Starting phenix.real_space_refine on Sun Aug 24 00:02:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqi_18592/08_2025/8qqi_18592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqi_18592/08_2025/8qqi_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qqi_18592/08_2025/8qqi_18592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqi_18592/08_2025/8qqi_18592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qqi_18592/08_2025/8qqi_18592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqi_18592/08_2025/8qqi_18592.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.46, per 1000 atoms: 0.35 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: 1.21 Conformation dependent library (CDL) restraints added in 565.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.82 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: 2.83 Time building geometry restraints manager: 1.57 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=" CA GLY B 577 " pdb=" C GLY B 577 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.65e+00 bond pdb=" CA GLY D 577 " pdb=" C GLY D 577 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.23e+00 bond pdb=" N GLY D 577 " pdb=" CA GLY D 577 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.14e+00 bond pdb=" N GLY B 577 " pdb=" CA GLY B 577 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.03e+00 bond pdb=" O1 LRL A 601 " pdb=" S LRL A 601 " ideal model delta sigma weight residual 1.457 1.430 0.027 2.00e-02 2.50e+03 1.81e+00 ... (remaining 16021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 21231 1.49 - 2.98: 572 2.98 - 4.47: 58 4.47 - 5.96: 19 5.96 - 7.44: 10 Bond angle restraints: 21890 Sorted by residual: angle pdb=" C ASN A 165 " pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C ASN C 165 " pdb=" N LEU C 166 " pdb=" CA LEU C 166 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" N GLY B 577 " pdb=" CA GLY B 577 " pdb=" C GLY B 577 " ideal model delta sigma weight residual 111.67 115.22 -3.55 9.20e-01 1.18e+00 1.49e+01 angle pdb=" N GLY D 577 " pdb=" CA GLY D 577 " pdb=" C GLY D 577 " ideal model delta sigma weight residual 111.67 115.20 -3.53 9.20e-01 1.18e+00 1.47e+01 angle pdb=" CA ASN C 169 " pdb=" C ASN C 169 " pdb=" N GLY C 170 " ideal model delta sigma weight residual 115.90 120.28 -4.38 1.21e+00 6.83e-01 1.31e+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: 1620 0.036 - 0.072: 610 0.072 - 0.108: 131 0.108 - 0.144: 82 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: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.980 Find NCS groups from input model: 0.230 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.003 0.039 16026 Z= 0.165 Angle : 0.597 7.445 21890 Z= 0.331 Chirality : 0.043 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 aren 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 covalent geometry : bond 0.00322 (16026) covalent geometry : angle 0.59707 (21890) hydrogen bonds : bond 0.25933 ( 634) hydrogen bonds : angle 7.15225 ( 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 : 0.623 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: 0.8774 (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: 0.8519 time to fit residues: 289.3358 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 : 0.591 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 333 ASN A 389 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 = 0.3714 r_free = 0.3714 target = 0.145743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110671 restraints weight = 19617.710| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.90 r_work: 0.3076 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16026 Z= 0.197 Angle : 0.633 9.305 21890 Z= 0.338 Chirality : 0.044 0.181 2450 Planarity : 0.006 0.057 2680 Dihedral : 16.329 137.651 2657 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.30 % Allowed : 12.69 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.18), residues: 1824 helix: -0.37 (0.17), residues: 814 sheet: -0.43 (0.39), residues: 204 loop : -2.07 (0.18), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 38 TYR 0.012 0.002 TYR A 266 PHE 0.010 0.002 PHE A 330 TRP 0.015 0.002 TRP B 725 HIS 0.007 0.002 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00465 (16026) covalent geometry : angle 0.63349 (21890) hydrogen bonds : bond 0.07560 ( 634) hydrogen bonds : angle 4.50538 ( 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 206 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: A 314 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: A 395 GLU cc_start: 0.6965 (tp30) cc_final: 0.6720 (tp30) REVERT: B 447 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8042 (tmtt) REVERT: B 508 THR cc_start: 0.8305 (m) cc_final: 0.8031 (p) REVERT: B 667 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7983 (ttp-170) REVERT: B 724 ASP cc_start: 0.7891 (t70) cc_final: 0.7255 (m-30) REVERT: B 748 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 783 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7132 (m-30) REVERT: C 23 ASP cc_start: 0.8104 (m-30) cc_final: 0.7732 (m-30) REVERT: C 121 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7918 (mtm-85) REVERT: C 249 GLU cc_start: 0.7477 (pm20) cc_final: 0.7088 (pm20) REVERT: C 285 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7149 (mtt180) REVERT: C 401 PRO cc_start: 0.8612 (Cg_exo) cc_final: 0.8400 (Cg_endo) REVERT: C 490 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7593 (tmm160) REVERT: C 511 GLU cc_start: 0.7962 (tt0) cc_final: 0.7395 (mp0) REVERT: D 447 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7189 (mmtt) REVERT: D 538 LYS cc_start: 0.8166 (mttp) cc_final: 0.7950 (mtmt) REVERT: D 544 GLN cc_start: 0.8122 (mt0) cc_final: 0.7911 (mt0) REVERT: D 588 ASN cc_start: 0.7530 (m-40) cc_final: 0.7298 (m110) REVERT: D 607 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8188 (mtmt) REVERT: D 617 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6510 (tt0) REVERT: D 794 GLU cc_start: 0.7738 (tt0) cc_final: 0.7338 (tp30) outliers start: 51 outliers final: 23 residues processed: 192 average time/residue: 0.8666 time to fit residues: 179.1639 Evaluate side-chains 163 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 783 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 250 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 463 SER Chi-restraints excluded: chain D residue 547 LYS Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 617 GLU Chi-restraints excluded: chain D residue 724 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: 1.9990 chunk 142 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107476 restraints weight = 19756.679| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.87 r_work: 0.3030 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 16026 Z= 0.245 Angle : 0.689 9.189 21890 Z= 0.368 Chirality : 0.047 0.157 2450 Planarity : 0.006 0.062 2680 Dihedral : 16.444 143.743 2657 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.27 % Allowed : 13.34 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.19), residues: 1824 helix: 0.14 (0.18), residues: 820 sheet: -1.18 (0.34), residues: 256 loop : -2.15 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 38 TYR 0.015 0.002 TYR B 483 PHE 0.018 0.002 PHE D 706 TRP 0.012 0.002 TRP D 751 HIS 0.009 0.002 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00596 (16026) covalent geometry : angle 0.68938 (21890) hydrogen bonds : bond 0.08498 ( 634) hydrogen bonds : angle 4.42922 ( 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 205 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7735 (mtp180) REVERT: A 201 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 226 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7823 (mtp85) REVERT: A 314 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: A 372 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7873 (ttmm) REVERT: A 399 HIS cc_start: 0.7712 (m90) cc_final: 0.7079 (m90) REVERT: B 536 LYS cc_start: 0.8506 (tttm) cc_final: 0.8179 (tttt) REVERT: B 667 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8162 (ttp-170) REVERT: B 724 ASP cc_start: 0.7875 (t70) cc_final: 0.7238 (m-30) REVERT: B 740 LYS cc_start: 0.7695 (mttp) cc_final: 0.7389 (mttp) REVERT: B 748 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: C 249 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: C 285 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7185 (mtt180) REVERT: C 298 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.5462 (mptt) REVERT: C 490 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7365 (ttm170) REVERT: C 511 GLU cc_start: 0.8007 (tt0) cc_final: 0.7380 (mp0) REVERT: D 447 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7192 (mmtt) REVERT: D 588 ASN cc_start: 0.7617 (m-40) cc_final: 0.7365 (m110) REVERT: D 774 ASP cc_start: 0.7770 (p0) cc_final: 0.7230 (t70) outliers start: 66 outliers final: 35 residues processed: 188 average time/residue: 0.8957 time to fit residues: 181.2031 Evaluate side-chains 166 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 147 ASP 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 452 GLU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 510 LEU 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 B residue 765 VAL Chi-restraints excluded: chain C residue 16 GLU 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 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 345 MET 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 463 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 547 LYS Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 663 ILE 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: 0.8980 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 ASN C 357 HIS D 554 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109922 restraints weight = 19735.895| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.87 r_work: 0.3068 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16026 Z= 0.163 Angle : 0.571 9.614 21890 Z= 0.307 Chirality : 0.042 0.150 2450 Planarity : 0.005 0.056 2680 Dihedral : 16.195 134.762 2657 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.82 % Allowed : 14.64 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1824 helix: 0.64 (0.19), residues: 820 sheet: -0.94 (0.35), residues: 232 loop : -2.10 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 628 TYR 0.014 0.001 TYR B 483 PHE 0.018 0.001 PHE D 706 TRP 0.011 0.001 TRP B 647 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00374 (16026) covalent geometry : angle 0.57102 (21890) hydrogen bonds : bond 0.06559 ( 634) hydrogen bonds : angle 4.14059 ( 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 185 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 126 time to evaluate : 0.636 Fit side-chains REVERT: A 121 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7742 (mtp180) REVERT: A 201 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: A 226 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7758 (mtp85) REVERT: A 372 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7859 (ttmm) REVERT: A 399 HIS cc_start: 0.7612 (m90) cc_final: 0.7327 (m90) REVERT: B 508 THR cc_start: 0.8262 (m) cc_final: 0.7973 (p) REVERT: B 536 LYS cc_start: 0.8488 (tttm) cc_final: 0.8217 (tttt) REVERT: B 667 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8074 (ttp-170) REVERT: B 724 ASP cc_start: 0.7882 (t70) cc_final: 0.7196 (m-30) REVERT: B 740 LYS cc_start: 0.7660 (mttp) cc_final: 0.7387 (mttp) REVERT: B 748 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: B 783 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: C 121 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6852 (mtm-85) REVERT: C 147 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: C 157 ASP cc_start: 0.8071 (t70) cc_final: 0.7846 (t0) REVERT: C 285 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7187 (mtt180) REVERT: C 298 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.5247 (mptt) REVERT: C 490 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7360 (ttm170) REVERT: D 447 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7295 (mmtt) REVERT: D 588 ASN cc_start: 0.7611 (m-40) cc_final: 0.7364 (m110) REVERT: D 597 MET cc_start: 0.8106 (mtm) cc_final: 0.7805 (mtm) REVERT: D 706 PHE cc_start: 0.7854 (p90) cc_final: 0.7642 (p90) REVERT: D 774 ASP cc_start: 0.7597 (p0) cc_final: 0.7161 (t70) outliers start: 59 outliers final: 28 residues processed: 169 average time/residue: 0.9035 time to fit residues: 164.6395 Evaluate side-chains 161 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 284 LYS Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 510 LEU 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 707 ILE 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 B residue 783 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 250 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 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 463 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 5.9990 chunk 166 optimal weight: 0.0270 chunk 133 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 74 optimal weight: 0.2980 chunk 149 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113878 restraints weight = 19336.098| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.83 r_work: 0.3130 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16026 Z= 0.120 Angle : 0.506 10.909 21890 Z= 0.271 Chirality : 0.040 0.146 2450 Planarity : 0.004 0.050 2680 Dihedral : 15.938 139.985 2657 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.78 % Allowed : 15.74 % 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 aren not related in a simple way. whole: -0.65 (0.19), residues: 1824 helix: 1.08 (0.19), residues: 818 sheet: -0.87 (0.36), residues: 228 loop : -1.98 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 628 TYR 0.013 0.001 TYR B 483 PHE 0.015 0.001 PHE D 706 TRP 0.009 0.001 TRP B 647 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00257 (16026) covalent geometry : angle 0.50562 (21890) hydrogen bonds : bond 0.05139 ( 634) hydrogen bonds : angle 3.87194 ( 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 170 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.545 Fit side-chains REVERT: A 121 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7692 (mtp180) REVERT: A 226 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7705 (mtp85) REVERT: A 256 ARG cc_start: 0.7353 (mmm160) cc_final: 0.6694 (mmt180) REVERT: A 399 HIS cc_start: 0.7466 (m90) cc_final: 0.7148 (m90) REVERT: B 447 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8323 (tmtt) REVERT: B 450 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7840 (pt) REVERT: B 667 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8308 (ttm170) REVERT: B 724 ASP cc_start: 0.7716 (t70) cc_final: 0.6991 (m-30) REVERT: B 740 LYS cc_start: 0.7595 (mttp) cc_final: 0.7347 (mttp) REVERT: B 748 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: C 23 ASP cc_start: 0.8078 (m-30) cc_final: 0.7676 (m-30) REVERT: C 285 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7138 (mtt180) REVERT: C 298 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.5221 (mptt) REVERT: C 490 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7222 (tmm160) REVERT: D 447 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7352 (mmtt) REVERT: D 588 ASN cc_start: 0.7580 (m-40) cc_final: 0.7326 (m110) REVERT: D 597 MET cc_start: 0.8102 (mtm) cc_final: 0.7847 (mtm) REVERT: D 774 ASP cc_start: 0.7508 (p0) cc_final: 0.7174 (t70) REVERT: D 794 GLU cc_start: 0.7678 (tt0) cc_final: 0.7436 (tp30) outliers start: 43 outliers final: 24 residues processed: 159 average time/residue: 0.8685 time to fit residues: 148.6997 Evaluate side-chains 149 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 250 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 616 THR 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 248 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 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 557 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 134 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116483 restraints weight = 19368.902| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.81 r_work: 0.3183 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16026 Z= 0.101 Angle : 0.467 10.032 21890 Z= 0.252 Chirality : 0.039 0.144 2450 Planarity : 0.004 0.046 2680 Dihedral : 15.742 149.224 2657 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.72 % Allowed : 16.26 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.20), residues: 1824 helix: 1.37 (0.19), residues: 820 sheet: -0.65 (0.40), residues: 188 loop : -1.86 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 628 TYR 0.012 0.001 TYR B 483 PHE 0.019 0.001 PHE D 706 TRP 0.008 0.001 TRP B 647 HIS 0.002 0.001 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00207 (16026) covalent geometry : angle 0.46699 (21890) hydrogen bonds : bond 0.04246 ( 634) hydrogen bonds : angle 3.66291 ( 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 169 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.634 Fit side-chains REVERT: A 121 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7714 (mtp180) REVERT: A 226 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7665 (mtp85) REVERT: A 345 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8728 (mtp) REVERT: A 395 GLU cc_start: 0.6842 (tp30) cc_final: 0.6606 (tp30) REVERT: A 399 HIS cc_start: 0.7368 (m90) cc_final: 0.6997 (m90) REVERT: B 447 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8391 (tmtt) REVERT: B 569 ASN cc_start: 0.7996 (p0) cc_final: 0.7691 (p0) REVERT: B 724 ASP cc_start: 0.7697 (t70) cc_final: 0.6951 (m-30) REVERT: B 740 LYS cc_start: 0.7521 (mttp) cc_final: 0.7294 (mttp) REVERT: B 748 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: C 23 ASP cc_start: 0.8031 (m-30) cc_final: 0.7623 (m-30) REVERT: C 249 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: C 283 GLU cc_start: 0.7119 (mp0) cc_final: 0.6870 (mp0) REVERT: C 285 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7094 (mtt180) REVERT: C 298 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.5135 (mptt) REVERT: D 447 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7374 (mmtt) REVERT: D 588 ASN cc_start: 0.7563 (m-40) cc_final: 0.7363 (m110) REVERT: D 774 ASP cc_start: 0.7441 (p0) cc_final: 0.7130 (t70) outliers start: 42 outliers final: 17 residues processed: 155 average time/residue: 0.9010 time to fit residues: 150.4396 Evaluate side-chains 141 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER 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 248 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 298 LYS Chi-restraints excluded: chain D residue 453 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 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 = 0.3805 r_free = 0.3805 target = 0.148720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113291 restraints weight = 19257.425| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.77 r_work: 0.3179 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3124 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 : 0.507 9.474 21890 Z= 0.272 Chirality : 0.040 0.144 2450 Planarity : 0.004 0.048 2680 Dihedral : 15.875 140.846 2657 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.46 % Allowed : 16.84 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1824 helix: 1.40 (0.19), residues: 818 sheet: -0.56 (0.39), residues: 192 loop : -1.90 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.013 0.001 TYR B 483 PHE 0.012 0.001 PHE A 368 TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00275 (16026) covalent geometry : angle 0.50689 (21890) hydrogen bonds : bond 0.05195 ( 634) hydrogen bonds : angle 3.73714 ( 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 160 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7770 (mtp180) REVERT: A 226 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7762 (mtp85) REVERT: A 395 GLU cc_start: 0.6910 (tp30) cc_final: 0.6681 (tp30) REVERT: A 399 HIS cc_start: 0.7420 (m90) cc_final: 0.7065 (m90) REVERT: B 447 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8448 (tmtt) REVERT: B 569 ASN cc_start: 0.8028 (p0) cc_final: 0.7727 (p0) REVERT: B 724 ASP cc_start: 0.7855 (t70) cc_final: 0.7093 (m-30) REVERT: B 740 LYS cc_start: 0.7572 (mttp) cc_final: 0.7338 (mttp) REVERT: B 748 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: C 249 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: C 285 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7155 (mtt180) REVERT: C 298 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5148 (mptt) REVERT: D 447 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7416 (mmtt) REVERT: D 706 PHE cc_start: 0.7533 (p90) cc_final: 0.7325 (p90) REVERT: D 774 ASP cc_start: 0.7612 (p0) cc_final: 0.7213 (t70) REVERT: D 794 GLU cc_start: 0.7975 (tp30) cc_final: 0.7172 (mt-10) outliers start: 38 outliers final: 22 residues processed: 151 average time/residue: 0.8970 time to fit residues: 145.9926 Evaluate side-chains 149 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER 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 16 GLU Chi-restraints excluded: chain C residue 248 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 298 LYS Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 544 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 58 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 144 optimal weight: 0.3980 chunk 176 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 GLN D 588 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115050 restraints weight = 19430.325| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.82 r_work: 0.3153 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3156 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= 0.116 Angle : 0.488 9.211 21890 Z= 0.264 Chirality : 0.040 0.144 2450 Planarity : 0.004 0.047 2680 Dihedral : 15.818 142.017 2657 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.53 % Allowed : 17.29 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1824 helix: 1.51 (0.19), residues: 816 sheet: -0.51 (0.39), residues: 192 loop : -1.82 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 256 TYR 0.013 0.001 TYR B 483 PHE 0.012 0.001 PHE A 368 TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00249 (16026) covalent geometry : angle 0.48815 (21890) hydrogen bonds : bond 0.04914 ( 634) hydrogen bonds : angle 3.69841 ( 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 163 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: A 226 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7728 (mtp85) REVERT: A 395 GLU cc_start: 0.6819 (tp30) cc_final: 0.6569 (tp30) REVERT: A 399 HIS cc_start: 0.7370 (m90) cc_final: 0.7008 (m90) REVERT: A 452 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: B 569 ASN cc_start: 0.8018 (p0) cc_final: 0.7737 (p0) REVERT: B 667 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8177 (ttm170) REVERT: B 724 ASP cc_start: 0.7704 (t70) cc_final: 0.6953 (m-30) REVERT: B 740 LYS cc_start: 0.7482 (mttp) cc_final: 0.7273 (mttp) REVERT: B 748 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: C 249 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: C 285 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7062 (mtt180) REVERT: C 298 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.5205 (mptt) REVERT: C 490 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7177 (tmm160) REVERT: D 447 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7376 (mmtt) REVERT: D 794 GLU cc_start: 0.7893 (tp30) cc_final: 0.7209 (mt-10) outliers start: 39 outliers final: 26 residues processed: 154 average time/residue: 0.8658 time to fit residues: 143.3917 Evaluate side-chains 153 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU 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 C residue 16 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 248 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 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 544 GLN 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: 1.9990 chunk 157 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113027 restraints weight = 19370.722| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.77 r_work: 0.3176 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3184 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= 0.124 Angle : 0.506 9.816 21890 Z= 0.272 Chirality : 0.040 0.145 2450 Planarity : 0.004 0.048 2680 Dihedral : 15.863 139.516 2657 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.46 % Allowed : 17.23 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1824 helix: 1.52 (0.19), residues: 816 sheet: -0.53 (0.39), residues: 192 loop : -1.84 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 256 TYR 0.013 0.001 TYR B 483 PHE 0.019 0.001 PHE D 706 TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00271 (16026) covalent geometry : angle 0.50609 (21890) hydrogen bonds : bond 0.05200 ( 634) hydrogen bonds : angle 3.73434 ( 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 159 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7785 (mtp180) REVERT: A 226 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7788 (mtp85) REVERT: A 395 GLU cc_start: 0.6878 (tp30) cc_final: 0.6644 (tp30) REVERT: A 399 HIS cc_start: 0.7470 (m90) cc_final: 0.7121 (m90) REVERT: A 452 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: B 569 ASN cc_start: 0.7964 (p0) cc_final: 0.7719 (p0) REVERT: B 667 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8276 (ttm170) REVERT: B 724 ASP cc_start: 0.7850 (t70) cc_final: 0.7089 (m-30) REVERT: B 740 LYS cc_start: 0.7549 (mttp) cc_final: 0.7317 (mttp) REVERT: B 748 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: C 249 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: C 283 GLU cc_start: 0.7192 (mp0) cc_final: 0.6885 (mp0) REVERT: C 285 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7187 (mtt180) REVERT: C 298 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.5115 (mptt) REVERT: C 490 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7355 (tmm160) REVERT: D 447 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7416 (mmtt) REVERT: D 794 GLU cc_start: 0.8075 (tp30) cc_final: 0.7279 (mt-10) outliers start: 38 outliers final: 26 residues processed: 151 average time/residue: 0.9200 time to fit residues: 149.6525 Evaluate side-chains 151 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU 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 C residue 16 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 248 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 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 544 GLN 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: 1.9990 chunk 57 optimal weight: 0.8980 chunk 165 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 42 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114574 restraints weight = 19251.106| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.83 r_work: 0.3193 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16026 Z= 0.113 Angle : 0.492 9.577 21890 Z= 0.264 Chirality : 0.040 0.144 2450 Planarity : 0.004 0.046 2680 Dihedral : 15.786 142.891 2657 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.33 % Allowed : 17.36 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.20), residues: 1824 helix: 1.59 (0.19), residues: 816 sheet: -0.48 (0.39), residues: 192 loop : -1.81 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 628 TYR 0.013 0.001 TYR B 483 PHE 0.012 0.001 PHE A 368 TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00241 (16026) covalent geometry : angle 0.49182 (21890) hydrogen bonds : bond 0.04781 ( 634) hydrogen bonds : angle 3.68502 ( 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 151 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7758 (mtp180) REVERT: A 226 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7826 (mtp85) REVERT: A 395 GLU cc_start: 0.6917 (tp30) cc_final: 0.6690 (tp30) REVERT: A 399 HIS cc_start: 0.7371 (m90) cc_final: 0.7020 (m90) REVERT: A 452 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7299 (tp30) REVERT: B 569 ASN cc_start: 0.7974 (p0) cc_final: 0.7722 (p0) REVERT: B 575 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6601 (mp) REVERT: B 667 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8231 (ttm170) REVERT: B 724 ASP cc_start: 0.7828 (t70) cc_final: 0.7054 (m-30) REVERT: B 740 LYS cc_start: 0.7487 (mttp) cc_final: 0.7270 (mttp) REVERT: B 748 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: C 249 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: C 283 GLU cc_start: 0.7400 (mp0) cc_final: 0.7063 (mp0) REVERT: C 285 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7200 (mtt180) REVERT: C 298 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5081 (mptt) REVERT: C 490 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7254 (tmm160) REVERT: D 447 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7384 (mmtt) REVERT: D 794 GLU cc_start: 0.8061 (tp30) cc_final: 0.7266 (mt-10) outliers start: 36 outliers final: 24 residues processed: 145 average time/residue: 0.8078 time to fit residues: 126.0518 Evaluate side-chains 146 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 575 LEU 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 C residue 16 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 248 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 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 544 GLN 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 118 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 140 optimal weight: 0.0980 chunk 168 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115825 restraints weight = 19232.927| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.80 r_work: 0.3219 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16026 Z= 0.101 Angle : 0.467 8.940 21890 Z= 0.251 Chirality : 0.039 0.143 2450 Planarity : 0.004 0.044 2680 Dihedral : 15.689 149.067 2657 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.62 % Allowed : 18.13 % Favored : 80.25 % 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 aren not related in a simple way. whole: 0.01 (0.20), residues: 1824 helix: 1.68 (0.19), residues: 822 sheet: -0.42 (0.39), residues: 192 loop : -1.73 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 628 TYR 0.011 0.001 TYR B 483 PHE 0.017 0.001 PHE D 706 TRP 0.008 0.001 TRP B 647 HIS 0.002 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00208 (16026) covalent geometry : angle 0.46730 (21890) hydrogen bonds : bond 0.04193 ( 634) hydrogen bonds : angle 3.58192 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5571.36 seconds wall clock time: 95 minutes 21.67 seconds (5721.67 seconds total)