Starting phenix.real_space_refine on Mon Jun 9 23:37:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9z_39086/06_2025/8y9z_39086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9z_39086/06_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_39086/06_2025/8y9z_39086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9z_39086/06_2025/8y9z_39086.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9z_39086/06_2025/8y9z_39086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9z_39086/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.27, per 1000 atoms: 0.66 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: 2.38 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: 1.13 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: 3.62 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: 1.470 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.750 ------------------------------------------------------------------------------- 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 : 1.195 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: 0.2548 time to fit residues: 101.5580 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 : 2.140 ------------------------------------------------------------------------------- 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: 0.3188 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 1.104 Fit side-chains REVERT: A 99 GLU cc_start: 0.8033 (tt0) cc_final: 0.7781 (tm-30) REVERT: A 137 ASP cc_start: 0.8651 (m-30) cc_final: 0.8319 (m-30) REVERT: A 310 ASP cc_start: 0.7816 (t0) cc_final: 0.7574 (t0) REVERT: A 350 MET cc_start: 0.7945 (ttp) cc_final: 0.7594 (ttt) REVERT: A 416 LYS cc_start: 0.8169 (tttm) cc_final: 0.7829 (ttpp) REVERT: A 544 GLU cc_start: 0.7624 (tp30) cc_final: 0.7225 (mp0) REVERT: A 572 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7636 (tppt) REVERT: A 604 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7907 (ttt-90) REVERT: A 629 ASN cc_start: 0.8210 (m-40) cc_final: 0.7956 (m-40) REVERT: A 679 LYS cc_start: 0.7359 (mmmm) cc_final: 0.6862 (mttm) REVERT: A 729 ASP cc_start: 0.7729 (t0) cc_final: 0.6868 (m-30) REVERT: A 731 MET cc_start: 0.8698 (mmm) cc_final: 0.8192 (mmm) REVERT: A 751 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7146 (mm-30) REVERT: Y 98 TRP cc_start: 0.6931 (m-10) cc_final: 0.6681 (m-10) REVERT: Y 165 TRP cc_start: 0.7526 (t60) cc_final: 0.7214 (t60) REVERT: Y 250 GLU cc_start: 0.5191 (OUTLIER) cc_final: 0.4865 (pm20) REVERT: Y 299 TRP cc_start: 0.8364 (t60) cc_final: 0.8019 (t60) REVERT: Y 342 LYS cc_start: 0.8588 (tmmt) cc_final: 0.8040 (mptt) REVERT: Y 390 ASN cc_start: 0.8212 (t0) cc_final: 0.7841 (t0) REVERT: Y 413 MET cc_start: 0.8042 (tmm) cc_final: 0.7677 (tmm) REVERT: Y 423 ARG cc_start: 0.8550 (mpt90) cc_final: 0.8313 (mpt-90) REVERT: V 31 MET cc_start: 0.7573 (tpp) cc_final: 0.7365 (tpt) outliers start: 24 outliers final: 13 residues processed: 196 average time/residue: 0.2679 time to fit residues: 72.7964 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 : 1.205 ------------------------------------------------------------------------------- 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: 0.0570 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN V 83 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 = 0.3976 r_free = 0.3976 target = 0.174654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127667 restraints weight = 14088.613| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.52 r_work: 0.3171 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11259 Z= 0.128 Angle : 0.526 7.038 15215 Z= 0.275 Chirality : 0.041 0.153 1730 Planarity : 0.004 0.061 1942 Dihedral : 6.193 92.875 1537 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.53 % Allowed : 12.58 % 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: 0.07 (0.23), residues: 1372 helix: 1.08 (0.19), residues: 766 sheet: -0.39 (0.47), residues: 130 loop : -1.52 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 78 HIS 0.002 0.001 HIS B 74 PHE 0.010 0.001 PHE A 711 TYR 0.018 0.001 TYR V 32 ARG 0.006 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 572) hydrogen bonds : angle 3.90227 ( 1680) SS BOND : bond 0.00606 ( 1) SS BOND : angle 0.37962 ( 2) covalent geometry : bond 0.00294 (11258) covalent geometry : angle 0.52554 (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 214 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8041 (tt0) cc_final: 0.7839 (tm-30) REVERT: A 137 ASP cc_start: 0.8661 (m-30) cc_final: 0.8352 (m-30) REVERT: A 310 ASP cc_start: 0.8012 (t0) cc_final: 0.7732 (t0) REVERT: A 416 LYS cc_start: 0.8192 (tttm) cc_final: 0.7838 (ttpp) REVERT: A 544 GLU cc_start: 0.7724 (tp30) cc_final: 0.7298 (mp0) REVERT: A 624 ARG cc_start: 0.8353 (ttt90) cc_final: 0.7738 (ttt180) REVERT: A 629 ASN cc_start: 0.8171 (m-40) cc_final: 0.7910 (m-40) REVERT: A 679 LYS cc_start: 0.7420 (mmmm) cc_final: 0.7083 (mttm) REVERT: A 725 MET cc_start: 0.7273 (mtt) cc_final: 0.6751 (mtp) REVERT: A 729 ASP cc_start: 0.7751 (t0) cc_final: 0.6920 (m-30) REVERT: A 755 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: A 761 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8280 (mm-30) REVERT: Y 75 MET cc_start: 0.6850 (mmm) cc_final: 0.6206 (tpt) REVERT: Y 98 TRP cc_start: 0.6929 (m-10) cc_final: 0.6672 (m-10) REVERT: Y 135 LEU cc_start: 0.8203 (tt) cc_final: 0.7741 (mm) REVERT: Y 165 TRP cc_start: 0.7634 (t60) cc_final: 0.7317 (t60) REVERT: Y 299 TRP cc_start: 0.8351 (t60) cc_final: 0.8043 (t60) REVERT: Y 336 MET cc_start: 0.8191 (mtp) cc_final: 0.7969 (mtp) REVERT: Y 342 LYS cc_start: 0.8602 (tmmt) cc_final: 0.8062 (mptt) REVERT: Y 390 ASN cc_start: 0.8179 (t0) cc_final: 0.7806 (t0) REVERT: Y 413 MET cc_start: 0.8036 (tmm) cc_final: 0.7671 (tmm) REVERT: Y 415 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7699 (tp40) REVERT: Y 423 ARG cc_start: 0.8557 (mpt90) cc_final: 0.8315 (mpt-90) REVERT: B 58 MET cc_start: 0.5801 (tmm) cc_final: 0.5410 (ttp) outliers start: 30 outliers final: 18 residues processed: 204 average time/residue: 0.2364 time to fit residues: 67.7602 Evaluate side-chains 188 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 658 VAL Chi-restraints excluded: chain A residue 755 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 83 optimal weight: 0.0470 chunk 70 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.174636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126179 restraints weight = 13907.179| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.47 r_work: 0.3171 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2221 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= 0.112 Angle : 0.512 7.142 15215 Z= 0.264 Chirality : 0.040 0.142 1730 Planarity : 0.003 0.047 1942 Dihedral : 5.916 94.482 1535 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.45 % Allowed : 13.85 % Favored : 83.70 % 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: 0.36 (0.23), residues: 1372 helix: 1.38 (0.19), residues: 766 sheet: 0.01 (0.50), residues: 118 loop : -1.56 (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 0.010 0.001 PHE Y 112 TYR 0.017 0.001 TYR V 32 ARG 0.004 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 572) hydrogen bonds : angle 3.75491 ( 1680) SS BOND : bond 0.00713 ( 1) SS BOND : angle 0.36773 ( 2) covalent geometry : bond 0.00254 (11258) covalent geometry : angle 0.51182 (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 198 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 79 MET cc_start: 0.8062 (mtm) cc_final: 0.7832 (mtm) REVERT: A 137 ASP cc_start: 0.8594 (m-30) cc_final: 0.8370 (m-30) REVERT: A 310 ASP cc_start: 0.8140 (t0) cc_final: 0.7861 (t0) REVERT: A 416 LYS cc_start: 0.8161 (tttm) cc_final: 0.7794 (ttpp) REVERT: A 424 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 482 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 544 GLU cc_start: 0.7675 (tp30) cc_final: 0.7256 (mp0) REVERT: A 624 ARG cc_start: 0.8252 (ttt90) cc_final: 0.7726 (ttt180) REVERT: A 629 ASN cc_start: 0.8199 (m-40) cc_final: 0.7960 (m-40) REVERT: A 679 LYS cc_start: 0.7485 (mmmm) cc_final: 0.7140 (mttm) REVERT: A 689 MET cc_start: 0.7435 (tpt) cc_final: 0.7212 (tpt) REVERT: A 729 ASP cc_start: 0.7831 (t0) cc_final: 0.7044 (m-30) REVERT: A 731 MET cc_start: 0.8826 (mmm) cc_final: 0.8535 (mmm) REVERT: A 761 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8250 (mm-30) REVERT: Y 75 MET cc_start: 0.6581 (mmm) cc_final: 0.6152 (tpt) REVERT: Y 98 TRP cc_start: 0.7024 (m-10) cc_final: 0.6781 (m-10) REVERT: Y 298 LEU cc_start: 0.8442 (mt) cc_final: 0.8061 (tp) REVERT: Y 299 TRP cc_start: 0.8324 (t60) cc_final: 0.8058 (t60) REVERT: Y 342 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8053 (mptt) REVERT: Y 358 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: Y 390 ASN cc_start: 0.8369 (t0) cc_final: 0.7959 (t0) REVERT: Y 413 MET cc_start: 0.7997 (tmm) cc_final: 0.7648 (tmm) REVERT: Y 415 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7683 (tp40) REVERT: Y 423 ARG cc_start: 0.8530 (mpt90) cc_final: 0.8300 (mpt-90) REVERT: B 58 MET cc_start: 0.5613 (tmm) cc_final: 0.5228 (ttp) outliers start: 29 outliers final: 18 residues processed: 190 average time/residue: 0.2514 time to fit residues: 67.3005 Evaluate side-chains 188 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 482 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 249 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 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: 6.9990 chunk 98 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3967 r_free = 0.3967 target = 0.174217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122263 restraints weight = 13757.896| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.43 r_work: 0.3142 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2366 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= 0.112 Angle : 0.505 7.162 15215 Z= 0.260 Chirality : 0.040 0.141 1730 Planarity : 0.003 0.037 1942 Dihedral : 5.856 97.607 1535 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.45 % Allowed : 14.10 % Favored : 83.45 % 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: 0.56 (0.23), residues: 1372 helix: 1.53 (0.19), residues: 771 sheet: -0.05 (0.48), residues: 132 loop : -1.48 (0.28), residues: 469 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 0.010 0.001 PHE Y 428 TYR 0.024 0.001 TYR V 32 ARG 0.008 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 572) hydrogen bonds : angle 3.66885 ( 1680) SS BOND : bond 0.00632 ( 1) SS BOND : angle 0.37530 ( 2) covalent geometry : bond 0.00255 (11258) covalent geometry : angle 0.50517 (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 201 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8602 (m-30) cc_final: 0.8391 (m-30) REVERT: A 151 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.7911 (p) REVERT: A 310 ASP cc_start: 0.8280 (t0) cc_final: 0.7974 (t0) REVERT: A 424 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 544 GLU cc_start: 0.7679 (tp30) cc_final: 0.7296 (mp0) REVERT: A 629 ASN cc_start: 0.8186 (m-40) cc_final: 0.7955 (m-40) REVERT: A 679 LYS cc_start: 0.7624 (mmmm) cc_final: 0.7140 (mttm) REVERT: A 689 MET cc_start: 0.7529 (tpt) cc_final: 0.7205 (tpt) REVERT: A 729 ASP cc_start: 0.7884 (t0) cc_final: 0.7075 (m-30) REVERT: A 731 MET cc_start: 0.8866 (mmm) cc_final: 0.8529 (mmm) REVERT: A 761 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8243 (mm-30) REVERT: Y 75 MET cc_start: 0.6597 (mmm) cc_final: 0.6263 (tpt) REVERT: Y 98 TRP cc_start: 0.7065 (m-10) cc_final: 0.6815 (m-10) REVERT: Y 106 ARG cc_start: 0.8134 (tmm160) cc_final: 0.7514 (ttm110) REVERT: Y 298 LEU cc_start: 0.8403 (mt) cc_final: 0.8078 (tp) REVERT: Y 299 TRP cc_start: 0.8325 (t60) cc_final: 0.8085 (t60) REVERT: Y 342 LYS cc_start: 0.8605 (tmmt) cc_final: 0.8071 (mptt) REVERT: Y 358 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: Y 390 ASN cc_start: 0.8367 (t0) cc_final: 0.7955 (t0) REVERT: Y 413 MET cc_start: 0.8021 (tmm) cc_final: 0.7663 (tmm) REVERT: Y 415 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7728 (tp40) REVERT: Y 423 ARG cc_start: 0.8536 (mpt90) cc_final: 0.8318 (mpt-90) REVERT: B 58 MET cc_start: 0.5720 (tmm) cc_final: 0.5363 (ttp) outliers start: 29 outliers final: 20 residues processed: 194 average time/residue: 0.2425 time to fit residues: 66.3976 Evaluate side-chains 188 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 25 LEU 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 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: 0.6980 chunk 43 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 126 optimal weight: 0.0970 chunk 66 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 Y 88 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.173919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127908 restraints weight = 13914.476| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.75 r_work: 0.3120 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11259 Z= 0.111 Angle : 0.514 9.905 15215 Z= 0.261 Chirality : 0.041 0.152 1730 Planarity : 0.003 0.037 1942 Dihedral : 5.683 100.635 1533 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.45 % Allowed : 14.19 % Favored : 83.36 % 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: 0.69 (0.23), residues: 1372 helix: 1.63 (0.19), residues: 772 sheet: -0.01 (0.48), residues: 132 loop : -1.43 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 78 HIS 0.002 0.000 HIS B 74 PHE 0.009 0.001 PHE Y 428 TYR 0.011 0.001 TYR Y 359 ARG 0.003 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 572) hydrogen bonds : angle 3.64584 ( 1680) SS BOND : bond 0.00577 ( 1) SS BOND : angle 0.40553 ( 2) covalent geometry : bond 0.00252 (11258) covalent geometry : angle 0.51434 (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 200 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 ASP cc_start: 0.8298 (t0) cc_final: 0.7991 (t0) REVERT: A 424 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7849 (tm-30) REVERT: A 482 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 544 GLU cc_start: 0.7663 (tp30) cc_final: 0.7214 (mp0) REVERT: A 629 ASN cc_start: 0.8181 (m-40) cc_final: 0.7954 (m-40) REVERT: A 650 GLU cc_start: 0.7857 (mp0) cc_final: 0.7609 (pm20) REVERT: A 679 LYS cc_start: 0.7603 (mmmm) cc_final: 0.7117 (mttm) REVERT: A 689 MET cc_start: 0.7517 (tpt) cc_final: 0.7264 (tpt) REVERT: A 725 MET cc_start: 0.7180 (mtt) cc_final: 0.6564 (mtp) REVERT: A 729 ASP cc_start: 0.7869 (t0) cc_final: 0.7069 (m-30) REVERT: A 731 MET cc_start: 0.8810 (mmm) cc_final: 0.8433 (mmm) REVERT: A 761 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8285 (mm-30) REVERT: Y 75 MET cc_start: 0.6524 (mmm) cc_final: 0.6229 (tpt) REVERT: Y 98 TRP cc_start: 0.7063 (m-10) cc_final: 0.6803 (m-10) REVERT: Y 106 ARG cc_start: 0.8071 (tmm160) cc_final: 0.7473 (ttm110) REVERT: Y 298 LEU cc_start: 0.8282 (mt) cc_final: 0.7975 (tp) REVERT: Y 299 TRP cc_start: 0.8307 (t60) cc_final: 0.8075 (t60) REVERT: Y 342 LYS cc_start: 0.8591 (tmmt) cc_final: 0.8035 (mptt) REVERT: Y 358 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: Y 390 ASN cc_start: 0.8393 (t0) cc_final: 0.7976 (t0) REVERT: Y 413 MET cc_start: 0.7999 (tmm) cc_final: 0.7654 (tmm) REVERT: Y 415 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7676 (tp40) REVERT: Y 423 ARG cc_start: 0.8562 (mpt90) cc_final: 0.8351 (mpt-90) REVERT: B 58 MET cc_start: 0.5533 (tmm) cc_final: 0.5249 (ttp) outliers start: 29 outliers final: 20 residues processed: 194 average time/residue: 0.2364 time to fit residues: 64.9973 Evaluate side-chains 188 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 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 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 E residue 51 ILE 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: 8.9990 chunk 93 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 169 GLN V 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.173692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122320 restraints weight = 13984.896| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.70 r_work: 0.3147 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11259 Z= 0.116 Angle : 0.525 8.956 15215 Z= 0.266 Chirality : 0.041 0.154 1730 Planarity : 0.003 0.038 1942 Dihedral : 5.663 104.571 1533 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.36 % Allowed : 14.61 % Favored : 83.02 % 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: 1.69 (0.19), residues: 772 sheet: -0.02 (0.48), residues: 132 loop : -1.40 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 78 HIS 0.002 0.000 HIS B 74 PHE 0.009 0.001 PHE Y 428 TYR 0.011 0.001 TYR Y 359 ARG 0.010 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 572) hydrogen bonds : angle 3.61648 ( 1680) SS BOND : bond 0.00576 ( 1) SS BOND : angle 0.41001 ( 2) covalent geometry : bond 0.00267 (11258) covalent geometry : angle 0.52523 (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 194 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.7903 (p) REVERT: A 310 ASP cc_start: 0.8347 (t0) cc_final: 0.8071 (t0) REVERT: A 424 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 482 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8740 (mp) REVERT: A 544 GLU cc_start: 0.7706 (tp30) cc_final: 0.7319 (mp0) REVERT: A 629 ASN cc_start: 0.8265 (m-40) cc_final: 0.8039 (m-40) REVERT: A 679 LYS cc_start: 0.7643 (mmmm) cc_final: 0.7135 (mttm) REVERT: A 689 MET cc_start: 0.7718 (tpt) cc_final: 0.7439 (tpt) REVERT: A 725 MET cc_start: 0.7168 (mtt) cc_final: 0.6537 (mtp) REVERT: A 729 ASP cc_start: 0.7939 (t0) cc_final: 0.7119 (m-30) REVERT: A 761 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8313 (mm-30) REVERT: Y 75 MET cc_start: 0.6643 (mmm) cc_final: 0.6344 (tpt) REVERT: Y 98 TRP cc_start: 0.7002 (m-10) cc_final: 0.6777 (m-10) REVERT: Y 298 LEU cc_start: 0.8247 (mt) cc_final: 0.7938 (tp) REVERT: Y 299 TRP cc_start: 0.8317 (t60) cc_final: 0.8096 (t60) REVERT: Y 342 LYS cc_start: 0.8630 (tmmt) cc_final: 0.8123 (mptt) REVERT: Y 358 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: Y 390 ASN cc_start: 0.8430 (t0) cc_final: 0.8002 (t0) REVERT: Y 413 MET cc_start: 0.8044 (tmm) cc_final: 0.7699 (tmm) REVERT: Y 415 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7795 (tp40) REVERT: E 17 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8354 (mtmm) REVERT: B 58 MET cc_start: 0.5593 (tmm) cc_final: 0.5378 (ttp) outliers start: 28 outliers final: 23 residues processed: 187 average time/residue: 0.2430 time to fit residues: 65.1005 Evaluate side-chains 190 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 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 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 25 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 126 optimal weight: 0.0050 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.173942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128048 restraints weight = 13928.929| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.62 r_work: 0.3149 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11259 Z= 0.114 Angle : 0.531 10.119 15215 Z= 0.266 Chirality : 0.041 0.149 1730 Planarity : 0.003 0.038 1942 Dihedral : 5.647 109.624 1533 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.45 % Allowed : 14.95 % Favored : 82.60 % 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: 0.82 (0.24), residues: 1372 helix: 1.76 (0.19), residues: 772 sheet: -0.02 (0.48), residues: 132 loop : -1.40 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 78 HIS 0.002 0.000 HIS A 464 PHE 0.012 0.001 PHE A 549 TYR 0.011 0.001 TYR Y 359 ARG 0.005 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 572) hydrogen bonds : angle 3.59229 ( 1680) SS BOND : bond 0.00579 ( 1) SS BOND : angle 0.41717 ( 2) covalent geometry : bond 0.00262 (11258) covalent geometry : angle 0.53095 (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 196 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 151 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.7798 (p) REVERT: A 310 ASP cc_start: 0.8391 (t0) cc_final: 0.8107 (t0) REVERT: A 424 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 544 GLU cc_start: 0.7573 (tp30) cc_final: 0.7144 (mp0) REVERT: A 629 ASN cc_start: 0.8183 (m-40) cc_final: 0.7946 (m-40) REVERT: A 679 LYS cc_start: 0.7628 (mmmm) cc_final: 0.7111 (mttm) REVERT: A 689 MET cc_start: 0.7594 (tpt) cc_final: 0.7324 (tpt) REVERT: A 725 MET cc_start: 0.7047 (mtt) cc_final: 0.6335 (mtp) REVERT: A 729 ASP cc_start: 0.7804 (t0) cc_final: 0.6978 (m-30) REVERT: A 761 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8238 (mm-30) REVERT: Y 75 MET cc_start: 0.6570 (mmm) cc_final: 0.6130 (tpt) REVERT: Y 98 TRP cc_start: 0.7037 (m-10) cc_final: 0.6797 (m-10) REVERT: Y 298 LEU cc_start: 0.8151 (mt) cc_final: 0.7864 (tp) REVERT: Y 299 TRP cc_start: 0.8291 (t60) cc_final: 0.8075 (t60) REVERT: Y 342 LYS cc_start: 0.8571 (tmmt) cc_final: 0.8019 (mptt) REVERT: Y 358 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: Y 390 ASN cc_start: 0.8473 (t0) cc_final: 0.8018 (t0) REVERT: Y 413 MET cc_start: 0.7907 (tmm) cc_final: 0.7613 (tmm) REVERT: Y 415 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7699 (tp40) REVERT: E 17 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8304 (mtmm) outliers start: 29 outliers final: 23 residues processed: 189 average time/residue: 0.2470 time to fit residues: 67.0645 Evaluate side-chains 188 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 25 LEU 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: 0.5980 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.173259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126011 restraints weight = 14008.536| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.60 r_work: 0.3136 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2704 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= 0.123 Angle : 0.548 11.173 15215 Z= 0.274 Chirality : 0.041 0.147 1730 Planarity : 0.004 0.043 1942 Dihedral : 5.671 113.129 1533 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.36 % Allowed : 14.95 % Favored : 82.69 % 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: 0.81 (0.24), residues: 1372 helix: 1.74 (0.19), residues: 772 sheet: -0.03 (0.48), residues: 132 loop : -1.38 (0.29), residues: 468 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 0.010 0.001 PHE A 711 TYR 0.011 0.001 TYR Y 359 ARG 0.010 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 572) hydrogen bonds : angle 3.60629 ( 1680) SS BOND : bond 0.00553 ( 1) SS BOND : angle 0.42212 ( 2) covalent geometry : bond 0.00289 (11258) covalent geometry : angle 0.54826 (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 192 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.146 Fit side-chains REVERT: A 151 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.7765 (p) REVERT: A 310 ASP cc_start: 0.8460 (t0) cc_final: 0.8173 (t0) REVERT: A 424 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 482 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8743 (mt) REVERT: A 544 GLU cc_start: 0.7566 (tp30) cc_final: 0.7129 (mp0) REVERT: A 552 GLU cc_start: 0.7832 (tp30) cc_final: 0.7591 (tp30) REVERT: A 629 ASN cc_start: 0.8174 (m-40) cc_final: 0.7932 (m-40) REVERT: A 679 LYS cc_start: 0.7613 (mmmm) cc_final: 0.7103 (mttm) REVERT: A 689 MET cc_start: 0.7574 (tpt) cc_final: 0.7285 (tpt) REVERT: A 725 MET cc_start: 0.7037 (mtt) cc_final: 0.6371 (mtp) REVERT: A 729 ASP cc_start: 0.7794 (t0) cc_final: 0.6972 (m-30) REVERT: A 731 MET cc_start: 0.8611 (mmm) cc_final: 0.8347 (mmm) REVERT: A 761 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8209 (mm-30) REVERT: Y 75 MET cc_start: 0.6441 (mmm) cc_final: 0.6088 (tpt) REVERT: Y 98 TRP cc_start: 0.6968 (m-10) cc_final: 0.6722 (m-10) REVERT: Y 135 LEU cc_start: 0.8230 (tt) cc_final: 0.7986 (tp) REVERT: Y 298 LEU cc_start: 0.8139 (mt) cc_final: 0.7844 (tp) REVERT: Y 299 TRP cc_start: 0.8281 (t60) cc_final: 0.8068 (t60) REVERT: Y 342 LYS cc_start: 0.8544 (tmmt) cc_final: 0.7977 (mptt) REVERT: Y 358 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: Y 390 ASN cc_start: 0.8544 (t0) cc_final: 0.8042 (t0) REVERT: Y 413 MET cc_start: 0.7869 (tmm) cc_final: 0.7562 (tmm) REVERT: Y 415 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7686 (tp40) REVERT: E 17 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8356 (mtmm) outliers start: 28 outliers final: 24 residues processed: 186 average time/residue: 0.2329 time to fit residues: 61.5776 Evaluate side-chains 191 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 25 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 18 optimal weight: 0.7980 chunk 98 optimal weight: 0.0980 chunk 118 optimal weight: 0.1980 chunk 88 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 0.0070 chunk 115 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.173086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126265 restraints weight = 14015.158| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.64 r_work: 0.3148 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11259 Z= 0.122 Angle : 0.551 10.968 15215 Z= 0.275 Chirality : 0.041 0.146 1730 Planarity : 0.003 0.040 1942 Dihedral : 5.666 115.964 1533 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.36 % Allowed : 15.12 % Favored : 82.52 % 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: 1.77 (0.19), residues: 772 sheet: 0.26 (0.51), residues: 117 loop : -1.39 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 78 HIS 0.002 0.001 HIS A 464 PHE 0.019 0.001 PHE A 549 TYR 0.011 0.001 TYR Y 359 ARG 0.005 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 572) hydrogen bonds : angle 3.60214 ( 1680) SS BOND : bond 0.00548 ( 1) SS BOND : angle 0.41591 ( 2) covalent geometry : bond 0.00285 (11258) covalent geometry : angle 0.55104 (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 194 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.171 Fit side-chains REVERT: A 151 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.7747 (p) REVERT: A 310 ASP cc_start: 0.8533 (t0) cc_final: 0.8279 (t0) REVERT: A 424 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 544 GLU cc_start: 0.7572 (tp30) cc_final: 0.7121 (mp0) REVERT: A 552 GLU cc_start: 0.7829 (tp30) cc_final: 0.7591 (tp30) REVERT: A 679 LYS cc_start: 0.7630 (mmmm) cc_final: 0.7109 (mttm) REVERT: A 689 MET cc_start: 0.7575 (tpt) cc_final: 0.7291 (tpt) REVERT: A 725 MET cc_start: 0.7016 (mtt) cc_final: 0.6346 (mtp) REVERT: A 729 ASP cc_start: 0.7792 (t0) cc_final: 0.6980 (m-30) REVERT: A 731 MET cc_start: 0.8592 (mmm) cc_final: 0.8347 (mmm) REVERT: A 761 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8170 (mm-30) REVERT: Y 72 MET cc_start: 0.8973 (tpt) cc_final: 0.8771 (tpt) REVERT: Y 75 MET cc_start: 0.6476 (mmm) cc_final: 0.6103 (tpt) REVERT: Y 98 TRP cc_start: 0.6958 (m-10) cc_final: 0.6712 (m-10) REVERT: Y 135 LEU cc_start: 0.8260 (tt) cc_final: 0.8025 (tp) REVERT: Y 298 LEU cc_start: 0.8140 (mt) cc_final: 0.7840 (tp) REVERT: Y 299 TRP cc_start: 0.8286 (t60) cc_final: 0.8077 (t60) REVERT: Y 342 LYS cc_start: 0.8542 (tmmt) cc_final: 0.7981 (mptt) REVERT: Y 358 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: Y 390 ASN cc_start: 0.8551 (t0) cc_final: 0.8053 (t0) REVERT: Y 413 MET cc_start: 0.7874 (tmm) cc_final: 0.7572 (tmm) REVERT: Y 415 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7686 (tp40) REVERT: E 17 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8315 (mtmm) REVERT: V 107 TRP cc_start: 0.8590 (m-10) cc_final: 0.8029 (m-10) outliers start: 28 outliers final: 24 residues processed: 186 average time/residue: 0.2413 time to fit residues: 63.9203 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 : 1.152 ------------------------------------------------------------------------------- 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 25 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.171819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124904 restraints weight = 14041.810| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.61 r_work: 0.3129 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11259 Z= 0.142 Angle : 0.573 11.033 15215 Z= 0.287 Chirality : 0.042 0.156 1730 Planarity : 0.004 0.047 1942 Dihedral : 5.710 117.983 1533 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.28 % Allowed : 15.54 % Favored : 82.18 % 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: 1.67 (0.19), residues: 773 sheet: 0.20 (0.51), residues: 117 loop : -1.39 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 78 HIS 0.002 0.001 HIS A 464 PHE 0.012 0.001 PHE A 711 TYR 0.012 0.001 TYR Y 359 ARG 0.011 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 572) hydrogen bonds : angle 3.64751 ( 1680) SS BOND : bond 0.00527 ( 1) SS BOND : angle 0.41592 ( 2) covalent geometry : bond 0.00340 (11258) covalent geometry : angle 0.57342 (15213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5467.91 seconds wall clock time: 94 minutes 43.98 seconds (5683.98 seconds total)