Starting phenix.real_space_refine on Sun Jul 5 10:43:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7abr_11707/07_2026/7abr_11707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7abr_11707/07_2026/7abr_11707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7abr_11707/07_2026/7abr_11707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7abr_11707/07_2026/7abr_11707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7abr_11707/07_2026/7abr_11707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7abr_11707/07_2026/7abr_11707.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7abr_11707/07_2026/7abr_11707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7abr_11707/07_2026/7abr_11707.cif" } resolution = 3.7 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= 0.005 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: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 78 5.16 5 C 16898 2.51 5 N 4861 2.21 5 O 5343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27209 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4482 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 554} Chain breaks: 2 Chain: "B" Number of atoms: 4488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4488 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 554} Chain breaks: 2 Chain: "C" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4513 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 558} Chain breaks: 2 Chain: "D" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4582 Classifications: {'peptide': 586} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 566} Chain breaks: 2 Chain: "E" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4476 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 551} Chain breaks: 3 Chain: "F" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4213 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 518} Chain breaks: 6 Chain: "S" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'ATP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.37, per 1000 atoms: 0.27 Number of scatterers: 27209 At special positions: 0 Unit cell: (116.38, 149.178, 151.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 29 15.00 O 5343 8.00 N 4861 7.00 C 16898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6444 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 24 sheets defined 58.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.564A pdb=" N GLU A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 197 Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.759A pdb=" N ALA A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 306 Proline residue: A 302 - end of helix removed outlier: 3.882A pdb=" N ARG A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.620A pdb=" N LEU A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 363 removed outlier: 3.522A pdb=" N LEU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.635A pdb=" N ILE A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 408 Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 513 through 529 Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.567A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.697A pdb=" N LYS A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 623 through 635 removed outlier: 4.068A pdb=" N PHE A 627 " --> pdb=" O HIS A 623 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 628 " --> pdb=" O PRO A 624 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 698 through 705 removed outlier: 3.747A pdb=" N ILE A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 737 Processing helix chain 'A' and resid 744 through 756 removed outlier: 3.651A pdb=" N VAL A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 784 removed outlier: 4.261A pdb=" N ARG A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 167 removed outlier: 3.600A pdb=" N ASP B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.617A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.579A pdb=" N ARG B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 removed outlier: 3.810A pdb=" N VAL B 212 " --> pdb=" O GLU B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 212' Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 256 through 271 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 295 through 307 Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.569A pdb=" N ILE B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 4.032A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 381 Processing helix chain 'B' and resid 388 through 408 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 501 through 508 Processing helix chain 'B' and resid 513 through 529 Processing helix chain 'B' and resid 552 through 563 removed outlier: 3.509A pdb=" N ARG B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 removed outlier: 4.541A pdb=" N GLU B 579 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 580 " --> pdb=" O TYR B 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 576 through 580' Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.665A pdb=" N LYS B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 623 through 637 removed outlier: 4.064A pdb=" N PHE B 627 " --> pdb=" O HIS B 623 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN B 632 " --> pdb=" O ASN B 628 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 680 through 697 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.654A pdb=" N ILE B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 735 Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 744 through 755 removed outlier: 3.651A pdb=" N GLU B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 783 removed outlier: 3.650A pdb=" N ARG B 766 " --> pdb=" O ALA B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 4.207A pdb=" N SER C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 213 through 227 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 256 through 272 Processing helix chain 'C' and resid 281 through 285 removed outlier: 3.522A pdb=" N ILE C 285 " --> pdb=" O HIS C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 316 through 323 Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 343 through 363 removed outlier: 4.434A pdb=" N ARG C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 381 Processing helix chain 'C' and resid 388 through 407 removed outlier: 3.618A pdb=" N PHE C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.576A pdb=" N ILE C 476 " --> pdb=" O THR C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 510 Processing helix chain 'C' and resid 513 through 529 Processing helix chain 'C' and resid 550 through 564 removed outlier: 3.593A pdb=" N ALA C 555 " --> pdb=" O LYS C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 582 through 588 removed outlier: 4.334A pdb=" N LEU C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 removed outlier: 3.746A pdb=" N LYS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 4.070A pdb=" N LEU C 630 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 636 " --> pdb=" O GLN C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 697 Processing helix chain 'C' and resid 698 through 704 removed outlier: 3.760A pdb=" N ARG C 704 " --> pdb=" O GLU C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 736 removed outlier: 3.781A pdb=" N GLU C 736 " --> pdb=" O LYS C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 756 removed outlier: 3.755A pdb=" N VAL C 756 " --> pdb=" O ALA C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 783 removed outlier: 3.786A pdb=" N ARG C 766 " --> pdb=" O ALA C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 185 through 196 Processing helix chain 'D' and resid 213 through 227 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 256 through 271 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 300 through 307 removed outlier: 3.581A pdb=" N LEU D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 343 through 363 removed outlier: 4.536A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 381 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.529A pdb=" N ILE D 476 " --> pdb=" O THR D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 510 removed outlier: 4.077A pdb=" N LEU D 500 " --> pdb=" O THR D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 529 removed outlier: 3.584A pdb=" N VAL D 517 " --> pdb=" O GLN D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 563 Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 579 through 586 removed outlier: 3.637A pdb=" N THR D 583 " --> pdb=" O LYS D 580 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER D 584 " --> pdb=" O HIS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 623 through 637 removed outlier: 3.911A pdb=" N PHE D 627 " --> pdb=" O HIS D 623 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP D 636 " --> pdb=" O GLN D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 667 Processing helix chain 'D' and resid 680 through 697 removed outlier: 4.170A pdb=" N MET D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY D 691 " --> pdb=" O ASP D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 703 Processing helix chain 'D' and resid 715 through 736 Processing helix chain 'D' and resid 744 through 755 Processing helix chain 'D' and resid 763 through 773 Processing helix chain 'D' and resid 773 through 783 Processing helix chain 'E' and resid 170 through 176 removed outlier: 4.050A pdb=" N GLU E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 197 Processing helix chain 'E' and resid 209 through 213 removed outlier: 4.109A pdb=" N GLY E 213 " --> pdb=" O PRO E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 255 through 270 removed outlier: 3.544A pdb=" N GLU E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 285 removed outlier: 4.045A pdb=" N ILE E 285 " --> pdb=" O HIS E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 307 Proline residue: E 302 - end of helix Processing helix chain 'E' and resid 316 through 325 Processing helix chain 'E' and resid 343 through 359 Processing helix chain 'E' and resid 367 through 381 Processing helix chain 'E' and resid 388 through 407 removed outlier: 4.053A pdb=" N PHE E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 495 through 510 removed outlier: 4.805A pdb=" N GLU E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN E 504 " --> pdb=" O LEU E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 529 removed outlier: 3.882A pdb=" N VAL E 517 " --> pdb=" O GLN E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 563 Processing helix chain 'E' and resid 575 through 577 No H-bonds generated for 'chain 'E' and resid 575 through 577' Processing helix chain 'E' and resid 580 through 582 No H-bonds generated for 'chain 'E' and resid 580 through 582' Processing helix chain 'E' and resid 583 through 588 removed outlier: 4.101A pdb=" N VAL E 587 " --> pdb=" O THR E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 609 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 623 through 636 removed outlier: 3.861A pdb=" N PHE E 627 " --> pdb=" O HIS E 623 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL E 633 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP E 636 " --> pdb=" O GLN E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 697 Processing helix chain 'E' and resid 698 through 704 removed outlier: 3.553A pdb=" N ILE E 702 " --> pdb=" O ARG E 698 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 704 " --> pdb=" O GLU E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 737 removed outlier: 4.044A pdb=" N THR E 720 " --> pdb=" O LYS E 716 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU E 721 " --> pdb=" O LYS E 717 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU E 736 " --> pdb=" O LYS E 732 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 755 Processing helix chain 'E' and resid 762 through 773 removed outlier: 4.020A pdb=" N ARG E 766 " --> pdb=" O ALA E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 773 through 784 Processing helix chain 'F' and resid 160 through 167 Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.671A pdb=" N ILE F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 198 Processing helix chain 'F' and resid 213 through 227 Processing helix chain 'F' and resid 256 through 271 Processing helix chain 'F' and resid 280 through 285 Processing helix chain 'F' and resid 296 through 307 Proline residue: F 302 - end of helix Processing helix chain 'F' and resid 316 through 325 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 345 through 363 removed outlier: 3.749A pdb=" N GLN F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP F 356 " --> pdb=" O GLN F 352 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG F 357 " --> pdb=" O GLY F 353 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR F 358 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 382 removed outlier: 3.847A pdb=" N ARG F 380 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 382 " --> pdb=" O SER F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 407 removed outlier: 4.100A pdb=" N ARG F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 487 through 493 Processing helix chain 'F' and resid 494 through 496 No H-bonds generated for 'chain 'F' and resid 494 through 496' Processing helix chain 'F' and resid 497 through 508 removed outlier: 3.737A pdb=" N ASN F 501 " --> pdb=" O ASP F 497 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 503 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN F 504 " --> pdb=" O LEU F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 528 Processing helix chain 'F' and resid 550 through 563 Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'F' and resid 601 through 609 Processing helix chain 'F' and resid 619 through 622 Processing helix chain 'F' and resid 623 through 637 Processing helix chain 'F' and resid 683 through 697 removed outlier: 4.376A pdb=" N MET F 690 " --> pdb=" O LYS F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 698 through 704 removed outlier: 3.884A pdb=" N ILE F 702 " --> pdb=" O ARG F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 716 through 737 removed outlier: 3.727A pdb=" N THR F 720 " --> pdb=" O LYS F 716 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 734 " --> pdb=" O LEU F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 753 Processing helix chain 'F' and resid 765 through 773 Processing helix chain 'F' and resid 773 through 783 removed outlier: 3.588A pdb=" N ARG F 783 " --> pdb=" O GLU F 779 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 169 removed outlier: 3.575A pdb=" N MET A 240 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ILE A 312 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 276 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA A 314 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 278 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR A 316 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 208 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.330A pdb=" N SER A 365 " --> pdb=" O VAL A 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 573 removed outlier: 5.592A pdb=" N ILE A 570 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 617 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 572 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLY A 539 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N MET A 656 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 541 " --> pdb=" O MET A 656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 741 through 743 removed outlier: 3.508A pdb=" N LEU A 794 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 169 removed outlier: 3.772A pdb=" N ARG B 168 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARG B 238 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B 277 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET B 240 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP B 279 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 205 Processing sheet with id=AA7, first strand: chain 'B' and resid 570 through 573 removed outlier: 6.578A pdb=" N SER B 540 " --> pdb=" O GLU B 707 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 709 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE B 542 " --> pdb=" O ILE B 709 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 638 through 640 Processing sheet with id=AA9, first strand: chain 'B' and resid 740 through 743 Processing sheet with id=AB1, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.372A pdb=" N ARG C 238 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE C 277 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N MET C 240 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP C 279 " --> pdb=" O MET C 240 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU C 242 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN C 310 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 314 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR C 315 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU C 206 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 570 through 573 removed outlier: 6.803A pdb=" N ILE C 570 " --> pdb=" O LEU C 615 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP C 617 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE C 572 " --> pdb=" O ASP C 617 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 614 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR C 657 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU C 616 " --> pdb=" O THR C 657 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 707 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 542 " --> pdb=" O GLU C 707 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 638 through 640 Processing sheet with id=AB4, first strand: chain 'C' and resid 741 through 743 removed outlier: 6.922A pdb=" N GLU C 742 " --> pdb=" O LEU C 794 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 169 removed outlier: 6.357A pdb=" N ARG D 238 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE D 277 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N MET D 240 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP D 279 " --> pdb=" O MET D 240 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU D 242 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE D 312 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 276 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA D 314 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE D 278 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N THR D 316 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR D 315 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 208 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 570 through 573 removed outlier: 6.507A pdb=" N VAL D 614 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR D 657 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 616 " --> pdb=" O THR D 657 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE D 541 " --> pdb=" O MET D 656 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER D 658 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE D 543 " --> pdb=" O SER D 658 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 540 " --> pdb=" O GLU D 707 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE D 709 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE D 542 " --> pdb=" O ILE D 709 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 639 through 640 Processing sheet with id=AB8, first strand: chain 'D' and resid 792 through 796 Processing sheet with id=AB9, first strand: chain 'E' and resid 168 through 169 removed outlier: 5.591A pdb=" N ARG E 238 " --> pdb=" O ILE E 275 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE E 277 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N MET E 240 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP E 279 " --> pdb=" O MET E 240 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE E 312 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU E 276 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA E 314 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE E 278 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR E 315 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU E 206 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 570 through 573 removed outlier: 6.447A pdb=" N ILE E 570 " --> pdb=" O LEU E 615 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP E 617 " --> pdb=" O ILE E 570 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 572 " --> pdb=" O ASP E 617 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 614 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR E 657 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 616 " --> pdb=" O THR E 657 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER E 540 " --> pdb=" O GLU E 707 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE E 709 " --> pdb=" O SER E 540 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE E 542 " --> pdb=" O ILE E 709 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 740 through 743 removed outlier: 3.707A pdb=" N LEU E 794 " --> pdb=" O GLU E 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 276 through 279 Processing sheet with id=AC4, first strand: chain 'F' and resid 365 through 366 removed outlier: 7.101A pdb=" N SER F 365 " --> pdb=" O VAL F 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 569 through 573 removed outlier: 6.329A pdb=" N ILE F 570 " --> pdb=" O LEU F 615 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP F 617 " --> pdb=" O ILE F 570 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE F 572 " --> pdb=" O ASP F 617 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 614 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR F 657 " --> pdb=" O VAL F 614 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 616 " --> pdb=" O THR F 657 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE F 542 " --> pdb=" O GLU F 707 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 740 through 743 removed outlier: 6.264A pdb=" N SER F 740 " --> pdb=" O ILE F 792 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 794 " --> pdb=" O SER F 740 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU F 742 " --> pdb=" O LEU F 794 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL F 796 " --> pdb=" O GLU F 742 " (cutoff:3.500A) 1325 hydrogen bonds defined for protein. 3852 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: 5.44 Time building geometry restraints manager: 3.44 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: 9239 1.34 - 1.45: 3324 1.45 - 1.57: 14782 1.57 - 1.69: 47 1.69 - 1.81: 150 Bond restraints: 27542 Sorted by residual: bond pdb=" C4 ATP E1001 " pdb=" C5 ATP E1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" C4 ATP A1003 " pdb=" C5 ATP A1003 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C4 ATP D1003 " pdb=" C5 ATP D1003 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C4 ATP C1002 " pdb=" C5 ATP C1002 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C4 ATP D1002 " pdb=" N9 ATP D1002 " ideal model delta sigma weight residual 1.374 1.311 0.063 1.00e-02 1.00e+04 4.02e+01 ... (remaining 27537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.54: 37034 5.54 - 11.09: 133 11.09 - 16.63: 0 16.63 - 22.17: 9 22.17 - 27.72: 5 Bond angle restraints: 37181 Sorted by residual: angle pdb=" PB ATP C1002 " pdb=" O3B ATP C1002 " pdb=" PG ATP C1002 " ideal model delta sigma weight residual 139.87 112.15 27.72 1.00e+00 1.00e+00 7.68e+02 angle pdb=" PB ATP E1001 " pdb=" O3B ATP E1001 " pdb=" PG ATP E1001 " ideal model delta sigma weight residual 139.87 112.86 27.01 1.00e+00 1.00e+00 7.29e+02 angle pdb=" PB ATP A1003 " pdb=" O3B ATP A1003 " pdb=" PG ATP A1003 " ideal model delta sigma weight residual 139.87 116.82 23.05 1.00e+00 1.00e+00 5.31e+02 angle pdb=" PA ATP C1002 " pdb=" O3A ATP C1002 " pdb=" PB ATP C1002 " ideal model delta sigma weight residual 136.83 113.85 22.98 1.00e+00 1.00e+00 5.28e+02 angle pdb=" PA ATP E1001 " pdb=" O3A ATP E1001 " pdb=" PB ATP E1001 " ideal model delta sigma weight residual 136.83 114.23 22.60 1.00e+00 1.00e+00 5.11e+02 ... (remaining 37176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 15639 21.81 - 43.61: 1228 43.61 - 65.42: 115 65.42 - 87.23: 33 87.23 - 109.04: 3 Dihedral angle restraints: 17018 sinusoidal: 7097 harmonic: 9921 Sorted by residual: dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 49.04 -109.04 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" CA ASP A 327 " pdb=" C ASP A 327 " pdb=" N ALA A 328 " pdb=" CA ALA A 328 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TYR B 323 " pdb=" C TYR B 323 " pdb=" N ILE B 324 " pdb=" CA ILE B 324 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 17015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2715 0.043 - 0.085: 1210 0.085 - 0.128: 331 0.128 - 0.170: 61 0.170 - 0.213: 12 Chirality restraints: 4329 Sorted by residual: chirality pdb=" C3' ADP B 901 " pdb=" C2' ADP B 901 " pdb=" C4' ADP B 901 " pdb=" O3' ADP B 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE D 274 " pdb=" CA ILE D 274 " pdb=" CG1 ILE D 274 " pdb=" CG2 ILE D 274 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE C 274 " pdb=" CA ILE C 274 " pdb=" CG1 ILE C 274 " pdb=" CG2 ILE C 274 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 4326 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 590 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO B 591 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 590 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO A 591 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 770 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C GLN C 770 " 0.039 2.00e-02 2.50e+03 pdb=" O GLN C 770 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS C 771 " -0.013 2.00e-02 2.50e+03 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 615 2.63 - 3.20: 28457 3.20 - 3.77: 42258 3.77 - 4.33: 59168 4.33 - 4.90: 95316 Nonbonded interactions: 225814 Sorted by model distance: nonbonded pdb=" O PHE A 543 " pdb=" OG SER A 658 " model vdw 2.066 3.040 nonbonded pdb=" OE2 GLU C 700 " pdb=" NE ARG C 704 " model vdw 2.084 3.120 nonbonded pdb=" OE1 GLU C 635 " pdb=" NH1 ARG D 763 " model vdw 2.095 3.120 nonbonded pdb=" OG1 THR B 215 " pdb=" O1A ATP A1003 " model vdw 2.102 3.040 nonbonded pdb=" O GLU C 721 " pdb=" OG SER C 724 " model vdw 2.105 3.040 ... (remaining 225809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'B' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'C' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'D' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'E' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'F' and (resid 159 through 660 or resid 683 through 806)) } 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 group one per residue 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.760 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.013 0.898 27549 Z= 0.860 Angle : 1.090 27.715 37181 Z= 0.712 Chirality : 0.050 0.213 4329 Planarity : 0.005 0.063 4789 Dihedral : 14.928 109.037 10574 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.64 % Favored : 90.13 % Rotamer: Outliers : 0.51 % Allowed : 11.60 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 are not related in a simple way. whole: -3.56 (0.12), residues: 3373 helix: -2.07 (0.10), residues: 1783 sheet: -2.12 (0.23), residues: 385 loop : -2.61 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 733 TYR 0.033 0.003 TYR F 611 PHE 0.032 0.003 PHE D 649 TRP 0.006 0.002 TRP A 483 HIS 0.008 0.002 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.01051 / 0.50 (27542) covalent geometry : angle 1.09005 / 0.71 (37181) hydrogen bonds : bond 0.16435 / 10.90 ( 1325) hydrogen bonds : angle 7.60438 / 5.45 ( 3852) Misc. bond : bond 0.43822 / 28.76 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 423 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8603 (mmm) cc_final: 0.8217 (mmm) REVERT: A 246 THR cc_start: 0.8722 (p) cc_final: 0.8341 (p) REVERT: A 535 LYS cc_start: 0.7818 (mtmm) cc_final: 0.7406 (mmmt) REVERT: A 593 TYR cc_start: 0.7493 (m-80) cc_final: 0.7225 (m-80) REVERT: B 240 MET cc_start: 0.8703 (mmm) cc_final: 0.7972 (mmt) REVERT: B 381 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7302 (p90) REVERT: C 501 ASN cc_start: 0.7025 (t0) cc_final: 0.6758 (t0) REVERT: C 502 MET cc_start: 0.8633 (tmm) cc_final: 0.8352 (tmm) REVERT: C 705 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 666 LYS cc_start: 0.7278 (tptm) cc_final: 0.7030 (tptp) REVERT: D 781 LEU cc_start: 0.8972 (tp) cc_final: 0.8639 (tt) REVERT: E 381 TYR cc_start: 0.8716 (m-80) cc_final: 0.8489 (m-80) REVERT: E 397 GLU cc_start: 0.7953 (tt0) cc_final: 0.7732 (tt0) REVERT: E 472 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8579 (p) REVERT: E 474 ASP cc_start: 0.7722 (p0) cc_final: 0.7506 (p0) REVERT: E 573 ASP cc_start: 0.8138 (m-30) cc_final: 0.7882 (m-30) REVERT: F 242 LEU cc_start: 0.8296 (pt) cc_final: 0.7937 (pp) REVERT: F 269 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8385 (tmm-80) REVERT: F 308 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7241 (tt0) REVERT: F 331 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 15 outliers final: 8 residues processed: 435 average time/residue: 0.2299 time to fit residues: 146.4944 Evaluate side-chains 269 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 705 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 202 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 ASN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 682 HIS A 703 ASN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 ASN A 787 HIS B 203 ASN B 223 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS C 203 ASN C 227 ASN C 352 GLN C 501 ASN C 513 GLN C 581 HIS C 787 HIS D 228 ASN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS E 501 ASN E 772 HIS F 159 ASN F 228 ASN F 338 GLN F 352 GLN ** F 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN F 682 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084327 restraints weight = 66689.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.086625 restraints weight = 35411.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088444 restraints weight = 21215.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088471 restraints weight = 16126.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088502 restraints weight = 14432.992| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27549 Z= 0.161 Angle : 0.708 12.172 37181 Z= 0.362 Chirality : 0.045 0.208 4329 Planarity : 0.005 0.051 4789 Dihedral : 7.572 106.195 3818 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.25 % Allowed : 15.39 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.90 (0.14), residues: 3373 helix: -0.62 (0.11), residues: 1830 sheet: -1.74 (0.24), residues: 355 loop : -1.95 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 306 TYR 0.018 0.002 TYR F 611 PHE 0.023 0.002 PHE A 543 TRP 0.006 0.001 TRP D 483 HIS 0.010 0.001 HIS C 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (27542) covalent geometry : angle 0.70806 / 0.36 (37181) hydrogen bonds : bond 0.05127 / 3.44 ( 1325) hydrogen bonds : angle 5.83905 / 4.16 ( 3852) Misc. bond : bond 0.00237 / 0.17 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLN cc_start: 0.7945 (mm110) cc_final: 0.7622 (mm-40) REVERT: A 253 TYR cc_start: 0.7412 (m-80) cc_final: 0.6861 (m-80) REVERT: A 506 LEU cc_start: 0.9243 (mt) cc_final: 0.9040 (mt) REVERT: A 535 LYS cc_start: 0.7630 (mtmm) cc_final: 0.7180 (mmmt) REVERT: A 593 TYR cc_start: 0.7247 (m-80) cc_final: 0.6942 (m-80) REVERT: A 734 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7940 (mm) REVERT: B 258 GLU cc_start: 0.8884 (pm20) cc_final: 0.8342 (pm20) REVERT: B 323 TYR cc_start: 0.8362 (p90) cc_final: 0.7482 (p90) REVERT: B 381 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.6807 (p90) REVERT: B 488 VAL cc_start: 0.7373 (m) cc_final: 0.7080 (p) REVERT: C 351 LEU cc_start: 0.9332 (mt) cc_final: 0.9086 (mt) REVERT: C 393 ASP cc_start: 0.7669 (t0) cc_final: 0.7263 (t0) REVERT: C 501 ASN cc_start: 0.7148 (t0) cc_final: 0.6836 (t0) REVERT: C 685 MET cc_start: 0.7145 (mtm) cc_final: 0.6681 (mtm) REVERT: D 654 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9183 (tt) REVERT: D 721 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: E 258 GLU cc_start: 0.7577 (pp20) cc_final: 0.7306 (pp20) REVERT: E 295 ASP cc_start: 0.6655 (m-30) cc_final: 0.6350 (m-30) REVERT: E 298 ASN cc_start: 0.8374 (m110) cc_final: 0.8173 (m110) REVERT: E 571 ARG cc_start: 0.8340 (ttt-90) cc_final: 0.7963 (ttt-90) REVERT: F 242 LEU cc_start: 0.8498 (pt) cc_final: 0.7805 (pp) REVERT: F 269 ARG cc_start: 0.8804 (tpp80) cc_final: 0.8393 (tmm-80) REVERT: F 320 TYR cc_start: 0.8680 (t80) cc_final: 0.8463 (t80) REVERT: F 331 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7294 (tm-30) REVERT: F 624 PRO cc_start: 0.7568 (Cg_exo) cc_final: 0.7286 (Cg_endo) outliers start: 66 outliers final: 34 residues processed: 403 average time/residue: 0.1888 time to fit residues: 119.9321 Evaluate side-chains 314 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 787 HIS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 721 GLU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 722 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 632 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.104500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.084122 restraints weight = 66708.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086386 restraints weight = 35447.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087816 restraints weight = 21099.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088088 restraints weight = 17022.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088068 restraints weight = 14918.758| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27549 Z= 0.144 Angle : 0.652 11.522 37181 Z= 0.330 Chirality : 0.044 0.246 4329 Planarity : 0.004 0.044 4789 Dihedral : 7.229 101.581 3810 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.59 % Allowed : 18.19 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.27 (0.14), residues: 3373 helix: -0.07 (0.12), residues: 1835 sheet: -1.55 (0.24), residues: 365 loop : -1.68 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 571 TYR 0.020 0.001 TYR D 381 PHE 0.014 0.001 PHE A 543 TRP 0.003 0.001 TRP B 483 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (27542) covalent geometry : angle 0.65200 / 0.33 (37181) hydrogen bonds : bond 0.04497 / 3.01 ( 1325) hydrogen bonds : angle 5.45470 / 3.89 ( 3852) Misc. bond : bond 0.00128 / 0.05 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 320 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLN cc_start: 0.7895 (mm110) cc_final: 0.7622 (mm-40) REVERT: A 253 TYR cc_start: 0.7442 (m-80) cc_final: 0.6919 (m-80) REVERT: A 535 LYS cc_start: 0.7475 (mtmm) cc_final: 0.7011 (mmmt) REVERT: A 569 MET cc_start: 0.8805 (tmm) cc_final: 0.8587 (tmm) REVERT: A 593 TYR cc_start: 0.7184 (m-80) cc_final: 0.6901 (m-80) REVERT: B 381 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.6647 (p90) REVERT: B 488 VAL cc_start: 0.7621 (m) cc_final: 0.7347 (p) REVERT: C 393 ASP cc_start: 0.7550 (t0) cc_final: 0.7242 (t0) REVERT: C 685 MET cc_start: 0.7199 (mtm) cc_final: 0.6807 (mtm) REVERT: D 649 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7589 (p90) REVERT: D 654 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9174 (tt) REVERT: E 219 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7815 (mt-10) REVERT: E 258 GLU cc_start: 0.7684 (pp20) cc_final: 0.7458 (pp20) REVERT: E 295 ASP cc_start: 0.6638 (m-30) cc_final: 0.6363 (m-30) REVERT: E 298 ASN cc_start: 0.8240 (m110) cc_final: 0.7528 (m110) REVERT: E 474 ASP cc_start: 0.7493 (p0) cc_final: 0.7131 (p0) REVERT: E 483 TRP cc_start: 0.8672 (t60) cc_final: 0.8356 (t60) REVERT: F 269 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8272 (tmm-80) REVERT: F 304 LEU cc_start: 0.9362 (mt) cc_final: 0.9105 (tt) REVERT: F 320 TYR cc_start: 0.8647 (t80) cc_final: 0.8445 (t80) REVERT: F 321 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7737 (mtt180) REVERT: F 331 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7221 (tm-30) REVERT: F 578 MET cc_start: 0.8001 (tpt) cc_final: 0.7400 (tpt) REVERT: F 624 PRO cc_start: 0.7488 (Cg_exo) cc_final: 0.7177 (Cg_endo) outliers start: 76 outliers final: 43 residues processed: 379 average time/residue: 0.1789 time to fit residues: 109.9392 Evaluate side-chains 318 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 722 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 334 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN F 581 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.083277 restraints weight = 66637.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.085280 restraints weight = 35958.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087494 restraints weight = 22022.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087533 restraints weight = 16737.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087513 restraints weight = 14288.197| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27549 Z= 0.169 Angle : 0.652 10.612 37181 Z= 0.328 Chirality : 0.044 0.225 4329 Planarity : 0.004 0.047 4789 Dihedral : 7.169 99.333 3810 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.48 % Allowed : 19.08 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.97 (0.14), residues: 3373 helix: 0.19 (0.12), residues: 1837 sheet: -1.49 (0.24), residues: 363 loop : -1.57 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 571 TYR 0.013 0.001 TYR D 381 PHE 0.012 0.001 PHE A 543 TRP 0.004 0.001 TRP C 483 HIS 0.006 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (27542) covalent geometry : angle 0.65157 / 0.33 (37181) hydrogen bonds : bond 0.04393 / 2.95 ( 1325) hydrogen bonds : angle 5.36349 / 3.83 ( 3852) Misc. bond : bond 0.00144 / 0.06 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 296 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLN cc_start: 0.7883 (mm110) cc_final: 0.7645 (mm-40) REVERT: A 253 TYR cc_start: 0.7505 (m-80) cc_final: 0.6955 (m-80) REVERT: A 535 LYS cc_start: 0.7470 (mtmm) cc_final: 0.6972 (mmmt) REVERT: A 569 MET cc_start: 0.8822 (tmm) cc_final: 0.8513 (tmm) REVERT: A 593 TYR cc_start: 0.7234 (m-80) cc_final: 0.6972 (m-80) REVERT: B 381 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.6655 (p90) REVERT: B 488 VAL cc_start: 0.7646 (m) cc_final: 0.7365 (p) REVERT: C 240 MET cc_start: 0.8845 (mmt) cc_final: 0.8579 (mmm) REVERT: C 319 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: C 331 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8211 (pm20) REVERT: C 393 ASP cc_start: 0.7637 (t0) cc_final: 0.7371 (t0) REVERT: C 685 MET cc_start: 0.7281 (mtm) cc_final: 0.6924 (mtm) REVERT: D 649 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7539 (p90) REVERT: D 654 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9162 (tt) REVERT: E 483 TRP cc_start: 0.8711 (t60) cc_final: 0.8418 (t60) REVERT: F 269 ARG cc_start: 0.8690 (tpp80) cc_final: 0.8266 (tmm-80) REVERT: F 276 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9095 (tt) REVERT: F 304 LEU cc_start: 0.9429 (mt) cc_final: 0.9135 (tt) REVERT: F 331 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7274 (tm-30) REVERT: F 578 MET cc_start: 0.8001 (tpt) cc_final: 0.7426 (tpt) outliers start: 102 outliers final: 59 residues processed: 376 average time/residue: 0.1682 time to fit residues: 104.1805 Evaluate side-chains 334 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 269 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 581 HIS Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 723 VAL Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 166 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 39 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN F 581 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084407 restraints weight = 66212.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086387 restraints weight = 36105.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088451 restraints weight = 22138.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088531 restraints weight = 16959.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088410 restraints weight = 14720.545| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27549 Z= 0.145 Angle : 0.640 10.008 37181 Z= 0.321 Chirality : 0.044 0.213 4329 Planarity : 0.004 0.048 4789 Dihedral : 7.074 96.463 3810 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.45 % Allowed : 19.93 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.75 (0.14), residues: 3373 helix: 0.35 (0.12), residues: 1839 sheet: -1.37 (0.24), residues: 366 loop : -1.44 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 321 TYR 0.010 0.001 TYR B 323 PHE 0.012 0.001 PHE B 697 TRP 0.003 0.001 TRP C 483 HIS 0.016 0.001 HIS F 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (27542) covalent geometry : angle 0.64036 / 0.32 (37181) hydrogen bonds : bond 0.04176 / 2.81 ( 1325) hydrogen bonds : angle 5.22367 / 3.73 ( 3852) Misc. bond : bond 0.00130 / 0.05 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 297 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7488 (m-80) cc_final: 0.6948 (m-80) REVERT: A 535 LYS cc_start: 0.7419 (mtmm) cc_final: 0.6901 (mmmt) REVERT: A 593 TYR cc_start: 0.7199 (m-80) cc_final: 0.6944 (m-80) REVERT: A 726 MET cc_start: 0.8578 (mpp) cc_final: 0.8310 (mpp) REVERT: B 381 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.6648 (p90) REVERT: B 721 GLU cc_start: 0.8258 (tp30) cc_final: 0.8032 (tp30) REVERT: C 319 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 393 ASP cc_start: 0.7618 (t0) cc_final: 0.7322 (t0) REVERT: C 685 MET cc_start: 0.7218 (mtm) cc_final: 0.6870 (mtm) REVERT: D 649 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7652 (p90) REVERT: D 654 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9150 (tt) REVERT: E 483 TRP cc_start: 0.8683 (t60) cc_final: 0.8468 (t60) REVERT: F 269 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8226 (tmm-80) REVERT: F 276 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9060 (tt) REVERT: F 304 LEU cc_start: 0.9384 (mt) cc_final: 0.9086 (tt) REVERT: F 326 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.5952 (pttm) REVERT: F 331 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 578 MET cc_start: 0.8011 (tpt) cc_final: 0.7498 (tpt) outliers start: 101 outliers final: 65 residues processed: 372 average time/residue: 0.1706 time to fit residues: 103.7305 Evaluate side-chains 343 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 272 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 695 ARG Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 24 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 328 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 309 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.104764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084347 restraints weight = 66687.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086419 restraints weight = 35575.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088456 restraints weight = 21692.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088591 restraints weight = 16447.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088503 restraints weight = 14022.468| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27549 Z= 0.151 Angle : 0.641 9.729 37181 Z= 0.320 Chirality : 0.044 0.243 4329 Planarity : 0.004 0.049 4789 Dihedral : 7.006 94.529 3809 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.55 % Allowed : 20.92 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.59 (0.15), residues: 3373 helix: 0.45 (0.12), residues: 1847 sheet: -1.30 (0.25), residues: 362 loop : -1.33 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 695 TYR 0.009 0.001 TYR E 596 PHE 0.012 0.001 PHE B 697 TRP 0.003 0.001 TRP C 483 HIS 0.005 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (27542) covalent geometry : angle 0.64119 / 0.32 (37181) hydrogen bonds : bond 0.04102 / 2.76 ( 1325) hydrogen bonds : angle 5.15959 / 3.69 ( 3852) Misc. bond : bond 0.00135 / 0.06 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 298 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7512 (m-80) cc_final: 0.6942 (m-80) REVERT: A 335 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: A 535 LYS cc_start: 0.7342 (mtmm) cc_final: 0.6721 (mmmt) REVERT: A 593 TYR cc_start: 0.7203 (m-80) cc_final: 0.6996 (m-80) REVERT: A 726 MET cc_start: 0.8503 (mpp) cc_final: 0.8279 (mpp) REVERT: B 381 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.6683 (p90) REVERT: B 721 GLU cc_start: 0.8253 (tp30) cc_final: 0.8024 (tp30) REVERT: C 166 LEU cc_start: 0.9236 (mt) cc_final: 0.8889 (mp) REVERT: C 319 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: C 393 ASP cc_start: 0.7615 (t0) cc_final: 0.7323 (t0) REVERT: C 685 MET cc_start: 0.7173 (mtm) cc_final: 0.6779 (mtm) REVERT: D 649 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7641 (p90) REVERT: D 654 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9161 (tt) REVERT: E 483 TRP cc_start: 0.8727 (t60) cc_final: 0.8450 (t60) REVERT: F 276 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (tt) REVERT: F 304 LEU cc_start: 0.9391 (mt) cc_final: 0.9110 (tt) REVERT: F 326 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5944 (pttm) REVERT: F 331 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7315 (tm-30) REVERT: F 578 MET cc_start: 0.7966 (tpt) cc_final: 0.7452 (tpt) outliers start: 104 outliers final: 70 residues processed: 376 average time/residue: 0.1728 time to fit residues: 106.2412 Evaluate side-chains 343 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 266 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 566 GLU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 695 ARG Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 723 VAL Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 160 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 153 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 172 optimal weight: 7.9990 chunk 250 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 GLN F 785 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.106418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086190 restraints weight = 66157.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088285 restraints weight = 35643.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090214 restraints weight = 21634.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090345 restraints weight = 16810.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090324 restraints weight = 14359.243| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27549 Z= 0.120 Angle : 0.626 10.720 37181 Z= 0.311 Chirality : 0.043 0.204 4329 Planarity : 0.004 0.050 4789 Dihedral : 6.862 90.613 3809 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.07 % Allowed : 21.95 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 are not related in a simple way. whole: -0.39 (0.15), residues: 3373 helix: 0.56 (0.12), residues: 1853 sheet: -1.16 (0.25), residues: 356 loop : -1.16 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 321 TYR 0.009 0.001 TYR B 323 PHE 0.012 0.001 PHE A 543 TRP 0.003 0.000 TRP D 483 HIS 0.004 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (27542) covalent geometry : angle 0.62608 / 0.31 (37181) hydrogen bonds : bond 0.03815 / 2.56 ( 1325) hydrogen bonds : angle 4.98518 / 3.57 ( 3852) Misc. bond : bond 0.00109 / 0.04 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 314 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7495 (m-80) cc_final: 0.6904 (m-10) REVERT: A 335 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: A 535 LYS cc_start: 0.7159 (mtmm) cc_final: 0.6592 (mmmt) REVERT: A 569 MET cc_start: 0.8798 (tmm) cc_final: 0.8448 (tmm) REVERT: A 593 TYR cc_start: 0.7247 (m-80) cc_final: 0.6130 (t80) REVERT: B 160 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8571 (p) REVERT: B 381 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.6489 (p90) REVERT: B 721 GLU cc_start: 0.8193 (tp30) cc_final: 0.7958 (tp30) REVERT: C 166 LEU cc_start: 0.9210 (mt) cc_final: 0.8862 (mp) REVERT: C 319 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: C 393 ASP cc_start: 0.7594 (t0) cc_final: 0.7282 (t0) REVERT: C 598 GLU cc_start: 0.7449 (mp0) cc_final: 0.7037 (pm20) REVERT: C 685 MET cc_start: 0.7293 (mtm) cc_final: 0.6699 (mtm) REVERT: D 649 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7538 (p90) REVERT: D 654 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9129 (tt) REVERT: E 483 TRP cc_start: 0.8680 (t60) cc_final: 0.8408 (t60) REVERT: F 276 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8985 (tt) REVERT: F 304 LEU cc_start: 0.9358 (mt) cc_final: 0.9113 (tt) REVERT: F 326 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6049 (pttm) REVERT: F 331 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7268 (tm-30) REVERT: F 578 MET cc_start: 0.7995 (tpt) cc_final: 0.7537 (tpt) REVERT: F 695 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7352 (mtm110) outliers start: 90 outliers final: 63 residues processed: 380 average time/residue: 0.1617 time to fit residues: 101.2174 Evaluate side-chains 349 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 277 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 407 PHE Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 695 ARG Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 312 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 270 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS B 790 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082168 restraints weight = 66910.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.083607 restraints weight = 37418.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.085568 restraints weight = 24607.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.085589 restraints weight = 19687.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085619 restraints weight = 17000.238| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27549 Z= 0.227 Angle : 0.697 10.607 37181 Z= 0.350 Chirality : 0.045 0.227 4329 Planarity : 0.004 0.047 4789 Dihedral : 7.071 93.013 3807 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.41 % Allowed : 22.35 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.44 (0.15), residues: 3373 helix: 0.53 (0.12), residues: 1858 sheet: -1.19 (0.25), residues: 361 loop : -1.20 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 608 TYR 0.016 0.002 TYR E 596 PHE 0.014 0.001 PHE B 697 TRP 0.007 0.001 TRP B 483 HIS 0.012 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (27542) covalent geometry : angle 0.69722 / 0.35 (37181) hydrogen bonds : bond 0.04306 / 2.89 ( 1325) hydrogen bonds : angle 5.18414 / 3.71 ( 3852) Misc. bond : bond 0.00187 / 0.08 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 271 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7619 (m-80) cc_final: 0.6987 (m-10) REVERT: A 335 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: A 569 MET cc_start: 0.8875 (tmm) cc_final: 0.8540 (tmm) REVERT: A 593 TYR cc_start: 0.7291 (m-80) cc_final: 0.6212 (t80) REVERT: A 726 MET cc_start: 0.8781 (mpp) cc_final: 0.8557 (pmm) REVERT: B 381 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.6781 (p90) REVERT: C 166 LEU cc_start: 0.9221 (mt) cc_final: 0.8863 (mp) REVERT: C 319 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: C 393 ASP cc_start: 0.7733 (t0) cc_final: 0.7508 (t0) REVERT: C 685 MET cc_start: 0.7193 (mtm) cc_final: 0.6819 (mtm) REVERT: D 654 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9185 (tt) REVERT: E 483 TRP cc_start: 0.8787 (t60) cc_final: 0.8493 (t60) REVERT: F 276 LEU cc_start: 0.9228 (tt) cc_final: 0.8984 (tt) REVERT: F 304 LEU cc_start: 0.9401 (mt) cc_final: 0.9125 (tt) REVERT: F 326 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.6120 (pttm) REVERT: F 331 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7232 (tm-30) REVERT: F 578 MET cc_start: 0.7948 (tpt) cc_final: 0.7489 (tpt) outliers start: 100 outliers final: 80 residues processed: 341 average time/residue: 0.1614 time to fit residues: 91.2027 Evaluate side-chains 348 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 263 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 407 PHE Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 695 ARG Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 117 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 288 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 326 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 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 = 0.3595 r_free = 0.3595 target = 0.105486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.085372 restraints weight = 66160.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.087195 restraints weight = 35736.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089309 restraints weight = 22191.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089407 restraints weight = 16644.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089386 restraints weight = 14624.098| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27549 Z= 0.127 Angle : 0.648 11.194 37181 Z= 0.321 Chirality : 0.043 0.281 4329 Planarity : 0.004 0.049 4789 Dihedral : 6.920 88.830 3807 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.11 % Allowed : 22.80 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 are not related in a simple way. whole: -0.28 (0.15), residues: 3373 helix: 0.64 (0.12), residues: 1858 sheet: -1.10 (0.25), residues: 362 loop : -1.11 (0.20), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 608 TYR 0.012 0.001 TYR E 596 PHE 0.012 0.001 PHE B 697 TRP 0.005 0.001 TRP D 483 HIS 0.018 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (27542) covalent geometry : angle 0.64831 / 0.32 (37181) hydrogen bonds : bond 0.03871 / 2.60 ( 1325) hydrogen bonds : angle 4.99264 / 3.58 ( 3852) Misc. bond : bond 0.00112 / 0.04 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 293 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7497 (m-80) cc_final: 0.6877 (m-10) REVERT: A 335 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8040 (mp10) REVERT: A 535 LYS cc_start: 0.7353 (mtmm) cc_final: 0.6726 (mmmt) REVERT: A 569 MET cc_start: 0.8872 (tmm) cc_final: 0.8503 (tmm) REVERT: A 593 TYR cc_start: 0.7228 (m-80) cc_final: 0.6028 (t80) REVERT: A 726 MET cc_start: 0.8663 (mpp) cc_final: 0.8410 (pmm) REVERT: B 381 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.6632 (p90) REVERT: B 721 GLU cc_start: 0.8169 (tp30) cc_final: 0.7963 (tp30) REVERT: C 166 LEU cc_start: 0.9206 (mt) cc_final: 0.8843 (mp) REVERT: C 319 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: C 393 ASP cc_start: 0.7581 (t0) cc_final: 0.7254 (t0) REVERT: C 685 MET cc_start: 0.7246 (mtm) cc_final: 0.6690 (mtm) REVERT: D 654 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9149 (tt) REVERT: E 483 TRP cc_start: 0.8717 (t60) cc_final: 0.8455 (t60) REVERT: F 304 LEU cc_start: 0.9340 (mt) cc_final: 0.9004 (tt) REVERT: F 326 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.6152 (pttm) REVERT: F 331 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7218 (tm-30) REVERT: F 578 MET cc_start: 0.7952 (tpt) cc_final: 0.7679 (tpt) outliers start: 91 outliers final: 74 residues processed: 361 average time/residue: 0.1745 time to fit residues: 103.7039 Evaluate side-chains 350 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 271 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 713 SER Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 407 PHE Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 695 ARG Chi-restraints excluded: chain F residue 723 VAL Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 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 = 0.3589 r_free = 0.3589 target = 0.105292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085073 restraints weight = 66238.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.087068 restraints weight = 36214.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088429 restraints weight = 22302.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088724 restraints weight = 18315.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088748 restraints weight = 15783.866| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27549 Z= 0.145 Angle : 0.659 11.294 37181 Z= 0.327 Chirality : 0.044 0.233 4329 Planarity : 0.004 0.052 4789 Dihedral : 6.901 88.945 3807 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.94 % Allowed : 23.11 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 are not related in a simple way. whole: -0.19 (0.15), residues: 3373 helix: 0.68 (0.12), residues: 1862 sheet: -0.92 (0.25), residues: 361 loop : -1.06 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG D 608 TYR 0.020 0.001 TYR E 596 PHE 0.021 0.001 PHE B 386 TRP 0.004 0.001 TRP F 483 HIS 0.013 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (27542) covalent geometry : angle 0.65939 / 0.33 (37181) hydrogen bonds : bond 0.03896 / 2.62 ( 1325) hydrogen bonds : angle 4.98332 / 3.57 ( 3852) Misc. bond : bond 0.00133 / 0.06 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 276 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7532 (m-80) cc_final: 0.6895 (m-10) REVERT: A 282 HIS cc_start: 0.7461 (p-80) cc_final: 0.7154 (p-80) REVERT: A 335 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: A 535 LYS cc_start: 0.7373 (mtmm) cc_final: 0.6708 (mmmt) REVERT: A 569 MET cc_start: 0.8849 (tmm) cc_final: 0.8472 (tmm) REVERT: B 381 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.6591 (p90) REVERT: C 166 LEU cc_start: 0.9209 (mt) cc_final: 0.8833 (mp) REVERT: C 319 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: C 393 ASP cc_start: 0.7557 (t0) cc_final: 0.7264 (t0) REVERT: C 685 MET cc_start: 0.7270 (mtm) cc_final: 0.6691 (mtm) REVERT: D 654 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9161 (tt) REVERT: E 483 TRP cc_start: 0.8711 (t60) cc_final: 0.8422 (t60) REVERT: F 304 LEU cc_start: 0.9349 (mt) cc_final: 0.9016 (tt) REVERT: F 326 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6153 (pttm) REVERT: F 331 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7221 (tm-30) REVERT: F 578 MET cc_start: 0.7876 (tpt) cc_final: 0.7579 (tpt) outliers start: 86 outliers final: 74 residues processed: 344 average time/residue: 0.1664 time to fit residues: 94.2134 Evaluate side-chains 345 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 266 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 713 SER Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 407 PHE Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 695 ARG Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 19 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 263 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 226 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 287 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084588 restraints weight = 65925.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086705 restraints weight = 36264.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088135 restraints weight = 22206.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.088546 restraints weight = 17706.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088485 restraints weight = 15390.565| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27549 Z= 0.142 Angle : 0.657 11.613 37181 Z= 0.324 Chirality : 0.043 0.215 4329 Planarity : 0.004 0.054 4789 Dihedral : 6.888 89.507 3807 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.80 % Allowed : 23.31 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 are not related in a simple way. whole: -0.16 (0.15), residues: 3373 helix: 0.70 (0.12), residues: 1860 sheet: -1.05 (0.25), residues: 373 loop : -0.99 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 608 TYR 0.010 0.001 TYR E 577 PHE 0.022 0.001 PHE B 386 TRP 0.003 0.001 TRP C 483 HIS 0.010 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (27542) covalent geometry : angle 0.65679 / 0.32 (37181) hydrogen bonds : bond 0.03852 / 2.59 ( 1325) hydrogen bonds : angle 4.95005 / 3.55 ( 3852) Misc. bond : bond 0.00129 / 0.05 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.65 seconds wall clock time: 70 minutes 13.41 seconds (4213.41 seconds total)