Starting phenix.real_space_refine on Thu Aug 6 13:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqi_18592/08_2026/8qqi_18592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqi_18592/08_2026/8qqi_18592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qqi_18592/08_2026/8qqi_18592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqi_18592/08_2026/8qqi_18592.map" model { file = "/net/cci-nas-00/data/ceres_data/8qqi_18592/08_2026/8qqi_18592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqi_18592/08_2026/8qqi_18592.cif" } resolution = 2.9 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= 0.039 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: 6 Type Number sf(0) Gaussians P 52 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 9678 2.51 5 N 2784 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15652 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4077 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Chain: "B" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3183 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 16, 'TRANS': 382} Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 531 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'LRL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 5.30, per 1000 atoms: 0.34 Number of scatterers: 15652 At special positions: 0 Unit cell: (126.48, 122.4, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 52 15.00 Mg 2 11.99 O 3076 8.00 N 2784 7.00 C 9678 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: 0.98 Conformation dependent library (CDL) restraints added in 785.4 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 22 sheets defined 49.3% alpha, 11.5% beta 20 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.661A pdb=" N ASP A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.516A pdb=" N ARG A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 82 through 91 removed outlier: 3.668A pdb=" N TYR A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.505A pdb=" N GLU A 133 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.787A pdb=" N LYS A 140 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 141' Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.660A pdb=" N ASN A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.828A pdb=" N GLU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.576A pdb=" N TYR A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 387 removed outlier: 3.609A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 355 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.854A pdb=" N VAL A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.657A pdb=" N ARG A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 427 " --> pdb=" O MET A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.526A pdb=" N GLN A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.573A pdb=" N LYS A 465 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 466 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR A 467 " --> pdb=" O GLN A 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 467' Processing helix chain 'A' and resid 469 through 494 removed outlier: 3.789A pdb=" N LYS A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.576A pdb=" N ARG A 503 " --> pdb=" O MET A 499 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.705A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.658A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 475 removed outlier: 3.708A pdb=" N ALA B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 518 removed outlier: 3.589A pdb=" N HIS B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 516 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.859A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 577 through 596 removed outlier: 3.765A pdb=" N GLU B 581 " --> pdb=" O GLY B 577 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.536A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 609 " --> pdb=" O MET B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.851A pdb=" N SER B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 640 removed outlier: 3.755A pdb=" N VAL B 626 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.662A pdb=" N ILE B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 696 removed outlier: 3.753A pdb=" N ARG B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 690 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.842A pdb=" N SER B 730 " --> pdb=" O LEU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.575A pdb=" N GLU B 744 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 745 " --> pdb=" O LEU B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 741 through 745' Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.507A pdb=" N TRP B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 753 " --> pdb=" O GLN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.724A pdb=" N ASP B 774 " --> pdb=" O ALA B 770 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 775 " --> pdb=" O ILE B 771 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 800 removed outlier: 3.587A pdb=" N ASN B 795 " --> pdb=" O PHE B 791 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 797 " --> pdb=" O GLU B 793 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 798 " --> pdb=" O GLU B 794 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 799 " --> pdb=" O ASN B 795 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 800 " --> pdb=" O ALA B 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 32 removed outlier: 3.660A pdb=" N ASP C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 24 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 removed outlier: 3.515A pdb=" N ARG C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY C 56 " --> pdb=" O MET C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.668A pdb=" N TYR C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.506A pdb=" N GLU C 133 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.787A pdb=" N LYS C 140 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.660A pdb=" N ASN C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.828A pdb=" N GLU C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 312 through 322 removed outlier: 3.576A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 387 removed outlier: 3.609A pdb=" N ILE C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 355 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE C 367 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 Processing helix chain 'C' and resid 402 through 411 removed outlier: 3.855A pdb=" N VAL C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 427 removed outlier: 3.656A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 427 " --> pdb=" O MET C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 removed outlier: 3.526A pdb=" N GLN C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 457 " --> pdb=" O GLN C 453 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.572A pdb=" N LYS C 465 " --> pdb=" O ARG C 462 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 466 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR C 467 " --> pdb=" O GLN C 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 467' Processing helix chain 'C' and resid 469 through 494 removed outlier: 3.788A pdb=" N LYS C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER C 494 " --> pdb=" O ARG C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 513 removed outlier: 3.575A pdb=" N ARG C 503 " --> pdb=" O MET C 499 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 504 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.706A pdb=" N SER D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.658A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER D 463 " --> pdb=" O ASP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 475 removed outlier: 3.708A pdb=" N ALA D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 518 removed outlier: 3.589A pdb=" N HIS D 505 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG D 516 " --> pdb=" O THR D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 524 removed outlier: 3.860A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 577 through 596 removed outlier: 3.764A pdb=" N GLU D 581 " --> pdb=" O GLY D 577 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 609 removed outlier: 3.535A pdb=" N LEU D 606 " --> pdb=" O PRO D 602 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 609 " --> pdb=" O MET D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 621 removed outlier: 3.852A pdb=" N SER D 621 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 640 removed outlier: 3.754A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 683 removed outlier: 3.663A pdb=" N ILE D 682 " --> pdb=" O ASP D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 696 removed outlier: 3.753A pdb=" N ARG D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 690 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 730 removed outlier: 3.841A pdb=" N SER D 730 " --> pdb=" O LEU D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 745 removed outlier: 3.574A pdb=" N GLU D 744 " --> pdb=" O GLY D 741 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET D 745 " --> pdb=" O LEU D 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 745' Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.508A pdb=" N TRP D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 753 " --> pdb=" O GLN D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 removed outlier: 3.725A pdb=" N ASP D 774 " --> pdb=" O ALA D 770 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN D 775 " --> pdb=" O ILE D 771 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 800 removed outlier: 3.587A pdb=" N ASN D 795 " --> pdb=" O PHE D 791 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 797 " --> pdb=" O GLU D 793 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS D 798 " --> pdb=" O GLU D 794 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 799 " --> pdb=" O ASN D 795 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 800 " --> pdb=" O ALA D 796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.554A pdb=" N THR A 9 " --> pdb=" O MET B 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 764 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 765 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA B 530 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 495 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 removed outlier: 3.543A pdb=" N SER A 171 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 173 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 333 removed outlier: 4.670A pdb=" N TYR A 241 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.860A pdb=" N ARG A 245 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 291 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA8, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.631A pdb=" N GLY A 442 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AB1, first strand: chain 'B' and resid 565 through 567 removed outlier: 3.607A pdb=" N PHE B 706 " --> pdb=" O HIS B 567 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 707 " --> pdb=" O GLN B 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.594A pdb=" N GLN B 646 " --> pdb=" O ARG B 667 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.626A pdb=" N THR C 9 " --> pdb=" O MET D 762 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 764 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 765 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D 495 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB5, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB6, first strand: chain 'C' and resid 171 through 174 removed outlier: 3.544A pdb=" N SER C 171 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 173 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 327 through 333 removed outlier: 4.669A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.859A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA C 291 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AC1, first strand: chain 'C' and resid 415 through 416 removed outlier: 3.632A pdb=" N GLY C 442 " --> pdb=" O TYR C 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AC3, first strand: chain 'D' and resid 565 through 567 removed outlier: 3.607A pdb=" N PHE D 706 " --> pdb=" O HIS D 567 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 707 " --> pdb=" O GLN D 714 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 650 removed outlier: 3.594A pdb=" N GLN D 646 " --> pdb=" O ARG D 667 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.35 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: 4053 1.33 - 1.45: 2882 1.45 - 1.57: 8877 1.57 - 1.69: 104 1.69 - 1.81: 110 Bond restraints: 16026 Sorted by residual: bond pdb=" C1' DC E 17 " pdb=" N1 DC E 17 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" C3' DC E 19 " pdb=" C2' DC E 19 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.26e+00 bond pdb=" C5' DG E 20 " pdb=" C4' DG E 20 " ideal model delta sigma weight residual 1.512 1.533 -0.021 7.00e-03 2.04e+04 8.70e+00 bond pdb=" C3' DT F 16 " pdb=" C2' DT F 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.54e+00 bond pdb=" C3' DA E 16 " pdb=" C2' DA E 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.27e+00 ... (remaining 16021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 21087 1.49 - 2.98: 713 2.98 - 4.47: 61 4.47 - 5.96: 19 5.96 - 7.44: 10 Bond angle restraints: 21890 Sorted by residual: angle pdb=" O4' DG F 12 " pdb=" C4' DG F 12 " pdb=" C3' DG F 12 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.49e+01 angle pdb=" N3 DT F 5 " pdb=" C4 DT F 5 " pdb=" O4 DT F 5 " ideal model delta sigma weight residual 119.90 122.74 -2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" O4' DA E 12 " pdb=" C4' DA E 12 " pdb=" C3' DA E 12 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N3 DT E 2 " pdb=" C4 DT E 2 " pdb=" O4 DT E 2 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" O4' DC E 7 " pdb=" C4' DC E 7 " pdb=" C3' DC E 7 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.99e+01 ... (remaining 21885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.43: 9382 32.43 - 64.86: 323 64.86 - 97.29: 9 97.29 - 129.72: 2 129.72 - 162.15: 4 Dihedral angle restraints: 9720 sinusoidal: 4406 harmonic: 5314 Sorted by residual: dihedral pdb=" C9 LRL C 601 " pdb=" N1 LRL C 601 " pdb=" S LRL C 601 " pdb=" O1 LRL C 601 " ideal model delta sinusoidal sigma weight residual -3.80 -165.95 162.15 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C9 LRL A 601 " pdb=" N1 LRL A 601 " pdb=" S LRL A 601 " pdb=" O1 LRL A 601 " ideal model delta sinusoidal sigma weight residual -3.80 -165.94 162.14 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" N1 LRL A 601 " pdb=" C10 LRL A 601 " pdb=" C9 LRL A 601 " pdb=" N3 LRL A 601 " ideal model delta sinusoidal sigma weight residual -49.10 -179.43 130.33 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 9717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1566 0.036 - 0.072: 632 0.072 - 0.108: 158 0.108 - 0.144: 87 0.144 - 0.180: 7 Chirality restraints: 2450 Sorted by residual: chirality pdb=" CB ILE A 203 " pdb=" CA ILE A 203 " pdb=" CG1 ILE A 203 " pdb=" CG2 ILE A 203 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CB ILE C 203 " pdb=" CA ILE C 203 " pdb=" CG1 ILE C 203 " pdb=" CG2 ILE C 203 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ASP A 391 " pdb=" N ASP A 391 " pdb=" C ASP A 391 " pdb=" CB ASP A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 2447 not shown) Planarity restraints: 2680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG E 20 " -0.029 2.00e-02 2.50e+03 1.36e-02 5.55e+00 pdb=" N9 DG E 20 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DG E 20 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DG E 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG E 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG E 20 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG E 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG E 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG E 20 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG E 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG E 20 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG E 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 42 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO C 43 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 42 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 43 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.029 5.00e-02 4.00e+02 ... (remaining 2677 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5195 2.88 - 3.38: 12329 3.38 - 3.89: 23260 3.89 - 4.39: 26227 4.39 - 4.90: 46605 Nonbonded interactions: 113616 Sorted by model distance: nonbonded pdb=" OG1 THR D 565 " pdb=" O GLU D 708 " model vdw 2.370 3.040 nonbonded pdb=" OG1 THR B 565 " pdb=" O GLU B 708 " model vdw 2.370 3.040 nonbonded pdb=" O LEU A 320 " pdb=" OG1 THR A 324 " model vdw 2.395 3.040 nonbonded pdb=" O LEU C 320 " pdb=" OG1 THR C 324 " model vdw 2.396 3.040 nonbonded pdb=" OE2 GLU D 424 " pdb="MG MG D 901 " model vdw 2.397 2.170 ... (remaining 113611 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.190 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.004 0.052 16026 Z= 0.264 Angle : 0.626 7.445 21890 Z= 0.412 Chirality : 0.045 0.180 2450 Planarity : 0.005 0.053 2680 Dihedral : 14.257 162.146 6296 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.16), residues: 1824 helix: -2.25 (0.14), residues: 804 sheet: 0.25 (0.39), residues: 212 loop : -2.01 (0.17), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.016 0.001 TYR D 483 PHE 0.012 0.001 PHE C 368 TRP 0.005 0.001 TRP D 647 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.26 (16026) covalent geometry : angle 0.62633 / 0.41 (21890) hydrogen bonds : bond 0.25933 / 17.31 ( 634) hydrogen bonds : angle 7.15225 / 4.85 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 724 ASP cc_start: 0.7765 (t70) cc_final: 0.7391 (m-30) REVERT: C 52 MET cc_start: 0.9022 (mtp) cc_final: 0.8775 (mtm) REVERT: D 461 MET cc_start: 0.8582 (ttt) cc_final: 0.8288 (ttm) outliers start: 2 outliers final: 1 residues processed: 317 average time/residue: 0.7722 time to fit residues: 262.7742 Evaluate side-chains 140 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 HIS A 267 GLN A 333 ASN A 484 GLN B 411 GLN B 465 GLN B 531 GLN B 542 GLN B 544 GLN B 652 HIS B 679 HIS B 737 GLN C 267 GLN C 333 ASN C 484 GLN D 411 GLN D 531 GLN D 544 GLN D 554 GLN D 567 HIS D 721 GLN D 737 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112724 restraints weight = 19642.469| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.96 r_work: 0.3104 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16026 Z= 0.199 Angle : 0.656 12.127 21890 Z= 0.355 Chirality : 0.047 0.223 2450 Planarity : 0.006 0.057 2680 Dihedral : 16.430 149.134 2657 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.17 % Allowed : 12.37 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.18), residues: 1824 helix: -0.38 (0.17), residues: 820 sheet: -0.56 (0.39), residues: 200 loop : -2.03 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 309 TYR 0.012 0.002 TYR B 483 PHE 0.009 0.002 PHE A 354 TRP 0.012 0.002 TRP B 725 HIS 0.006 0.002 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (16026) covalent geometry : angle 0.65557 / 0.36 (21890) hydrogen bonds : bond 0.07849 / 5.19 ( 634) hydrogen bonds : angle 4.68238 / 3.17 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: A 314 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: A 399 HIS cc_start: 0.7396 (m90) cc_final: 0.6860 (m90) REVERT: B 447 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8099 (tmtt) REVERT: B 724 ASP cc_start: 0.7832 (t70) cc_final: 0.7198 (m-30) REVERT: B 748 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: C 23 ASP cc_start: 0.8177 (m-30) cc_final: 0.7756 (m-30) REVERT: C 121 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6314 (mtm-85) REVERT: C 249 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: C 490 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7580 (ttm170) REVERT: C 511 GLU cc_start: 0.8019 (tt0) cc_final: 0.7463 (mp0) REVERT: D 461 MET cc_start: 0.8547 (ttt) cc_final: 0.8060 (ttm) REVERT: D 483 TYR cc_start: 0.7489 (t80) cc_final: 0.7195 (t80) REVERT: D 588 ASN cc_start: 0.7453 (m-40) cc_final: 0.7223 (m110) REVERT: D 607 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8045 (mtmt) outliers start: 49 outliers final: 21 residues processed: 179 average time/residue: 0.7094 time to fit residues: 137.4051 Evaluate side-chains 159 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 619 ASP Chi-restraints excluded: chain D residue 758 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 652 HIS D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113916 restraints weight = 19659.439| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.84 r_work: 0.3130 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16026 Z= 0.135 Angle : 0.535 9.737 21890 Z= 0.296 Chirality : 0.043 0.210 2450 Planarity : 0.004 0.052 2680 Dihedral : 16.267 141.036 2657 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.72 % Allowed : 13.54 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.19), residues: 1824 helix: 0.51 (0.18), residues: 812 sheet: -0.63 (0.39), residues: 200 loop : -1.92 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 38 TYR 0.012 0.001 TYR A 266 PHE 0.019 0.001 PHE D 706 TRP 0.009 0.001 TRP B 725 HIS 0.006 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (16026) covalent geometry : angle 0.53463 / 0.30 (21890) hydrogen bonds : bond 0.06218 / 4.09 ( 634) hydrogen bonds : angle 4.26009 / 2.86 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: A 201 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: A 314 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 399 HIS cc_start: 0.7365 (m90) cc_final: 0.6840 (m90) REVERT: B 447 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7958 (tmtt) REVERT: B 508 THR cc_start: 0.8186 (m) cc_final: 0.7902 (p) REVERT: B 536 LYS cc_start: 0.8213 (tttm) cc_final: 0.7983 (tttt) REVERT: B 724 ASP cc_start: 0.7838 (t70) cc_final: 0.7199 (m-30) REVERT: B 748 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: C 23 ASP cc_start: 0.8105 (m-30) cc_final: 0.7730 (m-30) REVERT: C 249 GLU cc_start: 0.7442 (pm20) cc_final: 0.7085 (pm20) REVERT: C 285 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7100 (mtt180) REVERT: C 490 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7452 (tmm160) REVERT: C 511 GLU cc_start: 0.7933 (tt0) cc_final: 0.7389 (mp0) REVERT: D 607 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8087 (mtmt) REVERT: D 794 GLU cc_start: 0.7676 (tt0) cc_final: 0.7292 (tp30) outliers start: 42 outliers final: 19 residues processed: 165 average time/residue: 0.7888 time to fit residues: 141.0544 Evaluate side-chains 150 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 619 ASP Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain D residue 758 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 0.0050 chunk 44 optimal weight: 4.9990 chunk 121 optimal weight: 0.0040 chunk 40 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN B 652 HIS D 554 GLN D 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112978 restraints weight = 19705.717| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.88 r_work: 0.3120 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16026 Z= 0.141 Angle : 0.544 10.930 21890 Z= 0.298 Chirality : 0.043 0.165 2450 Planarity : 0.004 0.052 2680 Dihedral : 16.210 137.348 2657 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.30 % Allowed : 13.92 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.19), residues: 1824 helix: 0.90 (0.19), residues: 810 sheet: -0.76 (0.39), residues: 200 loop : -1.90 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 38 TYR 0.012 0.001 TYR B 483 PHE 0.022 0.001 PHE D 706 TRP 0.008 0.001 TRP B 647 HIS 0.005 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (16026) covalent geometry : angle 0.54446 / 0.30 (21890) hydrogen bonds : bond 0.06012 / 3.97 ( 634) hydrogen bonds : angle 4.07794 / 2.74 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7600 (mtp180) REVERT: A 201 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: A 314 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 399 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.7082 (m90) REVERT: B 447 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7944 (tmtt) REVERT: B 508 THR cc_start: 0.8242 (m) cc_final: 0.7948 (p) REVERT: B 536 LYS cc_start: 0.8401 (tttm) cc_final: 0.8138 (tttt) REVERT: B 667 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8174 (ttm170) REVERT: B 724 ASP cc_start: 0.7689 (t70) cc_final: 0.7066 (m-30) REVERT: B 748 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: C 23 ASP cc_start: 0.8107 (m-30) cc_final: 0.7666 (m-30) REVERT: C 249 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: C 285 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7084 (mtt180) REVERT: C 490 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7322 (tmm160) REVERT: C 511 GLU cc_start: 0.7912 (tt0) cc_final: 0.7319 (mp0) REVERT: D 447 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7139 (mmtt) REVERT: D 607 LYS cc_start: 0.8294 (mtpt) cc_final: 0.8017 (mtmt) REVERT: D 706 PHE cc_start: 0.7689 (p90) cc_final: 0.7422 (p90) REVERT: D 794 GLU cc_start: 0.7618 (tt0) cc_final: 0.7252 (tp30) outliers start: 51 outliers final: 24 residues processed: 165 average time/residue: 0.8159 time to fit residues: 145.0481 Evaluate side-chains 159 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain D residue 758 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 133 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 149 optimal weight: 0.0170 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112276 restraints weight = 19575.863| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.85 r_work: 0.3127 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16026 Z= 0.131 Angle : 0.521 8.610 21890 Z= 0.287 Chirality : 0.042 0.164 2450 Planarity : 0.004 0.050 2680 Dihedral : 16.152 134.211 2657 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.98 % Allowed : 14.77 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1824 helix: 1.10 (0.19), residues: 816 sheet: -0.67 (0.38), residues: 204 loop : -1.92 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.012 0.001 TYR B 483 PHE 0.011 0.001 PHE A 368 TRP 0.008 0.001 TRP B 647 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (16026) covalent geometry : angle 0.52111 / 0.29 (21890) hydrogen bonds : bond 0.05674 / 3.74 ( 634) hydrogen bonds : angle 3.96929 / 2.67 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.614 Fit side-chains REVERT: A 121 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7635 (mtp180) REVERT: A 201 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: A 256 ARG cc_start: 0.7145 (mmt-90) cc_final: 0.6705 (mmp-170) REVERT: A 314 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 372 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7807 (ttmm) REVERT: A 395 GLU cc_start: 0.6735 (tp30) cc_final: 0.6402 (tp30) REVERT: A 399 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6843 (m90) REVERT: B 447 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7949 (tmtt) REVERT: B 500 ASP cc_start: 0.7772 (m-30) cc_final: 0.7569 (m-30) REVERT: B 508 THR cc_start: 0.8225 (m) cc_final: 0.7933 (p) REVERT: B 536 LYS cc_start: 0.8372 (tttm) cc_final: 0.8148 (tttt) REVERT: B 667 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7591 (ttp-170) REVERT: B 724 ASP cc_start: 0.7701 (t70) cc_final: 0.7068 (m-30) REVERT: B 740 LYS cc_start: 0.7467 (mttp) cc_final: 0.7150 (mmtp) REVERT: B 748 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: C 23 ASP cc_start: 0.8091 (m-30) cc_final: 0.7649 (m-30) REVERT: C 249 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: C 285 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7104 (mtt180) REVERT: C 490 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7291 (tmm160) REVERT: D 447 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7151 (mmtt) REVERT: D 483 TYR cc_start: 0.7258 (t80) cc_final: 0.7027 (t80) REVERT: D 510 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8177 (mp) REVERT: D 607 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7943 (mtmt) REVERT: D 794 GLU cc_start: 0.7645 (tt0) cc_final: 0.7296 (tp30) outliers start: 46 outliers final: 20 residues processed: 157 average time/residue: 0.7812 time to fit residues: 132.3491 Evaluate side-chains 154 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 134 optimal weight: 0.2980 chunk 138 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 165 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 357 HIS D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114010 restraints weight = 19591.121| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.84 r_work: 0.3149 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16026 Z= 0.115 Angle : 0.499 10.681 21890 Z= 0.275 Chirality : 0.041 0.161 2450 Planarity : 0.004 0.048 2680 Dihedral : 16.079 137.746 2657 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.04 % Allowed : 15.28 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1824 helix: 1.28 (0.19), residues: 818 sheet: -0.72 (0.39), residues: 196 loop : -1.85 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.011 0.001 TYR B 483 PHE 0.024 0.001 PHE D 706 TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.12 (16026) covalent geometry : angle 0.49876 / 0.27 (21890) hydrogen bonds : bond 0.05155 / 3.39 ( 634) hydrogen bonds : angle 3.86446 / 2.59 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.547 Fit side-chains REVERT: A 121 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7631 (mtp180) REVERT: A 201 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: A 314 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: A 395 GLU cc_start: 0.6757 (tp30) cc_final: 0.6431 (tp30) REVERT: A 399 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6811 (m90) REVERT: B 447 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7859 (tmtt) REVERT: B 508 THR cc_start: 0.8185 (m) cc_final: 0.7882 (p) REVERT: B 536 LYS cc_start: 0.8340 (tttm) cc_final: 0.8125 (tttt) REVERT: B 667 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8087 (ttm170) REVERT: B 724 ASP cc_start: 0.7711 (t70) cc_final: 0.7060 (m-30) REVERT: B 740 LYS cc_start: 0.7459 (mttp) cc_final: 0.7180 (mmtp) REVERT: B 748 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: C 23 ASP cc_start: 0.8107 (m-30) cc_final: 0.7648 (m-30) REVERT: C 249 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: C 285 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7086 (mtt180) REVERT: C 298 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.5436 (mptt) REVERT: D 447 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7174 (mmtt) REVERT: D 510 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8235 (mp) REVERT: D 607 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7841 (mtmt) REVERT: D 781 MET cc_start: 0.8180 (mmt) cc_final: 0.7807 (mmt) REVERT: D 794 GLU cc_start: 0.7628 (tt0) cc_final: 0.7295 (tp30) outliers start: 47 outliers final: 22 residues processed: 156 average time/residue: 0.7592 time to fit residues: 127.8317 Evaluate side-chains 156 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 182 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 517 GLN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112806 restraints weight = 19513.823| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.88 r_work: 0.3133 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16026 Z= 0.125 Angle : 0.514 10.231 21890 Z= 0.281 Chirality : 0.042 0.157 2450 Planarity : 0.004 0.048 2680 Dihedral : 16.056 137.206 2657 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.91 % Allowed : 15.61 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1824 helix: 1.36 (0.19), residues: 818 sheet: -0.64 (0.39), residues: 200 loop : -1.88 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.013 0.001 TYR B 483 PHE 0.022 0.001 PHE D 706 TRP 0.007 0.001 TRP B 647 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (16026) covalent geometry : angle 0.51365 / 0.28 (21890) hydrogen bonds : bond 0.05364 / 3.54 ( 634) hydrogen bonds : angle 3.82258 / 2.56 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 0.438 Fit side-chains REVERT: A 121 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7650 (mtp180) REVERT: A 201 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: A 314 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: A 395 GLU cc_start: 0.6840 (tp30) cc_final: 0.6639 (tp30) REVERT: A 399 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.7024 (m90) REVERT: B 447 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7871 (tmtt) REVERT: B 508 THR cc_start: 0.8188 (m) cc_final: 0.7885 (p) REVERT: B 536 LYS cc_start: 0.8362 (tttm) cc_final: 0.8152 (tttt) REVERT: B 667 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8115 (ttm170) REVERT: B 724 ASP cc_start: 0.7732 (t70) cc_final: 0.7074 (m-30) REVERT: B 740 LYS cc_start: 0.7475 (mttp) cc_final: 0.7211 (mmtp) REVERT: B 748 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: C 23 ASP cc_start: 0.8124 (m-30) cc_final: 0.7654 (m-30) REVERT: C 249 GLU cc_start: 0.7488 (pm20) cc_final: 0.7065 (pm20) REVERT: C 285 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7091 (mtt180) REVERT: C 298 LYS cc_start: 0.6564 (OUTLIER) cc_final: 0.5435 (mptt) REVERT: C 490 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7286 (tmm160) REVERT: D 447 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7200 (mmtt) REVERT: D 510 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8204 (mp) REVERT: D 588 ASN cc_start: 0.7343 (m-40) cc_final: 0.7111 (m110) REVERT: D 607 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7895 (mtmt) REVERT: D 794 GLU cc_start: 0.7638 (tt0) cc_final: 0.7301 (tp30) outliers start: 45 outliers final: 23 residues processed: 157 average time/residue: 0.7425 time to fit residues: 125.6179 Evaluate side-chains 155 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 58 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 52 optimal weight: 0.0570 chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 176 optimal weight: 0.3980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.150686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115428 restraints weight = 19385.520| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.83 r_work: 0.3210 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16026 Z= 0.109 Angle : 0.486 10.206 21890 Z= 0.268 Chirality : 0.041 0.153 2450 Planarity : 0.004 0.044 2680 Dihedral : 15.984 141.925 2657 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.53 % Allowed : 15.80 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1824 helix: 1.50 (0.19), residues: 816 sheet: -0.74 (0.39), residues: 196 loop : -1.79 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 256 TYR 0.012 0.001 TYR B 483 PHE 0.023 0.001 PHE D 706 TRP 0.007 0.001 TRP B 647 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (16026) covalent geometry : angle 0.48580 / 0.27 (21890) hydrogen bonds : bond 0.04771 / 3.13 ( 634) hydrogen bonds : angle 3.74091 / 2.51 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.432 Fit side-chains REVERT: A 121 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7719 (mtp180) REVERT: A 201 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: A 226 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7766 (mtp85) REVERT: A 314 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: A 399 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.7030 (m90) REVERT: B 447 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7954 (tmtt) REVERT: B 487 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7936 (mppt) REVERT: B 508 THR cc_start: 0.8188 (m) cc_final: 0.7962 (p) REVERT: B 667 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8119 (ttm170) REVERT: B 724 ASP cc_start: 0.7783 (t70) cc_final: 0.7113 (m-30) REVERT: B 740 LYS cc_start: 0.7503 (mttp) cc_final: 0.7248 (mmtp) REVERT: B 748 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: C 23 ASP cc_start: 0.8245 (m-30) cc_final: 0.7804 (m-30) REVERT: C 249 GLU cc_start: 0.7717 (pm20) cc_final: 0.7398 (pm20) REVERT: C 285 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7182 (mtt180) REVERT: C 298 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.5577 (mptt) REVERT: C 490 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7301 (tmm160) REVERT: D 447 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7380 (mmtt) REVERT: D 510 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8336 (mp) REVERT: D 588 ASN cc_start: 0.7413 (m-40) cc_final: 0.7203 (m110) REVERT: D 607 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8055 (mtmt) REVERT: D 794 GLU cc_start: 0.7793 (tt0) cc_final: 0.7489 (tp30) outliers start: 39 outliers final: 20 residues processed: 149 average time/residue: 0.7625 time to fit residues: 122.5646 Evaluate side-chains 152 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 23 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.150058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114551 restraints weight = 19387.386| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.84 r_work: 0.3198 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16026 Z= 0.116 Angle : 0.497 9.880 21890 Z= 0.273 Chirality : 0.041 0.152 2450 Planarity : 0.004 0.048 2680 Dihedral : 15.973 141.241 2657 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.40 % Allowed : 16.19 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1824 helix: 1.54 (0.19), residues: 816 sheet: -0.74 (0.39), residues: 196 loop : -1.78 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 256 TYR 0.012 0.001 TYR B 483 PHE 0.021 0.001 PHE D 706 TRP 0.007 0.001 TRP B 647 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (16026) covalent geometry : angle 0.49718 / 0.27 (21890) hydrogen bonds : bond 0.04978 / 3.28 ( 634) hydrogen bonds : angle 3.72007 / 2.49 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7713 (mtp180) REVERT: A 201 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: A 226 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7784 (mtp85) REVERT: A 314 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 399 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.7054 (m90) REVERT: B 447 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7896 (tmtt) REVERT: B 487 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7972 (mppt) REVERT: B 508 THR cc_start: 0.8212 (m) cc_final: 0.7975 (p) REVERT: B 667 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8158 (ttm170) REVERT: B 724 ASP cc_start: 0.7777 (t70) cc_final: 0.7107 (m-30) REVERT: B 740 LYS cc_start: 0.7517 (mttp) cc_final: 0.7259 (mmtp) REVERT: B 748 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: C 249 GLU cc_start: 0.7731 (pm20) cc_final: 0.7444 (pm20) REVERT: C 285 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7195 (mtt180) REVERT: C 298 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.5583 (mptt) REVERT: C 490 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7363 (tmm160) REVERT: D 447 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7391 (mmtt) REVERT: D 510 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8327 (mp) REVERT: D 588 ASN cc_start: 0.7407 (m-40) cc_final: 0.7191 (m110) REVERT: D 607 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8076 (mtmt) REVERT: D 794 GLU cc_start: 0.7828 (tt0) cc_final: 0.7500 (tp30) outliers start: 37 outliers final: 19 residues processed: 150 average time/residue: 0.7680 time to fit residues: 124.2903 Evaluate side-chains 151 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 165 optimal weight: 0.2980 chunk 144 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 135 optimal weight: 0.0060 chunk 123 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 132 optimal weight: 0.0060 chunk 42 optimal weight: 0.5980 overall best weight: 0.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.154964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121450 restraints weight = 19316.090| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.81 r_work: 0.3250 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16026 Z= 0.093 Angle : 0.452 9.944 21890 Z= 0.251 Chirality : 0.039 0.154 2450 Planarity : 0.003 0.038 2680 Dihedral : 15.860 152.963 2657 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.10 % Allowed : 17.42 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1824 helix: 1.74 (0.19), residues: 816 sheet: -0.64 (0.38), residues: 204 loop : -1.65 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.010 0.001 TYR B 483 PHE 0.019 0.001 PHE D 706 TRP 0.008 0.001 TRP B 647 HIS 0.003 0.000 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00159 / 0.09 (16026) covalent geometry : angle 0.45236 / 0.25 (21890) hydrogen bonds : bond 0.03721 / 2.43 ( 634) hydrogen bonds : angle 3.56939 / 2.38 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7741 (mtp180) REVERT: A 226 ARG cc_start: 0.8131 (mtt90) cc_final: 0.7812 (mtp85) REVERT: A 395 GLU cc_start: 0.6835 (tp30) cc_final: 0.6620 (tp30) REVERT: A 399 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6812 (m90) REVERT: B 447 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7977 (tmtt) REVERT: B 487 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7932 (mppt) REVERT: B 500 ASP cc_start: 0.7562 (m-30) cc_final: 0.7286 (m-30) REVERT: B 667 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: B 724 ASP cc_start: 0.7816 (t70) cc_final: 0.7074 (m-30) REVERT: B 740 LYS cc_start: 0.7432 (mttp) cc_final: 0.7170 (mmtp) REVERT: B 748 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: C 249 GLU cc_start: 0.7646 (pm20) cc_final: 0.7339 (pm20) REVERT: C 283 GLU cc_start: 0.7222 (mp0) cc_final: 0.6905 (mp0) REVERT: D 447 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7305 (mmtt) REVERT: D 588 ASN cc_start: 0.7508 (m-40) cc_final: 0.7299 (m110) REVERT: D 607 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8061 (mtmt) REVERT: D 794 GLU cc_start: 0.7794 (tt0) cc_final: 0.7487 (tp30) outliers start: 17 outliers final: 7 residues processed: 142 average time/residue: 0.8493 time to fit residues: 130.1108 Evaluate side-chains 129 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 521 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN D 554 GLN D 795 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116840 restraints weight = 19204.701| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.85 r_work: 0.3187 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16026 Z= 0.119 Angle : 0.499 9.496 21890 Z= 0.273 Chirality : 0.041 0.165 2450 Planarity : 0.004 0.048 2680 Dihedral : 15.930 145.589 2657 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.04 % Allowed : 18.07 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1824 helix: 1.70 (0.19), residues: 820 sheet: -0.67 (0.39), residues: 196 loop : -1.72 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 256 TYR 0.012 0.001 TYR B 483 PHE 0.018 0.001 PHE D 706 TRP 0.006 0.001 TRP B 647 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (16026) covalent geometry : angle 0.49929 / 0.27 (21890) hydrogen bonds : bond 0.04823 / 3.20 ( 634) hydrogen bonds : angle 3.63227 / 2.43 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5012.73 seconds wall clock time: 85 minutes 46.82 seconds (5146.82 seconds total)