: 29 outliers final: 23 residues processed: 191 average time/residue: 0.2356 time to fit residues: 63.5588 Evaluate side-chains 190 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 358 GLU Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain B residue 81 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 76 optimal weight: 0.0010 chunk 114 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116747 restraints weight = 13988.164| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.35 r_work: 0.3106 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11259 Z= 0.122 Angle : 0.549 12.129 15215 Z= 0.274 Chirality : 0.041 0.149 1730 Planarity : 0.003 0.042 1942 Dihedral : 5.700 115.363 1533 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.28 % Allowed : 15.96 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.23), residues: 1372 helix: 1.71 (0.19), residues: 765 sheet: 0.00 (0.50), residues: 121 loop : -1.53 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 78 HIS 0.002 0.001 HIS A 464 PHE 0.013 0.001 PHE A 549 TYR 0.012 0.001 TYR Y 365 ARG 0.010 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 572) hydrogen bonds : angle 3.64054 ( 1680) SS BOND : bond 0.00538 ( 1) SS BOND : angle 0.40980 ( 2) covalent geometry : bond 0.00285 (11258) covalent geometry : angle 0.54863 (15213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.260 Fit side-chains REVERT: A 151 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.7834 (p) REVERT: A 424 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 544 GLU cc_start: 0.7693 (tp30) cc_final: 0.7290 (mp0) REVERT: A 552 GLU cc_start: 0.7804 (tp30) cc_final: 0.7574 (tp30) REVERT: A 576 ARG cc_start: 0.7784 (mtp-110) cc_final: 0.7490 (mtp180) REVERT: A 653 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8180 (ttpp) REVERT: A 689 MET cc_start: 0.7670 (tpt) cc_final: 0.7385 (tpt) REVERT: A 725 MET cc_start: 0.7222 (mtt) cc_final: 0.6589 (mtp) REVERT: A 729 ASP cc_start: 0.7924 (t0) cc_final: 0.7166 (m-30) REVERT: A 761 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8309 (mm-30) REVERT: Y 75 MET cc_start: 0.6591 (mmm) cc_final: 0.6330 (tpt) REVERT: Y 98 TRP cc_start: 0.7016 (m-10) cc_final: 0.6787 (m-10) REVERT: Y 124 GLN cc_start: 0.7544 (pt0) cc_final: 0.7320 (pt0) REVERT: Y 135 LEU cc_start: 0.8299 (tt) cc_final: 0.8043 (tp) REVERT: Y 298 LEU cc_start: 0.8157 (mt) cc_final: 0.7849 (tp) REVERT: Y 299 TRP cc_start: 0.8322 (t60) cc_final: 0.8112 (t60) REVERT: Y 342 LYS cc_start: 0.8612 (tmmt) cc_final: 0.8083 (mptt) REVERT: Y 358 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: Y 390 ASN cc_start: 0.8500 (t0) cc_final: 0.8014 (t0) REVERT: Y 413 MET cc_start: 0.8043 (tmm) cc_final: 0.7756 (tmm) REVERT: E 17 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8312 (mtmm) REVERT: V 107 TRP cc_start: 0.8562 (m-10) cc_final: 0.8052 (m-10) outliers start: 27 outliers final: 21 residues processed: 188 average time/residue: 0.2493 time to fit residues: 66.3805 Evaluate side-chains 186 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 358 GLU Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain V residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 18 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 118 optimal weight: 0.0570 chunk 88 optimal weight: 0.0070 chunk 122 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 93 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124657 restraints weight = 13975.181| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.48 r_work: 0.3163 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11259 Z= 0.100 Angle : 0.544 11.753 15215 Z= 0.271 Chirality : 0.040 0.160 1730 Planarity : 0.003 0.039 1942 Dihedral : 5.630 117.038 1533 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.35 % Allowed : 16.72 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.24), residues: 1372 helix: 1.84 (0.19), residues: 766 sheet: 0.21 (0.50), residues: 121 loop : -1.49 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 78 HIS 0.002 0.000 HIS B 74 PHE 0.009 0.001 PHE Y 428 TYR 0.015 0.001 TYR V 32 ARG 0.005 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 572) hydrogen bonds : angle 3.52915 ( 1680) SS BOND : bond 0.00581 ( 1) SS BOND : angle 0.41323 ( 2) covalent geometry : bond 0.00214 (11258) covalent geometry : angle 0.54390 (15213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.309 Fit side-chains REVERT: A 424 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 544 GLU cc_start: 0.7653 (tp30) cc_final: 0.7299 (mp0) REVERT: A 552 GLU cc_start: 0.7756 (tp30) cc_final: 0.7525 (tp30) REVERT: A 653 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8200 (ttpp) REVERT: A 689 MET cc_start: 0.7682 (tpt) cc_final: 0.7358 (tpt) REVERT: A 725 MET cc_start: 0.7208 (mtt) cc_final: 0.6574 (mtp) REVERT: A 729 ASP cc_start: 0.7877 (t0) cc_final: 0.7119 (m-30) REVERT: A 761 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8262 (mm-30) REVERT: Y 75 MET cc_start: 0.6438 (mmm) cc_final: 0.6114 (tpt) REVERT: Y 135 LEU cc_start: 0.8259 (tt) cc_final: 0.8005 (tp) REVERT: Y 298 LEU cc_start: 0.8068 (mt) cc_final: 0.7752 (tp) REVERT: Y 299 TRP cc_start: 0.8303 (t60) cc_final: 0.8103 (t60) REVERT: Y 342 LYS cc_start: 0.8588 (tmmt) cc_final: 0.8078 (mptt) REVERT: Y 390 ASN cc_start: 0.8496 (t0) cc_final: 0.8000 (t0) REVERT: Y 413 MET cc_start: 0.8063 (tmm) cc_final: 0.7754 (tmm) REVERT: E 17 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8351 (mtmm) REVERT: V 107 TRP cc_start: 0.8578 (m-10) cc_final: 0.8034 (m-10) outliers start: 16 outliers final: 15 residues processed: 178 average time/residue: 0.2526 time to fit residues: 63.0206 Evaluate side-chains 175 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain B residue 81 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125245 restraints weight = 14027.517| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.61 r_work: 0.3134 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11259 Z= 0.134 Angle : 0.579 11.478 15215 Z= 0.288 Chirality : 0.042 0.175 1730 Planarity : 0.004 0.045 1942 Dihedral : 5.693 118.099 1533 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.35 % Allowed : 16.89 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.24), residues: 1372 helix: 1.74 (0.19), residues: 772 sheet: 0.15 (0.50), residues: 121 loop : -1.52 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Y 98 HIS 0.002 0.001 HIS A 464 PHE 0.009 0.001 PHE A 711 TYR 0.016 0.001 TYR V 32 ARG 0.010 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 572) hydrogen bonds : angle 3.60309 ( 1680) SS BOND : bond 0.00539 ( 1) SS BOND : angle 0.40440 ( 2) covalent geometry : bond 0.00319 (11258) covalent geometry : angle 0.57867 (15213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5226.95 seconds wall clock time: 91 minutes 13.78 seconds (5473.78 seconds total)