Starting phenix.real_space_refine on Fri Mar 6 02:22:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7abr_11707/03_2026/7abr_11707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7abr_11707/03_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_11707/03_2026/7abr_11707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7abr_11707/03_2026/7abr_11707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7abr_11707/03_2026/7abr_11707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7abr_11707/03_2026/7abr_11707.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 6.67, per 1000 atoms: 0.25 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: 2.35 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: 0.81 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: 5.15 Time building geometry restraints manager: 3.05 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: 15740 21.81 - 43.61: 1319 43.61 - 65.42: 133 65.42 - 87.23: 40 87.23 - 109.04: 3 Dihedral angle restraints: 17235 sinusoidal: 7314 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 17232 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: 2.180 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.010 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 15.373 109.037 10791 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 covalent geometry : bond 0.01051 (27542) covalent geometry : angle 1.09005 (37181) hydrogen bonds : bond 0.16435 ( 1325) hydrogen bonds : angle 7.60438 ( 3852) Misc. bond : bond 0.43822 ( 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 : 1.054 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: 0.2296 time to fit residues: 145.3282 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 : 0.990 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 228 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084207 restraints weight = 66722.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086377 restraints weight = 35440.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088546 restraints weight = 21525.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088577 restraints weight = 16441.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088583 restraints weight = 13926.472| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27549 Z= 0.167 Angle : 0.710 12.767 37181 Z= 0.365 Chirality : 0.045 0.223 4329 Planarity : 0.005 0.051 4789 Dihedral : 10.046 106.435 4035 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.25 % Allowed : 15.53 % Favored : 82.22 % 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: -1.92 (0.14), residues: 3373 helix: -0.64 (0.11), residues: 1830 sheet: -1.75 (0.24), residues: 355 loop : -1.95 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 783 TYR 0.018 0.002 TYR F 611 PHE 0.024 0.001 PHE A 543 TRP 0.006 0.001 TRP D 483 HIS 0.009 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00359 (27542) covalent geometry : angle 0.71030 (37181) hydrogen bonds : bond 0.05188 ( 1325) hydrogen bonds : angle 5.84640 ( 3852) Misc. bond : bond 0.00418 ( 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 420 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 354 time to evaluate : 1.082 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: 0.7961 (mm110) cc_final: 0.7639 (mm-40) REVERT: A 253 TYR cc_start: 0.7411 (m-80) cc_final: 0.6863 (m-80) REVERT: A 265 MET cc_start: 0.8373 (mmp) cc_final: 0.8125 (mmp) REVERT: A 506 LEU cc_start: 0.9249 (mt) cc_final: 0.9049 (mt) REVERT: A 535 LYS cc_start: 0.7627 (mtmm) cc_final: 0.7180 (mmmt) REVERT: A 593 TYR cc_start: 0.7246 (m-80) cc_final: 0.6945 (m-80) REVERT: B 258 GLU cc_start: 0.8881 (pm20) cc_final: 0.8343 (pm20) REVERT: B 323 TYR cc_start: 0.8355 (p90) cc_final: 0.7448 (p90) REVERT: B 381 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.6807 (p90) REVERT: B 488 VAL cc_start: 0.7370 (m) cc_final: 0.7076 (p) REVERT: C 351 LEU cc_start: 0.9337 (mt) cc_final: 0.9088 (mt) REVERT: C 393 ASP cc_start: 0.7667 (t0) cc_final: 0.7255 (t0) REVERT: C 501 ASN cc_start: 0.7166 (t0) cc_final: 0.6824 (t0) REVERT: C 685 MET cc_start: 0.7119 (mtm) cc_final: 0.6672 (mtm) REVERT: D 654 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9185 (tt) REVERT: D 721 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: E 258 GLU cc_start: 0.7582 (pp20) cc_final: 0.7307 (pp20) REVERT: E 295 ASP cc_start: 0.6644 (m-30) cc_final: 0.6334 (m-30) REVERT: E 571 ARG cc_start: 0.8339 (ttt-90) cc_final: 0.7962 (ttt-90) REVERT: F 242 LEU cc_start: 0.8497 (pt) cc_final: 0.7804 (pp) REVERT: F 269 ARG cc_start: 0.8804 (tpp80) cc_final: 0.8395 (tmm-80) REVERT: F 331 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7287 (tm-30) REVERT: F 624 PRO cc_start: 0.7577 (Cg_exo) cc_final: 0.7301 (Cg_endo) outliers start: 66 outliers final: 36 residues processed: 403 average time/residue: 0.1756 time to fit residues: 111.4042 Evaluate side-chains 311 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 272 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 311 CYS 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: 1.9990 chunk 282 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 246 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 HIS ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 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** E 270 GLN ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.085108 restraints weight = 66487.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087226 restraints weight = 35946.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.089124 restraints weight = 21783.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.089425 restraints weight = 16483.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089252 restraints weight = 14571.953| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2243 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= 0.161 Angle : 0.663 11.475 37181 Z= 0.336 Chirality : 0.044 0.191 4329 Planarity : 0.004 0.045 4789 Dihedral : 9.691 102.573 4027 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.00 % Allowed : 17.92 % Favored : 79.08 % 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: -1.33 (0.14), residues: 3373 helix: -0.12 (0.12), residues: 1836 sheet: -1.60 (0.24), residues: 365 loop : -1.69 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 571 TYR 0.020 0.002 TYR D 381 PHE 0.014 0.001 PHE A 543 TRP 0.004 0.001 TRP E 483 HIS 0.007 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00365 (27542) covalent geometry : angle 0.66280 (37181) hydrogen bonds : bond 0.04607 ( 1325) hydrogen bonds : angle 5.51507 ( 3852) Misc. bond : bond 0.00181 ( 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 400 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 312 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLN cc_start: 0.7886 (mm110) cc_final: 0.7619 (mm-40) REVERT: A 253 TYR cc_start: 0.7500 (m-80) cc_final: 0.6927 (m-80) REVERT: A 265 MET cc_start: 0.8499 (mmp) cc_final: 0.8272 (mmp) REVERT: A 535 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7054 (mmmt) REVERT: A 569 MET cc_start: 0.8807 (tmm) cc_final: 0.8589 (tmm) REVERT: A 593 TYR cc_start: 0.7230 (m-80) cc_final: 0.6942 (m-80) REVERT: A 734 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7824 (tp) REVERT: B 240 MET cc_start: 0.8677 (mmt) cc_final: 0.8429 (mmt) REVERT: B 381 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.6652 (p90) REVERT: B 488 VAL cc_start: 0.7472 (m) cc_final: 0.7198 (p) REVERT: C 393 ASP cc_start: 0.7585 (t0) cc_final: 0.7264 (t0) REVERT: C 685 MET cc_start: 0.7200 (mtm) cc_final: 0.6814 (mtm) REVERT: D 649 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7563 (p90) REVERT: D 654 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9181 (tt) REVERT: E 387 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.9001 (mm) REVERT: E 474 ASP cc_start: 0.7451 (p0) cc_final: 0.7092 (p0) REVERT: E 483 TRP cc_start: 0.8690 (t60) cc_final: 0.8387 (t60) REVERT: F 269 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8260 (tmm-80) REVERT: F 304 LEU cc_start: 0.9387 (mt) cc_final: 0.9092 (tt) REVERT: F 331 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7224 (tm-30) REVERT: F 624 PRO cc_start: 0.7497 (Cg_exo) cc_final: 0.7175 (Cg_endo) outliers start: 88 outliers final: 50 residues processed: 378 average time/residue: 0.1595 time to fit residues: 98.8488 Evaluate side-chains 326 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 271 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 478 MET 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 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 378 SER 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 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 649 PHE Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 739 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 387 LEU 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 603 THR Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 723 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 334 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 241 optimal weight: 0.0270 chunk 210 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 157 optimal weight: 0.0670 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.084744 restraints weight = 66220.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.086717 restraints weight = 35850.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088914 restraints weight = 21905.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088982 restraints weight = 16381.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.088942 restraints weight = 14324.665| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27549 Z= 0.141 Angle : 0.637 10.560 37181 Z= 0.322 Chirality : 0.044 0.193 4329 Planarity : 0.004 0.046 4789 Dihedral : 9.337 97.891 4027 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.21 % Allowed : 19.22 % Favored : 77.58 % 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: -0.91 (0.14), residues: 3373 helix: 0.22 (0.12), residues: 1835 sheet: -1.45 (0.24), residues: 368 loop : -1.51 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 571 TYR 0.012 0.001 TYR D 381 PHE 0.013 0.001 PHE A 543 TRP 0.003 0.001 TRP D 483 HIS 0.009 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00313 (27542) covalent geometry : angle 0.63729 (37181) hydrogen bonds : bond 0.04283 ( 1325) hydrogen bonds : angle 5.29429 ( 3852) Misc. bond : bond 0.00133 ( 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 412 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 318 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7475 (m-80) cc_final: 0.6938 (m-80) REVERT: A 265 MET cc_start: 0.8478 (mmp) cc_final: 0.8278 (mmp) REVERT: A 535 LYS cc_start: 0.7320 (mtmm) cc_final: 0.6880 (mmmt) REVERT: A 569 MET cc_start: 0.8816 (tmm) cc_final: 0.8500 (tmm) REVERT: A 593 TYR cc_start: 0.7180 (m-80) cc_final: 0.6943 (m-80) REVERT: B 381 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.6645 (p90) REVERT: B 488 VAL cc_start: 0.7611 (m) cc_final: 0.7345 (p) REVERT: C 316 THR cc_start: 0.8701 (m) cc_final: 0.8465 (p) REVERT: C 319 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: C 331 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: C 393 ASP cc_start: 0.7604 (t0) cc_final: 0.7304 (t0) REVERT: C 598 GLU cc_start: 0.7579 (mp0) cc_final: 0.7281 (pm20) REVERT: C 685 MET cc_start: 0.7214 (mtm) cc_final: 0.6836 (mtm) REVERT: D 553 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6983 (tm-30) REVERT: D 649 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7565 (p90) REVERT: D 654 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9137 (tt) REVERT: E 483 TRP cc_start: 0.8683 (t60) cc_final: 0.8379 (t60) REVERT: F 269 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8264 (tmm-80) REVERT: F 276 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9122 (tt) REVERT: F 304 LEU cc_start: 0.9360 (mt) cc_final: 0.9100 (tt) REVERT: F 326 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5896 (pttm) REVERT: F 331 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7349 (tm-30) outliers start: 94 outliers final: 48 residues processed: 390 average time/residue: 0.1640 time to fit residues: 103.9976 Evaluate side-chains 328 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 273 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 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 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 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 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 756 VAL Chi-restraints excluded: chain D residue 758 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 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 326 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 722 ILE 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: 5.9990 chunk 165 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 337 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN D 628 ASN E 228 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.105166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.084661 restraints weight = 65917.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086838 restraints weight = 35560.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088622 restraints weight = 21399.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.088947 restraints weight = 16478.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.088761 restraints weight = 14375.476| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27549 Z= 0.146 Angle : 0.645 10.557 37181 Z= 0.324 Chirality : 0.044 0.246 4329 Planarity : 0.004 0.048 4789 Dihedral : 9.168 95.978 4027 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.07 % Allowed : 21.02 % Favored : 75.90 % 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: 0.33 (0.12), residues: 1847 sheet: -1.30 (0.24), residues: 363 loop : -1.44 (0.19), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 695 TYR 0.017 0.001 TYR D 381 PHE 0.012 0.001 PHE B 697 TRP 0.003 0.001 TRP C 483 HIS 0.008 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00330 (27542) covalent geometry : angle 0.64539 (37181) hydrogen bonds : bond 0.04152 ( 1325) hydrogen bonds : angle 5.19979 ( 3852) Misc. bond : bond 0.00137 ( 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 387 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 297 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7513 (m-80) cc_final: 0.6953 (m-80) REVERT: A 265 MET cc_start: 0.8542 (mmp) cc_final: 0.8323 (mmp) REVERT: A 535 LYS cc_start: 0.7423 (mtmm) cc_final: 0.6894 (mmmt) REVERT: A 569 MET cc_start: 0.8851 (tmm) cc_final: 0.8447 (tmm) REVERT: A 593 TYR cc_start: 0.7231 (m-80) cc_final: 0.6968 (m-80) REVERT: A 596 TYR cc_start: 0.8496 (t80) cc_final: 0.7981 (t80) REVERT: A 726 MET cc_start: 0.8563 (mpp) cc_final: 0.8340 (mpp) REVERT: B 381 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.6657 (p90) REVERT: B 705 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8955 (mm) REVERT: C 166 LEU cc_start: 0.9241 (mt) cc_final: 0.8912 (mp) REVERT: C 331 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: C 393 ASP cc_start: 0.7608 (t0) cc_final: 0.7305 (t0) REVERT: C 685 MET cc_start: 0.7201 (mtm) cc_final: 0.6838 (mtm) REVERT: D 553 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7161 (tm-30) REVERT: D 649 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7773 (p90) REVERT: D 654 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9148 (tt) REVERT: E 483 TRP cc_start: 0.8679 (t60) cc_final: 0.8439 (t60) REVERT: F 269 ARG cc_start: 0.8670 (tpp80) cc_final: 0.8228 (tmm-80) REVERT: F 276 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9041 (tt) REVERT: F 304 LEU cc_start: 0.9351 (mt) cc_final: 0.9122 (tt) REVERT: F 326 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.5935 (pttm) REVERT: F 331 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7331 (tm-30) REVERT: F 578 MET cc_start: 0.7807 (tpt) cc_final: 0.7312 (tpt) outliers start: 90 outliers final: 64 residues processed: 364 average time/residue: 0.1681 time to fit residues: 100.8042 Evaluate side-chains 348 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 277 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 294 ILE 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 536 ARG 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 351 LEU 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 652 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 705 ILE 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 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 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 219 GLU 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 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 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 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 326 LYS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 603 THR 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: 3.9990 chunk 114 optimal weight: 7.9990 chunk 328 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 152 optimal weight: 0.0770 chunk 186 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 309 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.103955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083573 restraints weight = 66671.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.085710 restraints weight = 35911.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087570 restraints weight = 21657.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087629 restraints weight = 16825.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087602 restraints weight = 14524.228| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2897 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= 0.175 Angle : 0.650 9.734 37181 Z= 0.327 Chirality : 0.044 0.196 4329 Planarity : 0.004 0.048 4789 Dihedral : 9.081 94.886 4026 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.79 % Allowed : 21.57 % Favored : 74.64 % 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: 0.46 (0.12), residues: 1841 sheet: -1.22 (0.25), residues: 359 loop : -1.36 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 321 TYR 0.011 0.001 TYR D 593 PHE 0.013 0.001 PHE A 543 TRP 0.004 0.001 TRP C 483 HIS 0.007 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00400 (27542) covalent geometry : angle 0.64999 (37181) hydrogen bonds : bond 0.04208 ( 1325) hydrogen bonds : angle 5.16801 ( 3852) Misc. bond : bond 0.00154 ( 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 401 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 290 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7549 (m-80) cc_final: 0.6958 (m-80) REVERT: A 335 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: A 535 LYS cc_start: 0.7395 (mtmm) cc_final: 0.6741 (mmmt) REVERT: A 593 TYR cc_start: 0.7286 (m-80) cc_final: 0.7077 (m-80) REVERT: B 381 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.6772 (p90) REVERT: C 166 LEU cc_start: 0.9248 (mt) cc_final: 0.8903 (mp) REVERT: C 319 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: C 393 ASP cc_start: 0.7693 (t0) cc_final: 0.7417 (t0) REVERT: C 598 GLU cc_start: 0.7508 (mp0) cc_final: 0.7157 (pm20) REVERT: C 685 MET cc_start: 0.7164 (mtm) cc_final: 0.6771 (mtm) REVERT: C 798 ASP cc_start: 0.7048 (p0) cc_final: 0.6846 (p0) REVERT: D 649 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7685 (p90) REVERT: D 654 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9160 (tt) REVERT: E 483 TRP cc_start: 0.8766 (t60) cc_final: 0.8487 (t60) REVERT: F 276 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8987 (tt) REVERT: F 304 LEU cc_start: 0.9372 (mt) cc_final: 0.9133 (tt) REVERT: F 326 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.5986 (pttm) REVERT: F 331 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7313 (tm-30) REVERT: F 578 MET cc_start: 0.7829 (tpt) cc_final: 0.7312 (tpt) outliers start: 111 outliers final: 77 residues processed: 377 average time/residue: 0.1672 time to fit residues: 103.2286 Evaluate side-chains 347 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 263 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 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 351 LEU 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 484 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 619 ILE 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 654 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain D residue 219 GLU 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 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 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 723 VAL Chi-restraints excluded: chain D residue 756 VAL 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 392 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 722 ILE 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: 1.9990 chunk 28 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 250 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3599 r_free = 0.3599 target = 0.105677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085157 restraints weight = 66328.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.087165 restraints weight = 35849.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088974 restraints weight = 22122.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089256 restraints weight = 17327.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.089124 restraints weight = 15055.636| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27549 Z= 0.129 Angle : 0.641 10.857 37181 Z= 0.319 Chirality : 0.043 0.218 4329 Planarity : 0.004 0.048 4789 Dihedral : 8.813 91.259 4026 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.24 % Allowed : 22.29 % Favored : 74.47 % 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: -0.40 (0.15), residues: 3373 helix: 0.56 (0.12), residues: 1838 sheet: -1.06 (0.25), residues: 365 loop : -1.21 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 321 TYR 0.011 0.001 TYR E 596 PHE 0.012 0.001 PHE A 543 TRP 0.003 0.001 TRP D 483 HIS 0.004 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00284 (27542) covalent geometry : angle 0.64054 (37181) hydrogen bonds : bond 0.03902 ( 1325) hydrogen bonds : angle 5.03404 ( 3852) Misc. bond : bond 0.00123 ( 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 403 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 308 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7503 (m-80) cc_final: 0.6903 (m-10) REVERT: A 335 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: A 535 LYS cc_start: 0.7295 (mtmm) cc_final: 0.6707 (mmmt) REVERT: A 569 MET cc_start: 0.8844 (tmm) cc_final: 0.8462 (tmm) REVERT: A 593 TYR cc_start: 0.7261 (m-80) cc_final: 0.7029 (m-80) REVERT: B 381 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.6645 (p90) REVERT: B 721 GLU cc_start: 0.8236 (tp30) cc_final: 0.8010 (tp30) REVERT: C 166 LEU cc_start: 0.9213 (mt) cc_final: 0.8981 (mp) REVERT: C 319 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: C 393 ASP cc_start: 0.7576 (t0) cc_final: 0.7267 (t0) REVERT: C 685 MET cc_start: 0.7320 (mtm) cc_final: 0.6719 (mtm) REVERT: D 649 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7680 (p90) REVERT: D 654 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9133 (tt) REVERT: E 483 TRP cc_start: 0.8726 (t60) cc_final: 0.8455 (t60) REVERT: F 276 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9001 (tt) REVERT: F 304 LEU cc_start: 0.9341 (mt) cc_final: 0.9041 (tt) REVERT: F 326 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6105 (pttm) REVERT: F 331 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7296 (tm-30) REVERT: F 578 MET cc_start: 0.7956 (tpt) cc_final: 0.7441 (tpt) outliers start: 95 outliers final: 66 residues processed: 378 average time/residue: 0.1700 time to fit residues: 105.0850 Evaluate side-chains 345 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 272 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 379 ASP 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 351 LEU 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 575 SER Chi-restraints excluded: chain C residue 726 MET 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 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 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 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 594 VAL 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 803 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 312 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 280 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 208 optimal weight: 0.5980 chunk 175 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN E 270 GLN F 785 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086642 restraints weight = 66121.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.087473 restraints weight = 38764.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088479 restraints weight = 26589.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088857 restraints weight = 23076.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.088958 restraints weight = 19692.420| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27549 Z= 0.132 Angle : 0.640 10.803 37181 Z= 0.320 Chirality : 0.043 0.223 4329 Planarity : 0.004 0.048 4789 Dihedral : 8.699 89.219 4024 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.07 % Allowed : 22.90 % Favored : 74.03 % 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: -0.27 (0.15), residues: 3373 helix: 0.64 (0.12), residues: 1849 sheet: -0.96 (0.26), residues: 350 loop : -1.15 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 198 TYR 0.009 0.001 TYR E 577 PHE 0.011 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 covalent geometry : bond 0.00293 (27542) covalent geometry : angle 0.64023 (37181) hydrogen bonds : bond 0.03840 ( 1325) hydrogen bonds : angle 4.97289 ( 3852) Misc. bond : bond 0.00134 ( 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 375 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 285 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7540 (m-80) cc_final: 0.6916 (m-10) REVERT: A 265 MET cc_start: 0.8310 (mmp) cc_final: 0.7962 (mmm) REVERT: A 323 TYR cc_start: 0.8594 (m-80) cc_final: 0.8282 (m-10) REVERT: A 335 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: A 535 LYS cc_start: 0.7318 (mtmm) cc_final: 0.6798 (mmmt) REVERT: A 569 MET cc_start: 0.8848 (tmm) cc_final: 0.8420 (tmm) REVERT: A 593 TYR cc_start: 0.7286 (m-80) cc_final: 0.6853 (m-80) REVERT: A 726 MET cc_start: 0.8419 (mpp) cc_final: 0.8214 (pmm) REVERT: B 381 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.6566 (p90) REVERT: C 166 LEU cc_start: 0.9188 (mt) cc_final: 0.8965 (mp) REVERT: C 393 ASP cc_start: 0.7581 (t0) cc_final: 0.7281 (t0) REVERT: C 598 GLU cc_start: 0.7397 (mp0) cc_final: 0.7007 (pm20) REVERT: C 685 MET cc_start: 0.7362 (mtm) cc_final: 0.6760 (mtm) REVERT: E 483 TRP cc_start: 0.8674 (t60) cc_final: 0.8354 (t60) REVERT: E 571 ARG cc_start: 0.8315 (ttt-90) cc_final: 0.8104 (ttt-90) REVERT: F 304 LEU cc_start: 0.9322 (mt) cc_final: 0.9031 (tt) REVERT: F 326 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6148 (pttm) REVERT: F 331 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7232 (tm-30) REVERT: F 502 MET cc_start: 0.8250 (ppp) cc_final: 0.7976 (ppp) REVERT: F 578 MET cc_start: 0.7888 (tpt) cc_final: 0.7345 (tpt) outliers start: 90 outliers final: 72 residues processed: 351 average time/residue: 0.1646 time to fit residues: 95.3378 Evaluate side-chains 347 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 272 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 A residue 796 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 351 LEU 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 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 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 726 MET 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 247 VAL Chi-restraints excluded: chain D residue 311 CYS 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 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 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 270 GLN 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 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 723 VAL 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: 0.9990 chunk 281 optimal weight: 0.0060 chunk 105 optimal weight: 0.8980 chunk 288 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 311 optimal weight: 0.7980 chunk 326 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.106248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085973 restraints weight = 65960.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088269 restraints weight = 36286.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089552 restraints weight = 21824.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090012 restraints weight = 17543.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089962 restraints weight = 15226.286| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27549 Z= 0.123 Angle : 0.643 11.582 37181 Z= 0.318 Chirality : 0.043 0.274 4329 Planarity : 0.004 0.048 4789 Dihedral : 8.565 88.175 4024 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.76 % Allowed : 23.17 % Favored : 74.06 % 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: 0.67 (0.12), residues: 1857 sheet: -0.92 (0.26), residues: 346 loop : -1.05 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 321 TYR 0.010 0.001 TYR E 577 PHE 0.011 0.001 PHE B 697 TRP 0.003 0.001 TRP D 483 HIS 0.007 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00271 (27542) covalent geometry : angle 0.64266 (37181) hydrogen bonds : bond 0.03724 ( 1325) hydrogen bonds : angle 4.91779 ( 3852) Misc. bond : bond 0.00126 ( 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 376 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 295 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7465 (m-80) cc_final: 0.6819 (m-10) REVERT: A 265 MET cc_start: 0.8307 (mmp) cc_final: 0.7936 (mmm) REVERT: A 335 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: A 535 LYS cc_start: 0.7204 (mtmm) cc_final: 0.6649 (mmmt) REVERT: A 569 MET cc_start: 0.8837 (tmm) cc_final: 0.8389 (tmm) REVERT: A 596 TYR cc_start: 0.8480 (t80) cc_final: 0.8030 (t80) REVERT: B 381 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.6570 (p90) REVERT: B 721 GLU cc_start: 0.8190 (tp30) cc_final: 0.7965 (tp30) REVERT: C 393 ASP cc_start: 0.7547 (t0) cc_final: 0.7243 (t0) REVERT: C 685 MET cc_start: 0.7291 (mtm) cc_final: 0.6686 (mtm) REVERT: E 483 TRP cc_start: 0.8657 (t60) cc_final: 0.8361 (t60) REVERT: F 304 LEU cc_start: 0.9294 (mt) cc_final: 0.9012 (tt) REVERT: F 326 LYS cc_start: 0.6751 (pttt) cc_final: 0.6176 (pttm) REVERT: F 331 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7225 (tm-30) REVERT: F 502 MET cc_start: 0.8299 (ppp) cc_final: 0.8045 (ppp) REVERT: F 578 MET cc_start: 0.7905 (tpt) cc_final: 0.7400 (tpt) outliers start: 81 outliers final: 70 residues processed: 358 average time/residue: 0.1668 time to fit residues: 96.8903 Evaluate side-chains 345 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 273 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 A residue 796 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 351 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 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 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 726 MET 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 247 VAL 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 640 THR 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 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 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 344 VAL 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 803 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 264 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 791 HIS D 228 ASN D 628 ASN E 270 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.087316 restraints weight = 65944.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088366 restraints weight = 37769.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090004 restraints weight = 24874.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.090199 restraints weight = 20241.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090252 restraints weight = 17086.538| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27549 Z= 0.126 Angle : 0.647 11.818 37181 Z= 0.320 Chirality : 0.043 0.247 4329 Planarity : 0.004 0.050 4789 Dihedral : 8.481 87.860 4024 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.76 % Allowed : 23.41 % Favored : 73.82 % 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: -0.11 (0.15), residues: 3373 helix: 0.74 (0.12), residues: 1860 sheet: -0.81 (0.26), residues: 368 loop : -1.04 (0.20), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 321 TYR 0.016 0.001 TYR D 381 PHE 0.020 0.001 PHE B 386 TRP 0.003 0.001 TRP F 483 HIS 0.010 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00279 (27542) covalent geometry : angle 0.64702 (37181) hydrogen bonds : bond 0.03695 ( 1325) hydrogen bonds : angle 4.86343 ( 3852) Misc. bond : bond 0.00131 ( 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 370 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 289 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7410 (m-80) cc_final: 0.6749 (m-10) REVERT: A 265 MET cc_start: 0.8318 (mmp) cc_final: 0.7927 (mmm) REVERT: A 322 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8613 (mtpp) REVERT: A 335 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: A 535 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6646 (mmmt) REVERT: A 596 TYR cc_start: 0.8464 (t80) cc_final: 0.7990 (t80) REVERT: A 726 MET cc_start: 0.8547 (mpp) cc_final: 0.8346 (pmm) REVERT: A 736 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: B 381 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.6602 (p90) REVERT: B 721 GLU cc_start: 0.8188 (tp30) cc_final: 0.7961 (tp30) REVERT: C 393 ASP cc_start: 0.7542 (t0) cc_final: 0.7260 (t0) REVERT: C 535 LYS cc_start: 0.8405 (tppt) cc_final: 0.8158 (ttpp) REVERT: C 598 GLU cc_start: 0.7395 (mp0) cc_final: 0.6961 (pm20) REVERT: C 685 MET cc_start: 0.7322 (mtm) cc_final: 0.6715 (mtm) REVERT: E 483 TRP cc_start: 0.8663 (t60) cc_final: 0.8371 (t60) REVERT: F 304 LEU cc_start: 0.9303 (mt) cc_final: 0.9027 (tt) REVERT: F 326 LYS cc_start: 0.6945 (pttt) cc_final: 0.6411 (pttm) REVERT: F 331 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7274 (tm-30) REVERT: F 502 MET cc_start: 0.8276 (ppp) cc_final: 0.7935 (ppp) REVERT: F 578 MET cc_start: 0.7902 (tpt) cc_final: 0.7376 (tpt) REVERT: F 726 MET cc_start: 0.9050 (mtp) cc_final: 0.8806 (mtm) outliers start: 81 outliers final: 69 residues processed: 352 average time/residue: 0.1659 time to fit residues: 95.0203 Evaluate side-chains 341 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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 736 GLU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 351 LEU 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 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 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 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 723 VAL 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 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 270 GLN 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 392 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 344 VAL 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 803 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 19 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 263 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN E 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.088327 restraints weight = 65228.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089995 restraints weight = 37680.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.092014 restraints weight = 23928.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092289 restraints weight = 17816.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.092288 restraints weight = 15604.475| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27549 Z= 0.135 Angle : 0.654 12.000 37181 Z= 0.324 Chirality : 0.044 0.348 4329 Planarity : 0.004 0.050 4789 Dihedral : 8.473 89.374 4024 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.70 % Allowed : 23.62 % Favored : 73.69 % 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: -0.09 (0.15), residues: 3373 helix: 0.76 (0.12), residues: 1859 sheet: -0.92 (0.26), residues: 378 loop : -0.99 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 571 TYR 0.016 0.001 TYR D 381 PHE 0.012 0.001 PHE B 697 TRP 0.003 0.001 TRP C 483 HIS 0.014 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00308 (27542) covalent geometry : angle 0.65412 (37181) hydrogen bonds : bond 0.03704 ( 1325) hydrogen bonds : angle 4.86635 ( 3852) Misc. bond : bond 0.00147 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.87 seconds wall clock time: 66 minutes 50.07 seconds (4010.07 seconds total)