Starting phenix.real_space_refine on Wed Sep 17 20:21:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9z_39086/09_2025/8y9z_39086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9z_39086/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y9z_39086/09_2025/8y9z_39086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9z_39086/09_2025/8y9z_39086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y9z_39086/09_2025/8y9z_39086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9z_39086/09_2025/8y9z_39086.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.53, per 1000 atoms: 0.23 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: 1.07 Conformation dependent library (CDL) restraints added in 442.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.53 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: 1.77 Time building geometry restraints manager: 1.39 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: 2.150 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.005 0.000 ARG A 709 TYR 0.013 0.001 TYR Y 359 PHE 0.016 0.001 PHE Y 428 TRP 0.009 0.001 TRP V 36 HIS 0.005 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00607 (11258) covalent geometry : angle 0.66965 (15213) SS BOND : bond 0.00306 ( 1) SS BOND : angle 0.61402 ( 2) hydrogen bonds : bond 0.15037 ( 572) hydrogen bonds : angle 5.94641 ( 1680) *********************** 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 : 0.443 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: 0.1193 time to fit residues: 47.7700 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 : 0.405 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.176134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128165 restraints weight = 13818.958| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.53 r_work: 0.3166 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11259 Z= 0.123 Angle : 0.547 7.658 15215 Z= 0.291 Chirality : 0.041 0.156 1730 Planarity : 0.004 0.042 1942 Dihedral : 6.551 97.972 1545 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.03 % Allowed : 12.92 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.22), residues: 1372 helix: 0.57 (0.18), residues: 766 sheet: -0.49 (0.45), residues: 144 loop : -1.58 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 248 TYR 0.016 0.001 TYR V 32 PHE 0.010 0.001 PHE A 590 TRP 0.006 0.001 TRP E 20 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00272 (11258) covalent geometry : angle 0.54719 (15213) SS BOND : bond 0.00532 ( 1) SS BOND : angle 0.48812 ( 2) hydrogen bonds : bond 0.04334 ( 572) hydrogen bonds : angle 4.19030 ( 1680) *********************** 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 206 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.431 Fit side-chains REVERT: A 79 MET cc_start: 0.7407 (mmt) cc_final: 0.7130 (mtm) REVERT: A 99 GLU cc_start: 0.8043 (tt0) cc_final: 0.7778 (tm-30) REVERT: A 137 ASP cc_start: 0.8666 (m-30) cc_final: 0.8334 (m-30) REVERT: A 310 ASP cc_start: 0.7856 (t0) cc_final: 0.7615 (t0) REVERT: A 350 MET cc_start: 0.7947 (ttp) cc_final: 0.7590 (ttt) REVERT: A 416 LYS cc_start: 0.8153 (tttm) cc_final: 0.7807 (ttpp) REVERT: A 544 GLU cc_start: 0.7641 (tp30) cc_final: 0.7207 (mp0) REVERT: A 572 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7610 (tppt) REVERT: A 604 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7872 (ttt-90) REVERT: A 629 ASN cc_start: 0.8198 (m-40) cc_final: 0.7944 (m-40) REVERT: A 679 LYS cc_start: 0.7349 (mmmm) cc_final: 0.6844 (mttm) REVERT: A 729 ASP cc_start: 0.7717 (t0) cc_final: 0.6852 (m-30) REVERT: A 731 MET cc_start: 0.8663 (mmm) cc_final: 0.8157 (mmm) REVERT: A 751 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7129 (mm-30) REVERT: Y 98 TRP cc_start: 0.6937 (m-10) cc_final: 0.6682 (m-10) REVERT: Y 165 TRP cc_start: 0.7543 (t60) cc_final: 0.7228 (t60) REVERT: Y 250 GLU cc_start: 0.5178 (OUTLIER) cc_final: 0.4810 (pm20) REVERT: Y 299 TRP cc_start: 0.8364 (t60) cc_final: 0.8023 (t60) REVERT: Y 342 LYS cc_start: 0.8575 (tmmt) cc_final: 0.8016 (mptt) REVERT: Y 390 ASN cc_start: 0.8219 (t0) cc_final: 0.7844 (t0) REVERT: Y 413 MET cc_start: 0.8021 (tmm) cc_final: 0.7653 (tmm) REVERT: Y 423 ARG cc_start: 0.8522 (mpt90) cc_final: 0.8290 (mpt-90) REVERT: V 31 MET cc_start: 0.7565 (tpp) cc_final: 0.7344 (tpt) outliers start: 24 outliers final: 14 residues processed: 196 average time/residue: 0.1154 time to fit residues: 31.4367 Evaluate side-chains 181 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 112 LEU 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 E residue 51 ILE 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 53 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 96 optimal weight: 0.0000 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127556 restraints weight = 14168.618| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.61 r_work: 0.3166 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11259 Z= 0.119 Angle : 0.517 7.083 15215 Z= 0.271 Chirality : 0.041 0.159 1730 Planarity : 0.004 0.064 1942 Dihedral : 6.271 94.395 1539 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.53 % Allowed : 12.50 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.23), residues: 1372 helix: 1.07 (0.19), residues: 766 sheet: -0.36 (0.47), residues: 130 loop : -1.51 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 56 TYR 0.017 0.001 TYR V 32 PHE 0.010 0.001 PHE Y 428 TRP 0.008 0.001 TRP B 78 HIS 0.002 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00272 (11258) covalent geometry : angle 0.51675 (15213) SS BOND : bond 0.00636 ( 1) SS BOND : angle 0.34342 ( 2) hydrogen bonds : bond 0.03982 ( 572) hydrogen bonds : angle 3.91524 ( 1680) *********************** 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 203 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.369 Fit side-chains REVERT: A 99 GLU cc_start: 0.8070 (tt0) cc_final: 0.7830 (tm-30) REVERT: A 137 ASP cc_start: 0.8679 (m-30) cc_final: 0.8358 (m-30) REVERT: A 310 ASP cc_start: 0.8000 (t0) cc_final: 0.7731 (t0) REVERT: A 350 MET cc_start: 0.8019 (ttp) cc_final: 0.7609 (ttt) REVERT: A 416 LYS cc_start: 0.8170 (tttm) cc_final: 0.7818 (ttpp) REVERT: A 544 GLU cc_start: 0.7688 (tp30) cc_final: 0.7251 (mp0) REVERT: A 629 ASN cc_start: 0.8168 (m-40) cc_final: 0.7911 (m-40) REVERT: A 679 LYS cc_start: 0.7381 (mmmm) cc_final: 0.7058 (mttm) REVERT: A 689 MET cc_start: 0.7340 (tpt) cc_final: 0.6814 (tpt) REVERT: A 729 ASP cc_start: 0.7723 (t0) cc_final: 0.6909 (m-30) REVERT: A 761 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8255 (mm-30) REVERT: Y 75 MET cc_start: 0.6792 (mmm) cc_final: 0.6083 (tpt) REVERT: Y 98 TRP cc_start: 0.6915 (m-10) cc_final: 0.6665 (m-10) REVERT: Y 135 LEU cc_start: 0.8153 (tt) cc_final: 0.7681 (mm) REVERT: Y 165 TRP cc_start: 0.7568 (t60) cc_final: 0.7265 (t60) REVERT: Y 299 TRP cc_start: 0.8343 (t60) cc_final: 0.8031 (t60) REVERT: Y 342 LYS cc_start: 0.8583 (tmmt) cc_final: 0.8036 (mptt) REVERT: Y 390 ASN cc_start: 0.8267 (t0) cc_final: 0.7865 (t0) REVERT: Y 413 MET cc_start: 0.7986 (tmm) cc_final: 0.7615 (tmm) REVERT: Y 415 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7681 (tp40) REVERT: Y 423 ARG cc_start: 0.8541 (mpt90) cc_final: 0.8299 (mpt-90) REVERT: B 58 MET cc_start: 0.5625 (tmm) cc_final: 0.5189 (ttp) outliers start: 30 outliers final: 17 residues processed: 193 average time/residue: 0.1154 time to fit residues: 30.9457 Evaluate side-chains 185 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 658 VAL Chi-restraints excluded: chain A residue 722 SER 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 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.174527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123399 restraints weight = 14039.007| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.67 r_work: 0.3150 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11259 Z= 0.120 Angle : 0.518 7.077 15215 Z= 0.268 Chirality : 0.041 0.143 1730 Planarity : 0.004 0.047 1942 Dihedral : 5.931 93.893 1535 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.45 % Allowed : 13.09 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.23), residues: 1372 helix: 1.37 (0.19), residues: 766 sheet: -0.00 (0.50), residues: 118 loop : -1.53 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 516 TYR 0.018 0.001 TYR V 32 PHE 0.010 0.001 PHE A 711 TRP 0.009 0.001 TRP B 78 HIS 0.002 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00277 (11258) covalent geometry : angle 0.51839 (15213) SS BOND : bond 0.00617 ( 1) SS BOND : angle 0.38716 ( 2) hydrogen bonds : bond 0.03909 ( 572) hydrogen bonds : angle 3.77156 ( 1680) *********************** 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 201 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8653 (m-30) cc_final: 0.8377 (m-30) REVERT: A 310 ASP cc_start: 0.8091 (t0) cc_final: 0.7811 (t0) REVERT: A 416 LYS cc_start: 0.8197 (tttm) cc_final: 0.7854 (ttpp) REVERT: A 424 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 482 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8774 (mp) REVERT: A 544 GLU cc_start: 0.7745 (tp30) cc_final: 0.7346 (mp0) REVERT: A 629 ASN cc_start: 0.8271 (m-40) cc_final: 0.8051 (m-40) REVERT: A 679 LYS cc_start: 0.7511 (mmmm) cc_final: 0.7165 (mttm) REVERT: A 729 ASP cc_start: 0.7961 (t0) cc_final: 0.7152 (m-30) REVERT: A 761 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8304 (mm-30) REVERT: Y 75 MET cc_start: 0.6899 (mmm) cc_final: 0.6263 (tpt) REVERT: Y 98 TRP cc_start: 0.7027 (m-10) cc_final: 0.6771 (m-10) REVERT: Y 299 TRP cc_start: 0.8338 (t60) cc_final: 0.8127 (t60) REVERT: Y 336 MET cc_start: 0.8237 (mtp) cc_final: 0.8008 (mtp) REVERT: Y 342 LYS cc_start: 0.8627 (tmmt) cc_final: 0.8118 (mptt) REVERT: Y 390 ASN cc_start: 0.8300 (t0) cc_final: 0.7909 (t0) REVERT: Y 413 MET cc_start: 0.8050 (tmm) cc_final: 0.7689 (tmm) REVERT: Y 415 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7736 (tp40) REVERT: Y 423 ARG cc_start: 0.8560 (mpt90) cc_final: 0.8336 (mpt-90) REVERT: B 58 MET cc_start: 0.5669 (tmm) cc_final: 0.5282 (ttp) outliers start: 29 outliers final: 18 residues processed: 193 average time/residue: 0.1140 time to fit residues: 31.3084 Evaluate side-chains 187 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain Y residue 249 LEU Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain B residue 81 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 88 GLN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121483 restraints weight = 13889.064| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.75 r_work: 0.3074 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11259 Z= 0.154 Angle : 0.553 10.375 15215 Z= 0.284 Chirality : 0.042 0.143 1730 Planarity : 0.004 0.039 1942 Dihedral : 5.982 98.018 1535 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.79 % Allowed : 13.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.23), residues: 1372 helix: 1.42 (0.19), residues: 766 sheet: -0.23 (0.48), residues: 132 loop : -1.45 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 56 TYR 0.024 0.001 TYR V 32 PHE 0.013 0.001 PHE A 711 TRP 0.008 0.001 TRP B 78 HIS 0.004 0.001 HIS A 464 Details of bonding type rmsd covalent geometry : bond 0.00372 (11258) covalent geometry : angle 0.55310 (15213) SS BOND : bond 0.00576 ( 1) SS BOND : angle 0.40698 ( 2) hydrogen bonds : bond 0.04417 ( 572) hydrogen bonds : angle 3.78027 ( 1680) *********************** 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 200 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.7924 (p) REVERT: A 253 ASP cc_start: 0.7994 (t0) cc_final: 0.7718 (t0) REVERT: A 310 ASP cc_start: 0.8309 (t0) cc_final: 0.8031 (t0) REVERT: A 424 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 482 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8767 (mp) REVERT: A 544 GLU cc_start: 0.7761 (tp30) cc_final: 0.7371 (mp0) REVERT: A 576 ARG cc_start: 0.7699 (mtp180) cc_final: 0.7445 (mtp180) REVERT: A 629 ASN cc_start: 0.8297 (m-40) cc_final: 0.8074 (m-40) REVERT: A 679 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7166 (mttm) REVERT: A 689 MET cc_start: 0.7668 (tpt) cc_final: 0.7465 (tpt) REVERT: A 729 ASP cc_start: 0.8022 (t0) cc_final: 0.7230 (m-30) REVERT: A 761 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8346 (mm-30) REVERT: Y 75 MET cc_start: 0.6808 (mmm) cc_final: 0.6381 (tpt) REVERT: Y 98 TRP cc_start: 0.7066 (m-10) cc_final: 0.6801 (m-10) REVERT: Y 104 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.5162 (ppp) REVERT: Y 106 ARG cc_start: 0.8137 (tmm160) cc_final: 0.7556 (ttm110) REVERT: Y 299 TRP cc_start: 0.8385 (t60) cc_final: 0.8137 (t60) REVERT: Y 336 MET cc_start: 0.8298 (mtp) cc_final: 0.8057 (mtp) REVERT: Y 342 LYS cc_start: 0.8641 (tmmt) cc_final: 0.8117 (mptt) REVERT: Y 358 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: Y 390 ASN cc_start: 0.8366 (t0) cc_final: 0.7944 (t0) REVERT: Y 413 MET cc_start: 0.8112 (tmm) cc_final: 0.7749 (tmm) REVERT: Y 423 ARG cc_start: 0.8564 (mpt90) cc_final: 0.8349 (mpt-90) REVERT: B 58 MET cc_start: 0.5745 (tmm) cc_final: 0.5437 (ttp) outliers start: 33 outliers final: 22 residues processed: 189 average time/residue: 0.1171 time to fit residues: 30.8819 Evaluate side-chains 189 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 464 HIS 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 A residue 746 THR Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Y residue 139 MET 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 65 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 0.0010 chunk 104 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127793 restraints weight = 13986.132| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.65 r_work: 0.3138 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11259 Z= 0.115 Angle : 0.527 9.883 15215 Z= 0.267 Chirality : 0.041 0.150 1730 Planarity : 0.003 0.039 1942 Dihedral : 5.760 101.495 1533 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.03 % Allowed : 14.02 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.24), residues: 1372 helix: 1.56 (0.19), residues: 772 sheet: -0.12 (0.48), residues: 132 loop : -1.43 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 516 TYR 0.011 0.001 TYR Y 359 PHE 0.009 0.001 PHE Y 428 TRP 0.010 0.001 TRP B 78 HIS 0.002 0.000 HIS A 464 Details of bonding type rmsd covalent geometry : bond 0.00264 (11258) covalent geometry : angle 0.52721 (15213) SS BOND : bond 0.00526 ( 1) SS BOND : angle 0.45321 ( 2) hydrogen bonds : bond 0.03916 ( 572) hydrogen bonds : angle 3.69263 ( 1680) *********************** 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 197 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 ASP cc_start: 0.8342 (t0) cc_final: 0.8056 (t0) REVERT: A 424 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 544 GLU cc_start: 0.7663 (tp30) cc_final: 0.7212 (mp0) REVERT: A 629 ASN cc_start: 0.8247 (m-40) cc_final: 0.8031 (m-40) REVERT: A 679 LYS cc_start: 0.7632 (mmmm) cc_final: 0.7130 (mttm) REVERT: A 689 MET cc_start: 0.7541 (tpt) cc_final: 0.7243 (tpt) REVERT: A 725 MET cc_start: 0.7160 (mtt) cc_final: 0.6535 (mtp) REVERT: A 729 ASP cc_start: 0.7906 (t0) cc_final: 0.7096 (m-30) REVERT: A 761 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8272 (mm-30) REVERT: Y 75 MET cc_start: 0.6691 (mmm) cc_final: 0.6269 (tpt) REVERT: Y 98 TRP cc_start: 0.7040 (m-10) cc_final: 0.6805 (m-10) REVERT: Y 104 MET cc_start: 0.5488 (OUTLIER) cc_final: 0.5053 (ppp) REVERT: Y 106 ARG cc_start: 0.8142 (tmm160) cc_final: 0.7496 (ttm110) REVERT: Y 299 TRP cc_start: 0.8357 (t60) cc_final: 0.8052 (t60) REVERT: Y 336 MET cc_start: 0.8198 (mtp) cc_final: 0.7956 (mtp) REVERT: Y 342 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8022 (mptt) REVERT: Y 358 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: Y 390 ASN cc_start: 0.8419 (t0) cc_final: 0.7976 (t0) REVERT: Y 413 MET cc_start: 0.7958 (tmm) cc_final: 0.7670 (tmm) REVERT: Y 423 ARG cc_start: 0.8538 (mpt90) cc_final: 0.8327 (mpt-90) REVERT: E 17 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8371 (mtmm) REVERT: B 58 MET cc_start: 0.5571 (tmm) cc_final: 0.5269 (ttp) outliers start: 24 outliers final: 18 residues processed: 190 average time/residue: 0.1156 time to fit residues: 30.9169 Evaluate side-chains 187 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 395 ASN 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 104 MET 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 5 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126371 restraints weight = 13940.344| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.55 r_work: 0.3152 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11259 Z= 0.107 Angle : 0.529 9.188 15215 Z= 0.267 Chirality : 0.040 0.147 1730 Planarity : 0.003 0.039 1942 Dihedral : 5.711 104.530 1533 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.20 % Allowed : 14.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.24), residues: 1372 helix: 1.66 (0.19), residues: 772 sheet: -0.05 (0.48), residues: 132 loop : -1.42 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 56 TYR 0.011 0.001 TYR Y 359 PHE 0.009 0.001 PHE A 549 TRP 0.009 0.001 TRP B 78 HIS 0.002 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00238 (11258) covalent geometry : angle 0.52864 (15213) SS BOND : bond 0.00614 ( 1) SS BOND : angle 0.43628 ( 2) hydrogen bonds : bond 0.03730 ( 572) hydrogen bonds : angle 3.63850 ( 1680) *********************** 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 195 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 ASP cc_start: 0.8352 (t0) cc_final: 0.8061 (t0) REVERT: A 424 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 544 GLU cc_start: 0.7659 (tp30) cc_final: 0.7247 (mp0) REVERT: A 629 ASN cc_start: 0.8245 (m-40) cc_final: 0.8031 (m-40) REVERT: A 636 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 650 GLU cc_start: 0.7878 (mp0) cc_final: 0.7613 (pm20) REVERT: A 679 LYS cc_start: 0.7595 (mmmm) cc_final: 0.7100 (mttm) REVERT: A 689 MET cc_start: 0.7606 (tpt) cc_final: 0.7298 (tpt) REVERT: A 708 MET cc_start: 0.5626 (tpp) cc_final: 0.5368 (ttm) REVERT: A 725 MET cc_start: 0.7120 (mtt) cc_final: 0.6491 (mtp) REVERT: A 729 ASP cc_start: 0.7887 (t0) cc_final: 0.7050 (m-30) REVERT: A 731 MET cc_start: 0.8782 (mmm) cc_final: 0.8368 (mmm) REVERT: A 761 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8232 (mm-30) REVERT: Y 75 MET cc_start: 0.6549 (mmm) cc_final: 0.6243 (tpt) REVERT: Y 98 TRP cc_start: 0.7082 (m-10) cc_final: 0.6854 (m-10) REVERT: Y 104 MET cc_start: 0.5477 (OUTLIER) cc_final: 0.5035 (ppp) REVERT: Y 299 TRP cc_start: 0.8360 (t60) cc_final: 0.8144 (t60) REVERT: Y 336 MET cc_start: 0.8192 (mtp) cc_final: 0.7988 (mtp) REVERT: Y 342 LYS cc_start: 0.8593 (tmmt) cc_final: 0.8043 (mptt) REVERT: Y 358 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: Y 390 ASN cc_start: 0.8465 (t0) cc_final: 0.8022 (t0) REVERT: Y 413 MET cc_start: 0.7965 (tmm) cc_final: 0.7676 (tmm) REVERT: E 17 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8383 (mtmm) REVERT: V 4 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7308 (tp) REVERT: B 58 MET cc_start: 0.5511 (tmm) cc_final: 0.5282 (ttp) outliers start: 26 outliers final: 20 residues processed: 189 average time/residue: 0.1102 time to fit residues: 29.7791 Evaluate side-chains 188 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 104 MET 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 4 LEU 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 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 129 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** Y 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126569 restraints weight = 13866.968| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.45 r_work: 0.3166 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11259 Z= 0.109 Angle : 0.538 10.270 15215 Z= 0.268 Chirality : 0.041 0.157 1730 Planarity : 0.003 0.039 1942 Dihedral : 5.673 109.195 1533 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.11 % Allowed : 15.46 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.23), residues: 1372 helix: 1.74 (0.19), residues: 771 sheet: 0.26 (0.51), residues: 117 loop : -1.44 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 516 TYR 0.011 0.001 TYR Y 359 PHE 0.034 0.001 PHE A 549 TRP 0.010 0.001 TRP B 78 HIS 0.002 0.000 HIS Y 424 Details of bonding type rmsd covalent geometry : bond 0.00247 (11258) covalent geometry : angle 0.53790 (15213) SS BOND : bond 0.00600 ( 1) SS BOND : angle 0.43045 ( 2) hydrogen bonds : bond 0.03627 ( 572) hydrogen bonds : angle 3.59276 ( 1680) *********************** 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 195 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 310 ASP cc_start: 0.8366 (t0) cc_final: 0.8080 (t0) REVERT: A 424 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 544 GLU cc_start: 0.7566 (tp30) cc_final: 0.7141 (mp0) REVERT: A 629 ASN cc_start: 0.8190 (m-40) cc_final: 0.7973 (m-40) REVERT: A 679 LYS cc_start: 0.7595 (mmmm) cc_final: 0.7077 (mttm) REVERT: A 689 MET cc_start: 0.7636 (tpt) cc_final: 0.7355 (tpt) REVERT: A 725 MET cc_start: 0.7077 (mtt) cc_final: 0.6353 (mtp) REVERT: A 729 ASP cc_start: 0.7704 (t0) cc_final: 0.6958 (m-30) REVERT: A 761 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8210 (mm-30) REVERT: Y 98 TRP cc_start: 0.7054 (m-10) cc_final: 0.6832 (m-10) REVERT: Y 104 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4828 (ppp) REVERT: Y 342 LYS cc_start: 0.8560 (tmmt) cc_final: 0.7995 (mptt) REVERT: Y 358 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: Y 390 ASN cc_start: 0.8474 (t0) cc_final: 0.8021 (t0) REVERT: Y 413 MET cc_start: 0.7895 (tmm) cc_final: 0.7604 (tmm) REVERT: E 17 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8347 (mtmm) REVERT: V 4 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7306 (tp) outliers start: 25 outliers final: 20 residues processed: 188 average time/residue: 0.1073 time to fit residues: 28.8903 Evaluate side-chains 188 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 104 MET 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 4 LEU 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 12 optimal weight: 2.9990 chunk 91 optimal weight: 0.0050 chunk 94 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 101 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 124 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 = 0.3959 r_free = 0.3959 target = 0.173485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118238 restraints weight = 13811.536| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.26 r_work: 0.3130 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11259 Z= 0.120 Angle : 0.555 10.952 15215 Z= 0.275 Chirality : 0.041 0.149 1730 Planarity : 0.004 0.041 1942 Dihedral : 5.684 112.933 1533 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.11 % Allowed : 15.54 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.23), residues: 1372 helix: 1.75 (0.19), residues: 771 sheet: 0.04 (0.50), residues: 121 loop : -1.48 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 56 TYR 0.012 0.001 TYR Y 359 PHE 0.016 0.001 PHE A 549 TRP 0.012 0.001 TRP B 78 HIS 0.002 0.001 HIS A 464 Details of bonding type rmsd covalent geometry : bond 0.00280 (11258) covalent geometry : angle 0.55468 (15213) SS BOND : bond 0.00585 ( 1) SS BOND : angle 0.42655 ( 2) hydrogen bonds : bond 0.03756 ( 572) hydrogen bonds : angle 3.58811 ( 1680) *********************** 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 191 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 151 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7848 (p) REVERT: A 310 ASP cc_start: 0.8431 (t0) cc_final: 0.8161 (t0) REVERT: A 424 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 544 GLU cc_start: 0.7718 (tp30) cc_final: 0.7342 (mp0) REVERT: A 629 ASN cc_start: 0.8280 (m-40) cc_final: 0.8066 (m-40) REVERT: A 679 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7147 (mttm) REVERT: A 689 MET cc_start: 0.7706 (tpt) cc_final: 0.7421 (tpt) REVERT: A 725 MET cc_start: 0.7166 (mtt) cc_final: 0.6532 (mtp) REVERT: A 729 ASP cc_start: 0.7866 (t0) cc_final: 0.7124 (m-30) REVERT: A 761 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8289 (mm-30) REVERT: Y 98 TRP cc_start: 0.7052 (m-10) cc_final: 0.6838 (m-10) REVERT: Y 104 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.5074 (ppp) REVERT: Y 342 LYS cc_start: 0.8624 (tmmt) cc_final: 0.8119 (mptt) REVERT: Y 358 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: Y 390 ASN cc_start: 0.8401 (t0) cc_final: 0.7966 (t0) REVERT: Y 413 MET cc_start: 0.8042 (tmm) cc_final: 0.7756 (tmm) REVERT: E 17 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8403 (mtmm) REVERT: V 4 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7328 (tt) outliers start: 25 outliers final: 21 residues processed: 184 average time/residue: 0.1141 time to fit residues: 29.7102 Evaluate side-chains 189 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 104 MET 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 4 LEU 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 30 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124529 restraints weight = 13943.145| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.64 r_work: 0.3113 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11259 Z= 0.143 Angle : 0.576 11.193 15215 Z= 0.287 Chirality : 0.042 0.150 1730 Planarity : 0.004 0.039 1942 Dihedral : 5.732 116.901 1533 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.36 % Allowed : 15.71 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.24), residues: 1372 helix: 1.73 (0.19), residues: 771 sheet: -0.29 (0.47), residues: 136 loop : -1.51 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.013 0.001 TYR Y 359 PHE 0.012 0.001 PHE A 549 TRP 0.014 0.001 TRP B 78 HIS 0.003 0.001 HIS A 464 Details of bonding type rmsd covalent geometry : bond 0.00341 (11258) covalent geometry : angle 0.57590 (15213) SS BOND : bond 0.00548 ( 1) SS BOND : angle 0.42895 ( 2) hydrogen bonds : bond 0.04105 ( 572) hydrogen bonds : angle 3.62751 ( 1680) ********************** 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 197 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.367 Fit side-chains REVERT: A 151 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.7779 (p) REVERT: A 253 ASP cc_start: 0.7800 (t0) cc_final: 0.7484 (t0) REVERT: A 310 ASP cc_start: 0.8517 (t0) cc_final: 0.8276 (t0) REVERT: A 424 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 544 GLU cc_start: 0.7670 (tp30) cc_final: 0.7204 (mp0) REVERT: A 576 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7243 (mtp180) REVERT: A 636 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 689 MET cc_start: 0.7607 (tpt) cc_final: 0.7311 (tpt) REVERT: A 729 ASP cc_start: 0.7871 (t0) cc_final: 0.7047 (m-30) REVERT: A 731 MET cc_start: 0.8685 (mmm) cc_final: 0.8439 (mmm) REVERT: A 761 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8269 (mm-30) REVERT: Y 98 TRP cc_start: 0.6973 (m-10) cc_final: 0.6731 (m-10) REVERT: Y 104 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.5046 (ppp) REVERT: Y 135 LEU cc_start: 0.8278 (tt) cc_final: 0.8030 (tp) REVERT: Y 342 LYS cc_start: 0.8581 (tmmt) cc_final: 0.8026 (mptt) REVERT: Y 358 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: Y 390 ASN cc_start: 0.8596 (t0) cc_final: 0.8071 (t0) REVERT: Y 413 MET cc_start: 0.7955 (tmm) cc_final: 0.7697 (tmm) REVERT: E 17 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8276 (mtmm) REVERT: V 4 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7349 (tt) REVERT: V 107 TRP cc_start: 0.8562 (m-10) cc_final: 0.8057 (m-10) outliers start: 28 outliers final: 21 residues processed: 190 average time/residue: 0.1141 time to fit residues: 30.6381 Evaluate side-chains 192 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 104 MET 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 4 LEU Chi-restraints excluded: chain V residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 0.0470 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.173487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127987 restraints weight = 13810.104| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.28 r_work: 0.3179 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11259 Z= 0.112 Angle : 0.556 11.210 15215 Z= 0.275 Chirality : 0.041 0.146 1730 Planarity : 0.003 0.044 1942 Dihedral : 5.652 116.956 1533 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.20 % Allowed : 15.46 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.24), residues: 1372 helix: 1.79 (0.19), residues: 772 sheet: 0.07 (0.50), residues: 121 loop : -1.46 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 56 TYR 0.012 0.001 TYR Y 359 PHE 0.009 0.001 PHE Y 428 TRP 0.013 0.001 TRP B 78 HIS 0.002 0.000 HIS A 464 Details of bonding type rmsd covalent geometry : bond 0.00254 (11258) covalent geometry : angle 0.55559 (15213) SS BOND : bond 0.00551 ( 1) SS BOND : angle 0.42753 ( 2) hydrogen bonds : bond 0.03664 ( 572) hydrogen bonds : angle 3.56114 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2679.56 seconds wall clock time: 46 minutes 41.52 seconds (2801.52 seconds total)