Starting phenix.real_space_refine on Wed Mar 4 05:46:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9os7_70794/03_2026/9os7_70794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9os7_70794/03_2026/9os7_70794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9os7_70794/03_2026/9os7_70794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9os7_70794/03_2026/9os7_70794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9os7_70794/03_2026/9os7_70794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9os7_70794/03_2026/9os7_70794.map" } resolution = 3.66 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= 0.035 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7054 2.51 5 N 1783 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.01s 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: 10933 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4444 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PTRANS': 10, 'TRANS': 535} Chain breaks: 9 Chain: "C" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2045 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 3.12, per 1000 atoms: 0.29 Number of scatterers: 10933 At special positions: 0 Unit cell: (100.62, 131.58, 129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2060 8.00 N 1783 7.00 C 7054 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=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 501.7 milliseconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 13 sheets defined 42.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 32 through 35 Processing helix chain 'A' and resid 43 through 54 removed outlier: 3.747A pdb=" N GLU A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.684A pdb=" N LEU A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 215 through 223 removed outlier: 4.403A pdb=" N GLY A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.503A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.624A pdb=" N ILE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.509A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 removed outlier: 3.506A pdb=" N LEU A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 348 through 354 removed outlier: 4.021A pdb=" N TYR A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.743A pdb=" N GLN A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.897A pdb=" N PHE A 442 " --> pdb=" O PRO A 438 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 451 " --> pdb=" O LYS A 447 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 472 removed outlier: 3.591A pdb=" N ASP A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.863A pdb=" N LEU A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.976A pdb=" N LEU A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 514 " --> pdb=" O ARG A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.578A pdb=" N GLN A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 35 Processing helix chain 'B' and resid 43 through 54 removed outlier: 3.747A pdb=" N GLU B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.685A pdb=" N LEU B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 215 through 223 removed outlier: 4.402A pdb=" N GLY B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.502A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.625A pdb=" N ILE B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.509A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.507A pdb=" N LEU B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 348 through 354 removed outlier: 4.022A pdb=" N TYR B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 400 through 407 removed outlier: 3.742A pdb=" N GLN B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 406 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 Processing helix chain 'B' and resid 438 through 453 removed outlier: 3.896A pdb=" N PHE B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 453 " --> pdb=" O CYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.590A pdb=" N ASP B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.862A pdb=" N LEU B 476 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 517 removed outlier: 3.976A pdb=" N LEU B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 558 removed outlier: 3.578A pdb=" N GLN B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 604 removed outlier: 3.817A pdb=" N ALA C 595 " --> pdb=" O THR C 591 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 598 " --> pdb=" O ILE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 645 removed outlier: 3.539A pdb=" N LEU C 644 " --> pdb=" O SER C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 658 removed outlier: 4.290A pdb=" N PHE C 653 " --> pdb=" O ASP C 649 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 654 " --> pdb=" O PRO C 650 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN C 655 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 669 removed outlier: 3.549A pdb=" N PHE C 662 " --> pdb=" O GLY C 658 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 667 " --> pdb=" O ARG C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 691 removed outlier: 3.534A pdb=" N ASN C 685 " --> pdb=" O LYS C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 711 removed outlier: 3.656A pdb=" N ASN C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 711 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 744 removed outlier: 3.861A pdb=" N GLU C 728 " --> pdb=" O ASN C 724 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 729 " --> pdb=" O ILE C 725 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 736 " --> pdb=" O LYS C 732 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 769 removed outlier: 3.789A pdb=" N ILE C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 776 removed outlier: 3.533A pdb=" N LEU C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 801 removed outlier: 3.525A pdb=" N SER C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 790 " --> pdb=" O LEU C 786 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 815 Processing helix chain 'C' and resid 823 through 829 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 84 removed outlier: 6.663A pdb=" N VAL A 58 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU A 83 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE A 60 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 16 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 171 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 173 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.403A pdb=" N LEU A 203 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU A 522 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N PHE A 205 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N LEU A 520 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ALA A 536 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 522 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 253 through 257 removed outlier: 6.485A pdb=" N VAL A 328 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASP A 360 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N MET A 330 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 280 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL A 331 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 482 through 483 Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.661A pdb=" N VAL B 58 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 83 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B 60 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 16 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 171 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 173 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.403A pdb=" N LEU B 203 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU B 522 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N PHE B 205 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N LEU B 520 " --> pdb=" O ALA B 536 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA B 536 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 522 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 253 through 257 removed outlier: 6.486A pdb=" N VAL B 328 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASP B 360 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET B 330 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 280 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL B 331 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AB4, first strand: chain 'C' and resid 633 through 634 349 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3044 1.33 - 1.45: 1763 1.45 - 1.57: 6244 1.57 - 1.68: 6 1.68 - 1.80: 56 Bond restraints: 11113 Sorted by residual: bond pdb=" C PRO B 392 " pdb=" O PRO B 392 " ideal model delta sigma weight residual 1.235 1.260 -0.025 7.90e-03 1.60e+04 9.76e+00 bond pdb=" C PRO A 392 " pdb=" O PRO A 392 " ideal model delta sigma weight residual 1.235 1.259 -0.024 7.90e-03 1.60e+04 9.29e+00 bond pdb=" C ASN A 341 " pdb=" N PRO A 342 " ideal model delta sigma weight residual 1.333 1.307 0.026 1.01e-02 9.80e+03 6.88e+00 bond pdb=" CG LYS A 100 " pdb=" CD LYS A 100 " ideal model delta sigma weight residual 1.520 1.599 -0.079 3.00e-02 1.11e+03 6.86e+00 bond pdb=" C ASN B 341 " pdb=" N PRO B 342 " ideal model delta sigma weight residual 1.333 1.307 0.026 1.01e-02 9.80e+03 6.66e+00 ... (remaining 11108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 14749 3.59 - 7.17: 169 7.17 - 10.76: 27 10.76 - 14.34: 5 14.34 - 17.93: 3 Bond angle restraints: 14953 Sorted by residual: angle pdb=" CB LYS A 100 " pdb=" CG LYS A 100 " pdb=" CD LYS A 100 " ideal model delta sigma weight residual 111.30 129.23 -17.93 2.30e+00 1.89e-01 6.08e+01 angle pdb=" CB LYS B 100 " pdb=" CG LYS B 100 " pdb=" CD LYS B 100 " ideal model delta sigma weight residual 111.30 129.23 -17.93 2.30e+00 1.89e-01 6.08e+01 angle pdb=" C LYS B 92 " pdb=" N ASN B 93 " pdb=" CA ASN B 93 " ideal model delta sigma weight residual 121.70 135.65 -13.95 1.80e+00 3.09e-01 6.01e+01 angle pdb=" C LYS A 92 " pdb=" N ASN A 93 " pdb=" CA ASN A 93 " ideal model delta sigma weight residual 121.70 135.64 -13.94 1.80e+00 3.09e-01 6.00e+01 angle pdb=" CG LYS B 100 " pdb=" CD LYS B 100 " pdb=" CE LYS B 100 " ideal model delta sigma weight residual 111.30 123.01 -11.71 2.30e+00 1.89e-01 2.59e+01 ... (remaining 14948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5778 17.92 - 35.84: 644 35.84 - 53.76: 216 53.76 - 71.68: 76 71.68 - 89.60: 14 Dihedral angle restraints: 6728 sinusoidal: 2775 harmonic: 3953 Sorted by residual: dihedral pdb=" CA ILE A 365 " pdb=" C ILE A 365 " pdb=" N LEU A 366 " pdb=" CA LEU A 366 " ideal model delta harmonic sigma weight residual 180.00 -138.09 -41.91 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA ILE B 365 " pdb=" C ILE B 365 " pdb=" N LEU B 366 " pdb=" CA LEU B 366 " ideal model delta harmonic sigma weight residual -180.00 -138.19 -41.81 0 5.00e+00 4.00e-02 6.99e+01 dihedral pdb=" CA ILE C 634 " pdb=" C ILE C 634 " pdb=" N THR C 635 " pdb=" CA THR C 635 " ideal model delta harmonic sigma weight residual 180.00 -147.31 -32.69 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 6725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1399 0.080 - 0.160: 267 0.160 - 0.240: 22 0.240 - 0.319: 5 0.319 - 0.399: 2 Chirality restraints: 1695 Sorted by residual: chirality pdb=" CB ILE B 160 " pdb=" CA ILE B 160 " pdb=" CG1 ILE B 160 " pdb=" CG2 ILE B 160 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB ILE A 160 " pdb=" CA ILE A 160 " pdb=" CG1 ILE A 160 " pdb=" CG2 ILE A 160 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB ILE A 365 " pdb=" CA ILE A 365 " pdb=" CG1 ILE A 365 " pdb=" CG2 ILE A 365 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1692 not shown) Planarity restraints: 1885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 99 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" CD GLU B 99 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU B 99 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU B 99 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 99 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" CD GLU A 99 " 0.044 2.00e-02 2.50e+03 pdb=" OE1 GLU A 99 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 99 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 19 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C THR A 19 " -0.038 2.00e-02 2.50e+03 pdb=" O THR A 19 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 20 " 0.013 2.00e-02 2.50e+03 ... (remaining 1882 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2784 2.78 - 3.31: 9485 3.31 - 3.84: 18004 3.84 - 4.37: 20880 4.37 - 4.90: 35977 Nonbonded interactions: 87130 Sorted by model distance: nonbonded pdb=" OH TYR C 601 " pdb=" O TYR C 799 " model vdw 2.247 3.040 nonbonded pdb=" NZ LYS B 237 " pdb=" O TYR B 429 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS A 237 " pdb=" O TYR A 429 " model vdw 2.257 3.120 nonbonded pdb=" OH TYR B 135 " pdb=" O PRO B 180 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR A 135 " pdb=" O PRO A 180 " model vdw 2.286 3.040 ... (remaining 87125 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' selection = chain 'B' } 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: 4.940 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.010 0.079 11113 Z= 0.462 Angle : 1.154 17.931 14953 Z= 0.634 Chirality : 0.063 0.399 1695 Planarity : 0.006 0.053 1885 Dihedral : 18.466 89.605 4160 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.17 % Rotamer: Outliers : 9.32 % Allowed : 10.45 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.71 (0.18), residues: 1302 helix: -4.32 (0.10), residues: 489 sheet: -2.66 (0.34), residues: 196 loop : -2.07 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 460 TYR 0.016 0.002 TYR B 332 PHE 0.024 0.003 PHE B 372 TRP 0.020 0.003 TRP A 245 HIS 0.010 0.002 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.01014 (11113) covalent geometry : angle 1.15414 (14953) hydrogen bonds : bond 0.30543 ( 349) hydrogen bonds : angle 10.62272 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 227 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6079 (mtpp) REVERT: B 20 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7745 (m) REVERT: B 37 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 436 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8018 (p) REVERT: B 444 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8470 (t) REVERT: C 664 TYR cc_start: 0.6990 (t80) cc_final: 0.6342 (t80) REVERT: C 669 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6444 (mm-30) outliers start: 115 outliers final: 17 residues processed: 296 average time/residue: 0.1073 time to fit residues: 44.8015 Evaluate side-chains 136 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain C residue 647 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN A 225 ASN A 226 HIS A 271 ASN A 405 GLN A 483 HIS A 493 ASN A 502 ASN A 541 HIS B 11 ASN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 GLN B 483 HIS B 502 ASN B 541 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.152056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116594 restraints weight = 19721.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.114663 restraints weight = 12884.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.116743 restraints weight = 9884.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.117528 restraints weight = 7167.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.117974 restraints weight = 6505.204| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11113 Z= 0.160 Angle : 0.648 9.106 14953 Z= 0.349 Chirality : 0.045 0.199 1695 Planarity : 0.004 0.040 1885 Dihedral : 7.897 57.069 1456 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 2.84 % Allowed : 17.18 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.35 (0.20), residues: 1302 helix: -2.55 (0.17), residues: 526 sheet: -2.16 (0.37), residues: 196 loop : -1.73 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 753 TYR 0.014 0.001 TYR B 514 PHE 0.015 0.001 PHE A 139 TRP 0.014 0.002 TRP B 245 HIS 0.003 0.001 HIS C 585 Details of bonding type rmsd covalent geometry : bond 0.00356 (11113) covalent geometry : angle 0.64780 (14953) hydrogen bonds : bond 0.04866 ( 349) hydrogen bonds : angle 5.91520 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7860 (tp30) cc_final: 0.7460 (tp30) REVERT: A 53 GLU cc_start: 0.7416 (pp20) cc_final: 0.7125 (tp30) REVERT: A 174 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6550 (mtpp) REVERT: A 383 THR cc_start: 0.8752 (t) cc_final: 0.8467 (m) REVERT: A 389 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7043 (mt-10) REVERT: B 21 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8383 (ttpp) REVERT: B 112 GLN cc_start: 0.7895 (tp40) cc_final: 0.7668 (tp-100) REVERT: B 139 PHE cc_start: 0.8028 (m-80) cc_final: 0.7808 (m-80) REVERT: B 174 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7087 (tptp) REVERT: B 444 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8028 (t) REVERT: C 669 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7096 (mm-30) outliers start: 35 outliers final: 15 residues processed: 171 average time/residue: 0.0942 time to fit residues: 23.8526 Evaluate side-chains 135 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 723 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 125 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.150694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.114538 restraints weight = 20111.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112792 restraints weight = 13802.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.114416 restraints weight = 10163.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115377 restraints weight = 7989.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.115730 restraints weight = 7054.095| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11113 Z= 0.157 Angle : 0.611 8.843 14953 Z= 0.324 Chirality : 0.045 0.182 1695 Planarity : 0.003 0.033 1885 Dihedral : 6.228 57.332 1433 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.43 % Allowed : 20.34 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.55 (0.22), residues: 1302 helix: -1.58 (0.21), residues: 529 sheet: -2.00 (0.38), residues: 196 loop : -1.50 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 460 TYR 0.017 0.001 TYR B 514 PHE 0.016 0.001 PHE B 372 TRP 0.011 0.001 TRP B 245 HIS 0.002 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00359 (11113) covalent geometry : angle 0.61106 (14953) hydrogen bonds : bond 0.04247 ( 349) hydrogen bonds : angle 5.37892 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.6691 (p90) cc_final: 0.5995 (p90) REVERT: A 49 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: A 180 PRO cc_start: 0.6950 (Cg_endo) cc_final: 0.6637 (Cg_exo) REVERT: A 228 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7447 (ttt180) REVERT: A 389 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 88 PHE cc_start: 0.6736 (t80) cc_final: 0.6498 (t80) REVERT: B 112 GLN cc_start: 0.7951 (tp40) cc_final: 0.7673 (tp-100) REVERT: B 139 PHE cc_start: 0.8093 (m-80) cc_final: 0.7797 (m-80) REVERT: B 192 MET cc_start: 0.7665 (mmm) cc_final: 0.7230 (mmm) REVERT: B 257 MET cc_start: 0.8156 (mtt) cc_final: 0.7786 (mtt) REVERT: B 444 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.8010 (t) REVERT: C 669 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7288 (mm-30) outliers start: 30 outliers final: 18 residues processed: 157 average time/residue: 0.0917 time to fit residues: 22.0100 Evaluate side-chains 137 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 723 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 95 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 169 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.145777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.109326 restraints weight = 20203.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107626 restraints weight = 12959.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.109058 restraints weight = 10113.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.109686 restraints weight = 8310.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110199 restraints weight = 7648.222| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11113 Z= 0.208 Angle : 0.645 8.695 14953 Z= 0.339 Chirality : 0.047 0.201 1695 Planarity : 0.003 0.032 1885 Dihedral : 5.764 59.480 1420 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.73 % Allowed : 19.77 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.31 (0.22), residues: 1302 helix: -1.21 (0.22), residues: 529 sheet: -2.01 (0.38), residues: 196 loop : -1.50 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 460 TYR 0.023 0.002 TYR B 514 PHE 0.020 0.002 PHE B 372 TRP 0.011 0.002 TRP A 494 HIS 0.004 0.001 HIS B 483 Details of bonding type rmsd covalent geometry : bond 0.00488 (11113) covalent geometry : angle 0.64535 (14953) hydrogen bonds : bond 0.04190 ( 349) hydrogen bonds : angle 5.32958 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.6773 (p90) cc_final: 0.6043 (p90) REVERT: A 49 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: A 112 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7805 (tp-100) REVERT: A 180 PRO cc_start: 0.6980 (Cg_endo) cc_final: 0.6720 (Cg_exo) REVERT: A 228 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7167 (ttt180) REVERT: A 383 THR cc_start: 0.8778 (t) cc_final: 0.8463 (m) REVERT: A 389 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 21 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8524 (ttpp) REVERT: B 112 GLN cc_start: 0.8106 (tp40) cc_final: 0.7807 (tp-100) REVERT: B 134 ASN cc_start: 0.7652 (t0) cc_final: 0.7244 (t0) REVERT: B 139 PHE cc_start: 0.8124 (m-80) cc_final: 0.7804 (m-80) REVERT: B 192 MET cc_start: 0.7672 (mmm) cc_final: 0.7373 (mmm) REVERT: B 304 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 444 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8110 (t) REVERT: C 640 MET cc_start: 0.1760 (tpt) cc_final: 0.1154 (tpt) outliers start: 46 outliers final: 24 residues processed: 162 average time/residue: 0.0890 time to fit residues: 21.5419 Evaluate side-chains 140 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 723 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 71 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 11 ASN B 169 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN C 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.148226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.111373 restraints weight = 19930.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.110024 restraints weight = 13877.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.111751 restraints weight = 10423.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112639 restraints weight = 7572.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.112827 restraints weight = 6628.784| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11113 Z= 0.130 Angle : 0.582 8.579 14953 Z= 0.304 Chirality : 0.045 0.182 1695 Planarity : 0.003 0.032 1885 Dihedral : 5.305 48.606 1419 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.16 % Allowed : 21.80 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.95 (0.23), residues: 1302 helix: -0.83 (0.22), residues: 531 sheet: -1.90 (0.38), residues: 196 loop : -1.37 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 795 TYR 0.013 0.001 TYR C 652 PHE 0.015 0.001 PHE C 785 TRP 0.009 0.001 TRP A 215 HIS 0.008 0.001 HIS C 585 Details of bonding type rmsd covalent geometry : bond 0.00298 (11113) covalent geometry : angle 0.58227 (14953) hydrogen bonds : bond 0.03593 ( 349) hydrogen bonds : angle 5.00340 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7693 (tp-100) REVERT: A 180 PRO cc_start: 0.6941 (Cg_endo) cc_final: 0.6692 (Cg_exo) REVERT: A 383 THR cc_start: 0.8752 (t) cc_final: 0.8477 (m) REVERT: B 18 ASN cc_start: 0.8717 (t0) cc_final: 0.8428 (t0) REVERT: B 21 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8541 (ttpp) REVERT: B 112 GLN cc_start: 0.8116 (tp40) cc_final: 0.7886 (tp-100) REVERT: B 139 PHE cc_start: 0.8069 (m-80) cc_final: 0.7728 (m-80) REVERT: B 178 TYR cc_start: 0.8334 (m-80) cc_final: 0.8093 (m-80) REVERT: B 444 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7918 (t) outliers start: 39 outliers final: 23 residues processed: 165 average time/residue: 0.0880 time to fit residues: 21.9204 Evaluate side-chains 139 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 846 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 290 ASN B 169 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.145578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109164 restraints weight = 20162.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.107698 restraints weight = 12962.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.109032 restraints weight = 11396.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.109682 restraints weight = 8221.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.109642 restraints weight = 7302.203| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11113 Z= 0.192 Angle : 0.625 8.487 14953 Z= 0.326 Chirality : 0.046 0.219 1695 Planarity : 0.003 0.026 1885 Dihedral : 5.331 37.900 1419 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.73 % Allowed : 21.80 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.86 (0.23), residues: 1302 helix: -0.70 (0.23), residues: 533 sheet: -1.88 (0.38), residues: 196 loop : -1.37 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 701 TYR 0.020 0.001 TYR B 514 PHE 0.019 0.002 PHE B 372 TRP 0.018 0.002 TRP C 632 HIS 0.003 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00454 (11113) covalent geometry : angle 0.62469 (14953) hydrogen bonds : bond 0.03845 ( 349) hydrogen bonds : angle 5.13611 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7732 (tp-100) REVERT: A 180 PRO cc_start: 0.6931 (Cg_endo) cc_final: 0.6695 (Cg_exo) REVERT: A 383 THR cc_start: 0.8772 (t) cc_final: 0.8458 (m) REVERT: B 18 ASN cc_start: 0.8627 (t0) cc_final: 0.8401 (t0) REVERT: B 21 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8555 (ttpp) REVERT: B 112 GLN cc_start: 0.8167 (tp40) cc_final: 0.7949 (tp-100) REVERT: B 139 PHE cc_start: 0.8162 (m-80) cc_final: 0.7786 (m-80) REVERT: B 304 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8140 (mt) outliers start: 46 outliers final: 31 residues processed: 158 average time/residue: 0.0944 time to fit residues: 22.0503 Evaluate side-chains 145 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 846 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 134 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.146866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110663 restraints weight = 20149.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.109208 restraints weight = 12764.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110610 restraints weight = 10029.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.111492 restraints weight = 7951.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112206 restraints weight = 7322.415| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11113 Z= 0.151 Angle : 0.592 8.465 14953 Z= 0.309 Chirality : 0.045 0.201 1695 Planarity : 0.003 0.032 1885 Dihedral : 5.230 47.997 1418 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.32 % Allowed : 22.61 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.67 (0.23), residues: 1302 helix: -0.50 (0.23), residues: 534 sheet: -1.84 (0.37), residues: 196 loop : -1.29 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 701 TYR 0.017 0.001 TYR B 178 PHE 0.016 0.001 PHE C 785 TRP 0.011 0.002 TRP C 632 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00353 (11113) covalent geometry : angle 0.59219 (14953) hydrogen bonds : bond 0.03617 ( 349) hydrogen bonds : angle 4.98226 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7725 (tp-100) REVERT: A 180 PRO cc_start: 0.6875 (Cg_endo) cc_final: 0.6673 (Cg_exo) REVERT: A 187 LYS cc_start: 0.8702 (ptpt) cc_final: 0.8440 (ptpp) REVERT: A 383 THR cc_start: 0.8777 (t) cc_final: 0.8477 (m) REVERT: B 18 ASN cc_start: 0.8608 (t0) cc_final: 0.8380 (t0) REVERT: B 21 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8476 (ttpp) REVERT: B 64 LYS cc_start: 0.8611 (tppt) cc_final: 0.8340 (mmtm) REVERT: B 112 GLN cc_start: 0.8148 (tp40) cc_final: 0.7933 (tp-100) REVERT: B 134 ASN cc_start: 0.7945 (t0) cc_final: 0.7324 (p0) REVERT: B 304 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8164 (mt) REVERT: C 822 PHE cc_start: 0.7797 (t80) cc_final: 0.7595 (t80) outliers start: 41 outliers final: 30 residues processed: 156 average time/residue: 0.0904 time to fit residues: 20.8023 Evaluate side-chains 147 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 853 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 134 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.146448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110681 restraints weight = 20053.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.108300 restraints weight = 14473.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.109340 restraints weight = 10601.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.110246 restraints weight = 8796.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.110424 restraints weight = 7865.225| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11113 Z= 0.158 Angle : 0.601 8.414 14953 Z= 0.314 Chirality : 0.045 0.185 1695 Planarity : 0.003 0.028 1885 Dihedral : 5.205 45.909 1418 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.16 % Allowed : 22.69 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.57 (0.23), residues: 1302 helix: -0.37 (0.23), residues: 536 sheet: -1.86 (0.38), residues: 192 loop : -1.27 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 701 TYR 0.015 0.001 TYR B 514 PHE 0.018 0.001 PHE C 785 TRP 0.012 0.002 TRP C 632 HIS 0.003 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00371 (11113) covalent geometry : angle 0.60113 (14953) hydrogen bonds : bond 0.03616 ( 349) hydrogen bonds : angle 5.00755 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7747 (tp-100) REVERT: A 228 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7305 (ttt90) REVERT: A 383 THR cc_start: 0.8760 (t) cc_final: 0.8465 (m) REVERT: B 18 ASN cc_start: 0.8541 (t0) cc_final: 0.8296 (t0) REVERT: B 21 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (ttpp) REVERT: B 64 LYS cc_start: 0.8570 (tppt) cc_final: 0.8319 (mmtm) REVERT: B 86 GLU cc_start: 0.6706 (mp0) cc_final: 0.6350 (mp0) REVERT: B 112 GLN cc_start: 0.8172 (tp40) cc_final: 0.7943 (tp-100) REVERT: B 139 PHE cc_start: 0.7861 (m-80) cc_final: 0.7387 (m-80) REVERT: B 304 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8212 (mt) REVERT: C 822 PHE cc_start: 0.7799 (t80) cc_final: 0.7544 (t80) outliers start: 39 outliers final: 32 residues processed: 152 average time/residue: 0.0876 time to fit residues: 20.0622 Evaluate side-chains 151 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 853 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 0.0270 chunk 24 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 126 ASN B 73 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.149395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113450 restraints weight = 19892.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111492 restraints weight = 13909.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.113465 restraints weight = 10863.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114278 restraints weight = 7633.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.114752 restraints weight = 6862.229| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11113 Z= 0.108 Angle : 0.576 8.716 14953 Z= 0.298 Chirality : 0.044 0.220 1695 Planarity : 0.003 0.033 1885 Dihedral : 4.897 39.559 1418 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.43 % Allowed : 23.66 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % 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: -1.36 (0.24), residues: 1302 helix: -0.19 (0.23), residues: 536 sheet: -1.71 (0.38), residues: 192 loop : -1.17 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 701 TYR 0.018 0.001 TYR C 652 PHE 0.018 0.001 PHE C 785 TRP 0.009 0.001 TRP A 215 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00243 (11113) covalent geometry : angle 0.57634 (14953) hydrogen bonds : bond 0.03356 ( 349) hydrogen bonds : angle 4.80559 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.8302 (mp0) cc_final: 0.7907 (mt-10) REVERT: A 228 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7272 (ttt90) REVERT: A 383 THR cc_start: 0.8752 (t) cc_final: 0.8467 (m) REVERT: B 18 ASN cc_start: 0.8488 (t0) cc_final: 0.8280 (t0) REVERT: B 64 LYS cc_start: 0.8572 (tppt) cc_final: 0.8368 (mmtm) REVERT: B 112 GLN cc_start: 0.8141 (tp40) cc_final: 0.7922 (tp-100) REVERT: B 139 PHE cc_start: 0.7839 (m-80) cc_final: 0.7331 (m-80) REVERT: C 822 PHE cc_start: 0.7812 (t80) cc_final: 0.7600 (t80) outliers start: 30 outliers final: 25 residues processed: 151 average time/residue: 0.0912 time to fit residues: 20.5724 Evaluate side-chains 147 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 494 TRP Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 853 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 30 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 116 ASN A 126 ASN A 227 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.147840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.111460 restraints weight = 19904.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.109734 restraints weight = 13786.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111492 restraints weight = 10786.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.112225 restraints weight = 7756.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.112292 restraints weight = 6876.502| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11113 Z= 0.135 Angle : 0.596 8.938 14953 Z= 0.306 Chirality : 0.045 0.190 1695 Planarity : 0.003 0.027 1885 Dihedral : 4.925 36.004 1418 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.35 % Allowed : 24.55 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % 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: -1.28 (0.24), residues: 1302 helix: -0.10 (0.23), residues: 534 sheet: -1.70 (0.37), residues: 196 loop : -1.13 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 753 TYR 0.014 0.001 TYR A 152 PHE 0.019 0.001 PHE C 785 TRP 0.008 0.001 TRP C 632 HIS 0.007 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00312 (11113) covalent geometry : angle 0.59570 (14953) hydrogen bonds : bond 0.03477 ( 349) hydrogen bonds : angle 4.83159 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.8329 (mp0) cc_final: 0.7880 (mt-10) REVERT: A 176 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8269 (mmtm) REVERT: A 383 THR cc_start: 0.8741 (t) cc_final: 0.8460 (m) REVERT: B 21 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8450 (ttpp) REVERT: B 64 LYS cc_start: 0.8560 (tppt) cc_final: 0.8334 (mmtm) REVERT: B 112 GLN cc_start: 0.8109 (tp40) cc_final: 0.7784 (tp-100) REVERT: B 139 PHE cc_start: 0.7890 (m-80) cc_final: 0.7403 (m-80) REVERT: C 710 ARG cc_start: 0.7754 (tpp80) cc_final: 0.7495 (tpp80) REVERT: C 822 PHE cc_start: 0.7728 (t80) cc_final: 0.7523 (t80) outliers start: 29 outliers final: 23 residues processed: 147 average time/residue: 0.0949 time to fit residues: 20.7191 Evaluate side-chains 145 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 853 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 68 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 227 HIS A 483 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN C 814 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.144115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.108641 restraints weight = 20200.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106562 restraints weight = 13181.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.107874 restraints weight = 12965.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.108380 restraints weight = 8901.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108699 restraints weight = 8228.920| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11113 Z= 0.247 Angle : 0.692 8.543 14953 Z= 0.359 Chirality : 0.048 0.185 1695 Planarity : 0.003 0.028 1885 Dihedral : 5.364 37.637 1417 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.43 % Allowed : 24.23 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.55 (0.23), residues: 1302 helix: -0.33 (0.23), residues: 537 sheet: -1.90 (0.37), residues: 196 loop : -1.25 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 753 TYR 0.025 0.002 TYR B 514 PHE 0.025 0.002 PHE B 372 TRP 0.019 0.002 TRP C 632 HIS 0.008 0.002 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00585 (11113) covalent geometry : angle 0.69248 (14953) hydrogen bonds : bond 0.04109 ( 349) hydrogen bonds : angle 5.20690 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.25 seconds wall clock time: 31 minutes 18.04 seconds (1878.04 seconds total)