Starting phenix.real_space_refine on Tue Dec 31 11:39:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqi_18592/12_2024/8qqi_18592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqi_18592/12_2024/8qqi_18592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qqi_18592/12_2024/8qqi_18592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqi_18592/12_2024/8qqi_18592.map" model { file = "/net/cci-nas-00/data/ceres_data/8qqi_18592/12_2024/8qqi_18592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqi_18592/12_2024/8qqi_18592.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 13.15, per 1000 atoms: 0.84 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: 3.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.27 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: 5.84 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4053 1.33 - 1.45: 2882 1.45 - 1.57: 8877 1.57 - 1.69: 104 1.69 - 1.81: 110 Bond restraints: 16026 Sorted by residual: bond pdb=" 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 42.510 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.730 ------------------------------------------------------------------------------- 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= 0.203 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP D 647 HIS 0.003 0.001 HIS C 45 PHE 0.012 0.001 PHE C 368 TYR 0.016 0.001 TYR D 483 ARG 0.003 0.000 ARG C 46 *********************** 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 : 1.738 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: 1.8724 time to fit residues: 636.9970 Evaluate side-chains 139 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 155 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2408 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= 0.291 Angle : 0.626 9.361 21890 Z= 0.335 Chirality : 0.044 0.176 2450 Planarity : 0.006 0.056 2680 Dihedral : 16.311 137.330 2657 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 1824 helix: -0.36 (0.17), residues: 814 sheet: -0.54 (0.39), residues: 200 loop : -2.03 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 725 HIS 0.007 0.002 HIS A 262 PHE 0.010 0.002 PHE A 330 TYR 0.011 0.002 TYR A 266 ARG 0.007 0.001 ARG C 38 *********************** 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 207 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: A 314 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: B 667 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7929 (ttp-170) REVERT: B 724 ASP cc_start: 0.7758 (t70) cc_final: 0.7354 (m-30) REVERT: B 748 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: C 23 ASP cc_start: 0.7983 (m-30) cc_final: 0.7704 (m-30) REVERT: C 249 GLU cc_start: 0.7717 (pm20) cc_final: 0.7469 (pm20) REVERT: C 285 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6962 (mtt180) REVERT: C 490 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7547 (tmm160) REVERT: D 447 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7337 (mmtt) REVERT: D 607 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8421 (mtmt) REVERT: D 617 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6568 (tt0) outliers start: 51 outliers final: 23 residues processed: 193 average time/residue: 1.7430 time to fit residues: 363.4177 Evaluate side-chains 158 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 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 C residue 44 VAL 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 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 357 HIS D 554 GLN D 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16026 Z= 0.227 Angle : 0.560 8.889 21890 Z= 0.301 Chirality : 0.042 0.151 2450 Planarity : 0.005 0.055 2680 Dihedral : 16.039 134.600 2657 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.82 % Allowed : 13.54 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1824 helix: 0.42 (0.18), residues: 814 sheet: -0.68 (0.39), residues: 200 loop : -1.97 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 725 HIS 0.005 0.001 HIS A 80 PHE 0.015 0.001 PHE D 706 TYR 0.012 0.001 TYR B 483 ARG 0.005 0.000 ARG C 38 *********************** 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 196 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7678 (mtp180) REVERT: A 201 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: A 314 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: A 372 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8078 (ttmm) REVERT: B 667 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7932 (ttp-170) REVERT: B 724 ASP cc_start: 0.7773 (t70) cc_final: 0.7312 (m-30) REVERT: B 748 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: C 249 GLU cc_start: 0.7677 (pm20) cc_final: 0.7437 (pm20) REVERT: C 285 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6922 (mtt180) REVERT: C 298 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.5672 (mptt) REVERT: C 490 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7473 (tmm160) REVERT: C 511 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: D 447 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7394 (mmtt) REVERT: D 607 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8340 (mtmt) outliers start: 59 outliers final: 28 residues processed: 180 average time/residue: 1.8619 time to fit residues: 360.7574 Evaluate side-chains 153 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 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 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 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 C residue 511 GLU 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 663 ILE Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 ASN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16026 Z= 0.165 Angle : 0.504 9.261 21890 Z= 0.271 Chirality : 0.040 0.153 2450 Planarity : 0.004 0.049 2680 Dihedral : 15.851 139.642 2657 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.72 % Allowed : 15.35 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1824 helix: 0.90 (0.19), residues: 818 sheet: -0.66 (0.40), residues: 196 loop : -1.89 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 647 HIS 0.003 0.001 HIS A 80 PHE 0.018 0.001 PHE D 706 TYR 0.012 0.001 TYR B 483 ARG 0.005 0.000 ARG D 628 *********************** 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 165 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 1.822 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7668 (mtp180) REVERT: A 314 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: A 399 HIS cc_start: 0.7270 (m90) cc_final: 0.7048 (m90) REVERT: B 724 ASP cc_start: 0.7714 (t70) cc_final: 0.7226 (m-30) REVERT: B 748 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: C 285 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6904 (mtt180) REVERT: C 298 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.5709 (mptt) REVERT: D 447 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7481 (mmtt) REVERT: D 607 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8365 (mtmt) outliers start: 42 outliers final: 19 residues processed: 151 average time/residue: 1.7773 time to fit residues: 290.4168 Evaluate side-chains 138 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 616 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16026 Z= 0.245 Angle : 0.563 9.583 21890 Z= 0.302 Chirality : 0.042 0.152 2450 Planarity : 0.005 0.054 2680 Dihedral : 16.078 135.826 2657 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.11 % Allowed : 15.54 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1824 helix: 0.99 (0.19), residues: 818 sheet: -0.90 (0.38), residues: 212 loop : -1.94 (0.19), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 647 HIS 0.004 0.001 HIS A 80 PHE 0.014 0.001 PHE D 706 TYR 0.015 0.001 TYR B 483 ARG 0.004 0.000 ARG A 256 *********************** 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 165 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 1.785 Fit side-chains REVERT: A 121 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7721 (mtp180) REVERT: B 667 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7928 (ttp-170) REVERT: B 724 ASP cc_start: 0.7724 (t70) cc_final: 0.7212 (m-30) REVERT: B 748 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: C 285 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6945 (mtt180) REVERT: C 298 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.5595 (mptt) REVERT: C 490 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7368 (ttm170) REVERT: C 511 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: D 447 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7511 (mmtt) REVERT: D 607 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8448 (mtmt) outliers start: 48 outliers final: 24 residues processed: 151 average time/residue: 1.8061 time to fit residues: 294.6789 Evaluate side-chains 141 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain A residue 385 VAL 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 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 72 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 C residue 511 GLU 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 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 59 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 0.0670 chunk 43 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 517 GLN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3034 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= 0.141 Angle : 0.476 9.404 21890 Z= 0.257 Chirality : 0.040 0.145 2450 Planarity : 0.004 0.047 2680 Dihedral : 15.743 143.798 2657 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.59 % Allowed : 16.00 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1824 helix: 1.31 (0.19), residues: 818 sheet: -0.93 (0.38), residues: 204 loop : -1.79 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.002 0.001 HIS A 80 PHE 0.010 0.001 PHE A 368 TYR 0.013 0.001 TYR B 483 ARG 0.006 0.000 ARG D 628 *********************** 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 156 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.754 Fit side-chains REVERT: A 121 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7693 (mtp180) REVERT: B 500 ASP cc_start: 0.7723 (m-30) cc_final: 0.7503 (m-30) REVERT: B 667 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8208 (ttm170) REVERT: B 724 ASP cc_start: 0.7713 (t70) cc_final: 0.7172 (m-30) REVERT: B 748 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: C 23 ASP cc_start: 0.7971 (m-30) cc_final: 0.7723 (m-30) REVERT: C 285 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6921 (mtt180) REVERT: C 298 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.5476 (mptt) REVERT: C 490 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7110 (tmm160) REVERT: C 511 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: D 447 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7477 (mmtt) REVERT: D 510 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8502 (mp) REVERT: D 607 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8406 (mtmt) outliers start: 40 outliers final: 18 residues processed: 144 average time/residue: 1.8333 time to fit residues: 284.9558 Evaluate side-chains 138 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 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 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain C residue 44 VAL 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 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 511 GLU 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 692 THR 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 171 optimal weight: 6.9990 chunk 20 optimal weight: 0.0470 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3096 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= 0.149 Angle : 0.476 8.366 21890 Z= 0.258 Chirality : 0.040 0.144 2450 Planarity : 0.004 0.046 2680 Dihedral : 15.737 144.795 2657 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.40 % Allowed : 16.45 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1824 helix: 1.48 (0.19), residues: 818 sheet: -0.58 (0.40), residues: 188 loop : -1.80 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 80 PHE 0.016 0.001 PHE D 706 TYR 0.012 0.001 TYR B 483 ARG 0.003 0.000 ARG D 628 *********************** 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 150 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.498 Fit side-chains REVERT: A 121 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7663 (mtp180) REVERT: A 452 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6540 (tp30) REVERT: B 667 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8146 (ttm170) REVERT: B 724 ASP cc_start: 0.7722 (t70) cc_final: 0.7169 (m-30) REVERT: B 748 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: C 23 ASP cc_start: 0.7920 (m-30) cc_final: 0.7650 (m-30) REVERT: C 285 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6887 (mtt180) REVERT: C 298 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.5462 (mptt) REVERT: C 490 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7126 (tmm160) REVERT: D 447 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7555 (mmtt) outliers start: 37 outliers final: 21 residues processed: 142 average time/residue: 1.9050 time to fit residues: 291.4299 Evaluate side-chains 138 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 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 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 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 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 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 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 109 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3116 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= 0.204 Angle : 0.527 9.453 21890 Z= 0.283 Chirality : 0.041 0.147 2450 Planarity : 0.004 0.050 2680 Dihedral : 15.921 135.043 2657 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.59 % Allowed : 16.13 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1824 helix: 1.41 (0.19), residues: 818 sheet: -0.55 (0.39), residues: 192 loop : -1.90 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 80 PHE 0.011 0.001 PHE A 368 TYR 0.015 0.001 TYR B 483 ARG 0.005 0.000 ARG D 628 *********************** 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 159 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7717 (mtp180) REVERT: B 569 ASN cc_start: 0.7855 (p0) cc_final: 0.7621 (p0) REVERT: B 667 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8281 (ttm170) REVERT: B 702 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: B 724 ASP cc_start: 0.7729 (t70) cc_final: 0.7178 (m-30) REVERT: B 748 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: C 23 ASP cc_start: 0.7986 (m-30) cc_final: 0.7681 (m-30) REVERT: C 283 GLU cc_start: 0.7267 (mp0) cc_final: 0.6975 (mp0) REVERT: C 285 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6922 (mtt180) REVERT: C 298 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.5454 (mptt) REVERT: C 490 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7314 (tmm160) REVERT: D 447 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7507 (mmtt) outliers start: 40 outliers final: 26 residues processed: 152 average time/residue: 1.8525 time to fit residues: 304.0526 Evaluate side-chains 144 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 3.321 ------------------------------------------------------------------------------- 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 459 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain 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 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 510 LEU 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 169 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16026 Z= 0.154 Angle : 0.487 9.577 21890 Z= 0.263 Chirality : 0.040 0.144 2450 Planarity : 0.004 0.047 2680 Dihedral : 15.761 141.373 2657 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.46 % Allowed : 16.58 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1824 helix: 1.55 (0.19), residues: 818 sheet: -0.62 (0.39), residues: 188 loop : -1.81 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 262 PHE 0.017 0.001 PHE D 706 TYR 0.013 0.001 TYR B 483 ARG 0.002 0.000 ARG B 628 *********************** 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 150 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.849 Fit side-chains REVERT: A 121 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: A 452 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6551 (tp30) REVERT: B 500 ASP cc_start: 0.7828 (m-30) cc_final: 0.7610 (m-30) REVERT: B 667 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8206 (ttm170) REVERT: B 724 ASP cc_start: 0.7716 (t70) cc_final: 0.7155 (m-30) REVERT: B 748 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 23 ASP cc_start: 0.7941 (m-30) cc_final: 0.7673 (m-30) REVERT: C 283 GLU cc_start: 0.7230 (mp0) cc_final: 0.6955 (mp0) REVERT: C 285 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6908 (mtt180) REVERT: C 298 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.5362 (mptt) REVERT: C 490 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7261 (tmm160) REVERT: D 447 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7507 (mmtt) outliers start: 38 outliers final: 25 residues processed: 144 average time/residue: 1.8014 time to fit residues: 280.4974 Evaluate side-chains 141 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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 459 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain 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 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 510 LEU 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 174 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16026 Z= 0.312 Angle : 0.612 9.404 21890 Z= 0.328 Chirality : 0.044 0.149 2450 Planarity : 0.005 0.053 2680 Dihedral : 16.251 140.650 2657 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.33 % Allowed : 17.16 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1824 helix: 1.23 (0.19), residues: 820 sheet: -1.04 (0.36), residues: 216 loop : -1.98 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 751 HIS 0.005 0.001 HIS A 80 PHE 0.012 0.002 PHE A 368 TYR 0.017 0.002 TYR B 483 ARG 0.009 0.001 ARG A 256 ********************** 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 : 1.607 Fit side-chains REVERT: A 121 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7721 (mtp180) REVERT: B 667 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8058 (ttp-170) REVERT: B 724 ASP cc_start: 0.7737 (t70) cc_final: 0.7188 (m-30) REVERT: B 748 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: C 283 GLU cc_start: 0.7458 (mp0) cc_final: 0.7072 (mp0) REVERT: C 285 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6987 (mtt180) REVERT: C 298 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.5537 (mptt) REVERT: C 490 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7237 (ttm170) REVERT: D 447 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7522 (mmtt) outliers start: 36 outliers final: 27 residues processed: 145 average time/residue: 1.8293 time to fit residues: 286.6931 Evaluate side-chains 143 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 569 ASN 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 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 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 416 GLN Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 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 155 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 40 optimal weight: 0.4980 chunk 146 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114553 restraints weight = 19371.819| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.90 r_work: 0.3188 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 0.032 16026 Z= 0.148 Angle : 0.490 9.317 21890 Z= 0.265 Chirality : 0.040 0.144 2450 Planarity : 0.004 0.047 2680 Dihedral : 15.868 140.404 2657 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.01 % Allowed : 17.62 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1824 helix: 1.52 (0.19), residues: 818 sheet: -0.58 (0.39), residues: 192 loop : -1.88 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 399 PHE 0.017 0.001 PHE D 706 TYR 0.013 0.001 TYR B 483 ARG 0.006 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5600.99 seconds wall clock time: 101 minutes 9.91 seconds (6069.91 seconds total)