Starting phenix.real_space_refine on Thu Aug 6 06:58:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgj_52145/08_2026/9hgj_52145.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgj_52145/08_2026/9hgj_52145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hgj_52145/08_2026/9hgj_52145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgj_52145/08_2026/9hgj_52145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgj_52145/08_2026/9hgj_52145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgj_52145/08_2026/9hgj_52145.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 54 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 8437 2.51 5 N 2426 2.21 5 O 2575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13581 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6275 Classifications: {'peptide': 804} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 758} Chain breaks: 2 Chain: "B" Number of atoms: 6259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6259 Classifications: {'peptide': 802} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 755} Chain breaks: 2 Chain: "C" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 498 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.20 Number of scatterers: 13581 At special positions: 0 Unit cell: (117.3, 103.7, 124.95, 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 88 16.00 P 54 15.00 Mg 1 11.99 O 2575 8.00 N 2426 7.00 C 8437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 508.2 milliseconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2990 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 51.7% alpha, 8.5% beta 20 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.970A pdb=" N TYR A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.174A pdb=" N GLU A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 4.266A pdb=" N THR A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 4.942A pdb=" N HIS A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 161 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.766A pdb=" N TYR A 184 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.528A pdb=" N VAL A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.604A pdb=" N LEU A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 285 through 296 removed outlier: 3.662A pdb=" N ALA A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 318 removed outlier: 3.525A pdb=" N ALA A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.910A pdb=" N GLY A 340 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.705A pdb=" N VAL A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 412 through 422 removed outlier: 3.946A pdb=" N HIS A 418 " --> pdb=" O MET A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.781A pdb=" N PHE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.908A pdb=" N HIS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 472 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 5.695A pdb=" N ASN A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 518 removed outlier: 3.727A pdb=" N GLY A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.661A pdb=" N LEU A 522 " --> pdb=" O HIS A 518 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.730A pdb=" N ALA A 545 " --> pdb=" O PRO A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.542A pdb=" N PHE A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 558 " --> pdb=" O VAL A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 576 through 595 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 613 removed outlier: 3.717A pdb=" N ARG A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 653 removed outlier: 3.841A pdb=" N LEU A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 649 " --> pdb=" O CYS A 645 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 661 Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 679 through 690 removed outlier: 3.567A pdb=" N LEU A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 removed outlier: 3.734A pdb=" N LYS A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 739 removed outlier: 4.167A pdb=" N VAL A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.714A pdb=" N LEU A 760 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.166A pdb=" N GLY A 767 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 768 " --> pdb=" O THR A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.531A pdb=" N LEU A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 797 Processing helix chain 'A' and resid 822 through 832 Processing helix chain 'B' and resid 23 through 38 removed outlier: 3.503A pdb=" N TYR B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 50 removed outlier: 3.632A pdb=" N ARG B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 112 through 123 removed outlier: 4.263A pdb=" N THR B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 190 through 205 removed outlier: 4.412A pdb=" N ALA B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 256 through 264 removed outlier: 3.578A pdb=" N LEU B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.583A pdb=" N ALA B 284 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 319 removed outlier: 4.159A pdb=" N ILE B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.514A pdb=" N VAL B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 354 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 412 through 422 removed outlier: 3.618A pdb=" N HIS B 418 " --> pdb=" O MET B 414 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 5.147A pdb=" N TYR B 466 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.510A pdb=" N GLN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B 527 " --> pdb=" O ARG B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.761A pdb=" N GLU B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 558 removed outlier: 3.558A pdb=" N PHE B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 removed outlier: 4.037A pdb=" N ALA B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.630A pdb=" N ILE B 584 " --> pdb=" O ARG B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.950A pdb=" N ARG B 607 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS B 611 " --> pdb=" O ARG B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 654 removed outlier: 3.882A pdb=" N LEU B 643 " --> pdb=" O PRO B 639 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR B 649 " --> pdb=" O CYS B 645 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 677 removed outlier: 3.766A pdb=" N LEU B 673 " --> pdb=" O PRO B 669 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 690 removed outlier: 3.642A pdb=" N TYR B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL B 687 " --> pdb=" O TYR B 683 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE B 688 " --> pdb=" O MET B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 693 No H-bonds generated for 'chain 'B' and resid 691 through 693' Processing helix chain 'B' and resid 698 through 701 Processing helix chain 'B' and resid 702 through 714 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.743A pdb=" N ILE B 734 " --> pdb=" O ALA B 730 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 739 " --> pdb=" O ILE B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 770 removed outlier: 4.162A pdb=" N ASP B 770 " --> pdb=" O VAL B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 793 removed outlier: 3.997A pdb=" N LEU B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 812 removed outlier: 4.152A pdb=" N CYS B 811 " --> pdb=" O TRP B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 834 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 6.384A pdb=" N GLU A 56 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 174 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 150 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 251 removed outlier: 5.894A pdb=" N ARG A 248 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE A 398 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A 250 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N MET A 400 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A 365 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N TYR A 399 " --> pdb=" O MET A 365 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 367 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 301 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 325 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 615 through 620 Processing sheet with id=AA4, first strand: chain 'A' and resid 656 through 657 Processing sheet with id=AA5, first strand: chain 'A' and resid 743 through 746 Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 58 removed outlier: 6.831A pdb=" N THR B 54 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL B 236 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B 56 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B 76 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL B 235 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 78 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY B 237 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 150 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 300 through 304 removed outlier: 3.742A pdb=" N CYS B 301 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 365 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG B 248 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE B 398 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 250 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET B 400 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 327 removed outlier: 3.677A pdb=" N ILE B 346 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 621 removed outlier: 3.877A pdb=" N GLU B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 743 through 746 removed outlier: 3.627A pdb=" N GLN B 743 " --> pdb=" O ARG B 804 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 2478 1.33 - 1.48: 5615 1.48 - 1.64: 5766 1.64 - 1.80: 39 1.80 - 1.96: 93 Bond restraints: 13991 Sorted by residual: bond pdb=" C THR B 306 " pdb=" O THR B 306 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.28e-02 6.10e+03 2.77e+01 bond pdb=" O2G AGS B 901 " pdb=" PG AGS B 901 " ideal model delta sigma weight residual 1.604 1.502 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C VAL B 154 " pdb=" N GLU B 155 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.33e-02 5.65e+03 2.21e+01 bond pdb=" O3B AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 1.673 1.587 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CG HIS A 486 " pdb=" CD2 HIS A 486 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.78e+01 ... (remaining 13986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 17806 3.21 - 6.41: 1322 6.41 - 9.62: 93 9.62 - 12.82: 8 12.82 - 16.03: 2 Bond angle restraints: 19231 Sorted by residual: angle pdb=" O4' DT C 52 " pdb=" C1' DT C 52 " pdb=" N1 DT C 52 " ideal model delta sigma weight residual 108.00 101.73 6.27 7.00e-01 2.04e+00 8.04e+01 angle pdb=" O4' DG C 51 " pdb=" C1' DG C 51 " pdb=" N9 DG C 51 " ideal model delta sigma weight residual 108.00 113.27 -5.27 7.00e-01 2.04e+00 5.67e+01 angle pdb=" CA ASP A 377 " pdb=" CB ASP A 377 " pdb=" CG ASP A 377 " ideal model delta sigma weight residual 112.60 119.97 -7.37 1.00e+00 1.00e+00 5.43e+01 angle pdb=" C PRO A 840 " pdb=" CA PRO A 840 " pdb=" CB PRO A 840 " ideal model delta sigma weight residual 111.87 118.01 -6.14 8.40e-01 1.42e+00 5.34e+01 angle pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " pdb=" P DC D 30 " ideal model delta sigma weight residual 119.70 127.96 -8.26 1.20e+00 6.94e-01 4.74e+01 ... (remaining 19226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 7916 34.77 - 69.55: 341 69.55 - 104.32: 25 104.32 - 139.09: 0 139.09 - 173.87: 5 Dihedral angle restraints: 8287 sinusoidal: 3653 harmonic: 4634 Sorted by residual: dihedral pdb=" CA PRO A 206 " pdb=" C PRO A 206 " pdb=" N ARG A 207 " pdb=" CA ARG A 207 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG B 74 " pdb=" C ARG B 74 " pdb=" N CYS B 75 " pdb=" CA CYS B 75 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" N TRP B 839 " pdb=" C TRP B 839 " pdb=" CA TRP B 839 " pdb=" CB TRP B 839 " ideal model delta harmonic sigma weight residual 122.80 136.16 -13.36 0 2.50e+00 1.60e-01 2.86e+01 ... (remaining 8284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1760 0.134 - 0.269: 381 0.269 - 0.403: 41 0.403 - 0.538: 1 0.538 - 0.672: 2 Chirality restraints: 2185 Sorted by residual: chirality pdb=" P DT C 39 " pdb=" OP1 DT C 39 " pdb=" OP2 DT C 39 " pdb=" O5' DT C 39 " both_signs ideal model delta sigma weight residual True 2.34 -3.01 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" P DA D 19 " pdb=" OP1 DA D 19 " pdb=" OP2 DA D 19 " pdb=" O5' DA D 19 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" CA TRP A 839 " pdb=" N TRP A 839 " pdb=" C TRP A 839 " pdb=" CB TRP A 839 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 2182 not shown) Planarity restraints: 2300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 839 " -0.131 2.00e-02 2.50e+03 6.42e-02 1.03e+02 pdb=" CG TRP A 839 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 839 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 839 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP A 839 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 839 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A 839 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 839 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 839 " 0.060 2.00e-02 2.50e+03 pdb=" CH2 TRP A 839 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 839 " 0.126 2.00e-02 2.50e+03 6.34e-02 1.01e+02 pdb=" CG TRP B 839 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP B 839 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 839 " -0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP B 839 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP B 839 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 839 " -0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 839 " 0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 839 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 839 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 52 " 0.116 2.00e-02 2.50e+03 5.39e-02 7.26e+01 pdb=" N1 DT C 52 " -0.053 2.00e-02 2.50e+03 pdb=" C2 DT C 52 " -0.032 2.00e-02 2.50e+03 pdb=" O2 DT C 52 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DT C 52 " -0.029 2.00e-02 2.50e+03 pdb=" C4 DT C 52 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT C 52 " 0.089 2.00e-02 2.50e+03 pdb=" C5 DT C 52 " -0.038 2.00e-02 2.50e+03 pdb=" C7 DT C 52 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT C 52 " -0.035 2.00e-02 2.50e+03 ... (remaining 2297 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 9 2.48 - 3.08: 8206 3.08 - 3.69: 19094 3.69 - 4.29: 28596 4.29 - 4.90: 46527 Nonbonded interactions: 102432 Sorted by model distance: nonbonded pdb=" OE2 GLU A 175 " pdb="MG MG A 902 " model vdw 1.872 2.170 nonbonded pdb=" SG CYS B 111 " pdb=" CG GLN B 182 " model vdw 2.276 3.800 nonbonded pdb=" O PRO B 102 " pdb=" NH2 ARG B 149 " model vdw 2.361 3.120 nonbonded pdb=" CD2 PHE B 115 " pdb=" OD2 ASP B 174 " model vdw 2.371 3.340 nonbonded pdb=" OH TYR B 368 " pdb=" OD2 ASP B 401 " model vdw 2.419 3.040 ... (remaining 102427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 134 or resid 145 through 901)) selection = (chain 'B' and (resid 18 through 433 or resid 451 through 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.012 0.102 13991 Z= 0.742 Angle : 1.774 16.026 19231 Z= 1.169 Chirality : 0.109 0.672 2185 Planarity : 0.018 0.194 2300 Dihedral : 17.901 173.866 5297 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.19), residues: 1594 helix: -2.81 (0.15), residues: 708 sheet: -0.96 (0.36), residues: 190 loop : -0.84 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.004 ARG A 607 TYR 0.071 0.014 TYR A 609 PHE 0.061 0.011 PHE A 303 TRP 0.131 0.020 TRP A 839 HIS 0.034 0.005 HIS B 468 Details of bonding type rmsd/Z covalent geometry : bond 0.01152 / 0.74 (13991) covalent geometry : angle 1.77391 / 1.17 (19231) hydrogen bonds : bond 0.23020 / 15.60 ( 555) hydrogen bonds : angle 8.34942 / 6.06 ( 1529) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8334 (mtm110) cc_final: 0.8000 (ptm-80) REVERT: A 232 VAL cc_start: 0.9090 (t) cc_final: 0.8836 (m) REVERT: A 549 GLU cc_start: 0.9658 (mp0) cc_final: 0.9368 (mp0) REVERT: A 697 ASP cc_start: 0.9012 (t0) cc_final: 0.8584 (t0) REVERT: A 817 SER cc_start: 0.9247 (m) cc_final: 0.9029 (p) REVERT: B 56 GLU cc_start: 0.8320 (pt0) cc_final: 0.8043 (tm-30) REVERT: B 103 ASP cc_start: 0.8914 (t0) cc_final: 0.8683 (t0) REVERT: B 155 GLU cc_start: 0.9492 (mt-10) cc_final: 0.8856 (mp0) REVERT: B 182 GLN cc_start: 0.9366 (mm110) cc_final: 0.8977 (tm-30) REVERT: B 232 VAL cc_start: 0.9247 (t) cc_final: 0.8818 (m) REVERT: B 414 MET cc_start: 0.9578 (ttt) cc_final: 0.9324 (tpp) REVERT: B 642 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9208 (tp30) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1261 time to fit residues: 29.3538 Evaluate side-chains 100 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 HIS A 432 GLN A 486 HIS A 492 ASN A 727 HIS B 319 GLN B 361 HIS B 486 HIS B 727 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.105525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.076016 restraints weight = 44028.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.078876 restraints weight = 24638.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.080569 restraints weight = 18019.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.081550 restraints weight = 15141.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.081991 restraints weight = 13734.062| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13991 Z= 0.171 Angle : 0.788 9.409 19231 Z= 0.418 Chirality : 0.051 0.343 2185 Planarity : 0.005 0.046 2300 Dihedral : 20.003 175.190 2375 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.18 % Allowed : 8.16 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.20), residues: 1594 helix: -1.28 (0.18), residues: 723 sheet: -0.64 (0.34), residues: 219 loop : -0.86 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 515 TYR 0.018 0.002 TYR A 382 PHE 0.029 0.002 PHE A 131 TRP 0.019 0.002 TRP A 94 HIS 0.009 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (13991) covalent geometry : angle 0.78848 / 0.42 (19231) hydrogen bonds : bond 0.06088 / 4.18 ( 555) hydrogen bonds : angle 5.00823 / 3.61 ( 1529) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8936 (ttm) cc_final: 0.8713 (ttp) REVERT: A 817 SER cc_start: 0.8933 (m) cc_final: 0.8632 (p) REVERT: B 585 TYR cc_start: 0.8801 (m-80) cc_final: 0.8520 (m-80) REVERT: B 642 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7807 (tp30) outliers start: 16 outliers final: 7 residues processed: 123 average time/residue: 0.0913 time to fit residues: 17.5516 Evaluate side-chains 92 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 571 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 119 optimal weight: 0.0470 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 153 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.105341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.076075 restraints weight = 43863.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.078808 restraints weight = 24176.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.080550 restraints weight = 17613.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.081538 restraints weight = 14771.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.082121 restraints weight = 13389.773| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13991 Z= 0.137 Angle : 0.683 12.329 19231 Z= 0.358 Chirality : 0.046 0.329 2185 Planarity : 0.005 0.042 2300 Dihedral : 19.251 178.931 2375 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 1.54 % Allowed : 10.21 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.21), residues: 1594 helix: -0.62 (0.19), residues: 729 sheet: -0.45 (0.36), residues: 213 loop : -0.84 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 465 TYR 0.022 0.002 TYR B 786 PHE 0.030 0.001 PHE A 131 TRP 0.016 0.001 TRP B 839 HIS 0.015 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (13991) covalent geometry : angle 0.68322 / 0.36 (19231) hydrogen bonds : bond 0.04767 / 3.24 ( 555) hydrogen bonds : angle 4.50261 / 3.23 ( 1529) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8251 (tp30) cc_final: 0.8047 (tp30) REVERT: A 760 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8502 (pt) REVERT: A 817 SER cc_start: 0.8987 (m) cc_final: 0.8705 (p) REVERT: B 414 MET cc_start: 0.8244 (tpp) cc_final: 0.8040 (tpp) REVERT: B 585 TYR cc_start: 0.8819 (m-80) cc_final: 0.8424 (m-80) outliers start: 21 outliers final: 8 residues processed: 116 average time/residue: 0.0879 time to fit residues: 16.2128 Evaluate side-chains 96 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 634 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.104307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075270 restraints weight = 44735.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.077988 restraints weight = 24912.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.079719 restraints weight = 18286.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080683 restraints weight = 15342.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.081067 restraints weight = 13945.825| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13991 Z= 0.133 Angle : 0.642 9.391 19231 Z= 0.332 Chirality : 0.044 0.360 2185 Planarity : 0.004 0.039 2300 Dihedral : 18.817 176.925 2375 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 2.06 % Allowed : 11.46 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1594 helix: -0.25 (0.19), residues: 728 sheet: -0.24 (0.36), residues: 212 loop : -0.71 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 465 TYR 0.013 0.001 TYR B 585 PHE 0.024 0.001 PHE A 131 TRP 0.013 0.001 TRP B 839 HIS 0.011 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (13991) covalent geometry : angle 0.64241 / 0.33 (19231) hydrogen bonds : bond 0.04084 / 2.75 ( 555) hydrogen bonds : angle 4.29165 / 3.07 ( 1529) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8410 (tp30) cc_final: 0.8155 (tp30) REVERT: A 760 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8501 (pt) REVERT: A 817 SER cc_start: 0.8981 (m) cc_final: 0.8697 (p) REVERT: B 414 MET cc_start: 0.8354 (tpp) cc_final: 0.8134 (tpp) REVERT: B 585 TYR cc_start: 0.8782 (m-80) cc_final: 0.8435 (m-80) REVERT: B 642 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7823 (mm-30) REVERT: B 684 MET cc_start: 0.8823 (ptp) cc_final: 0.7706 (mmm) outliers start: 28 outliers final: 15 residues processed: 113 average time/residue: 0.0743 time to fit residues: 13.6121 Evaluate side-chains 102 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 23 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 HIS A 776 HIS B 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.104499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075208 restraints weight = 43852.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.078043 restraints weight = 23857.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.079770 restraints weight = 17337.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080819 restraints weight = 14511.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.081152 restraints weight = 13108.302| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13991 Z= 0.125 Angle : 0.625 8.992 19231 Z= 0.319 Chirality : 0.043 0.360 2185 Planarity : 0.004 0.040 2300 Dihedral : 18.494 179.843 2375 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 1.91 % Allowed : 13.01 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1594 helix: 0.04 (0.19), residues: 729 sheet: -0.14 (0.36), residues: 212 loop : -0.68 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 465 TYR 0.012 0.001 TYR B 585 PHE 0.020 0.001 PHE A 131 TRP 0.011 0.001 TRP B 839 HIS 0.011 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13991) covalent geometry : angle 0.62452 / 0.32 (19231) hydrogen bonds : bond 0.03810 / 2.57 ( 555) hydrogen bonds : angle 4.16624 / 2.97 ( 1529) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 GLU cc_start: 0.7565 (tp30) cc_final: 0.7314 (tp30) REVERT: A 760 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8522 (pt) REVERT: A 817 SER cc_start: 0.9009 (m) cc_final: 0.8742 (p) REVERT: B 408 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 414 MET cc_start: 0.8530 (tpp) cc_final: 0.8253 (tpp) REVERT: B 585 TYR cc_start: 0.8785 (m-80) cc_final: 0.8360 (m-80) REVERT: B 642 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7920 (mm-30) outliers start: 26 outliers final: 19 residues processed: 106 average time/residue: 0.0788 time to fit residues: 13.5189 Evaluate side-chains 106 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 3.9990 chunk 118 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 78 optimal weight: 0.0010 chunk 142 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS A 299 ASN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.101076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071891 restraints weight = 44312.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.074565 restraints weight = 24454.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.076216 restraints weight = 17844.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.077243 restraints weight = 14997.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077792 restraints weight = 13525.105| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13991 Z= 0.208 Angle : 0.686 9.297 19231 Z= 0.347 Chirality : 0.045 0.355 2185 Planarity : 0.005 0.043 2300 Dihedral : 18.334 179.922 2375 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 2.28 % Allowed : 13.59 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1594 helix: 0.09 (0.19), residues: 736 sheet: -0.16 (0.36), residues: 212 loop : -0.77 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 472 TYR 0.017 0.002 TYR A 168 PHE 0.018 0.001 PHE A 131 TRP 0.014 0.001 TRP A 839 HIS 0.011 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (13991) covalent geometry : angle 0.68633 / 0.35 (19231) hydrogen bonds : bond 0.04774 / 3.13 ( 555) hydrogen bonds : angle 4.33760 / 3.09 ( 1529) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 817 SER cc_start: 0.8996 (m) cc_final: 0.8769 (p) REVERT: B 414 MET cc_start: 0.8472 (tpp) cc_final: 0.8219 (tpp) REVERT: B 684 MET cc_start: 0.8275 (ptt) cc_final: 0.7219 (mmm) outliers start: 31 outliers final: 24 residues processed: 112 average time/residue: 0.0778 time to fit residues: 14.4097 Evaluate side-chains 103 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 5 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.101965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.073140 restraints weight = 43695.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.075816 restraints weight = 23810.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077538 restraints weight = 17283.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078558 restraints weight = 14402.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.079107 restraints weight = 13007.027| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13991 Z= 0.142 Angle : 0.625 9.891 19231 Z= 0.319 Chirality : 0.043 0.353 2185 Planarity : 0.004 0.038 2300 Dihedral : 18.162 178.267 2375 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 2.20 % Allowed : 14.03 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.21), residues: 1594 helix: 0.34 (0.20), residues: 727 sheet: -0.08 (0.37), residues: 212 loop : -0.73 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 472 TYR 0.012 0.001 TYR A 168 PHE 0.017 0.001 PHE A 131 TRP 0.012 0.001 TRP B 839 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13991) covalent geometry : angle 0.62497 / 0.32 (19231) hydrogen bonds : bond 0.03897 / 2.60 ( 555) hydrogen bonds : angle 4.21489 / 3.00 ( 1529) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 SER cc_start: 0.9098 (t) cc_final: 0.8873 (t) REVERT: B 414 MET cc_start: 0.8529 (tpp) cc_final: 0.8247 (tpp) REVERT: B 585 TYR cc_start: 0.8735 (m-80) cc_final: 0.8444 (m-80) REVERT: B 642 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7933 (mm-30) REVERT: B 684 MET cc_start: 0.8226 (ptt) cc_final: 0.7102 (mtp) outliers start: 30 outliers final: 27 residues processed: 111 average time/residue: 0.0720 time to fit residues: 13.1429 Evaluate side-chains 109 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 5 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 112 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.102653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073992 restraints weight = 43488.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076727 restraints weight = 24073.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078426 restraints weight = 17528.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079441 restraints weight = 14672.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.080011 restraints weight = 13246.186| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13991 Z= 0.112 Angle : 0.615 10.104 19231 Z= 0.309 Chirality : 0.042 0.349 2185 Planarity : 0.004 0.039 2300 Dihedral : 18.029 179.379 2375 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.06 % Allowed : 14.18 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.22), residues: 1594 helix: 0.52 (0.20), residues: 729 sheet: -0.01 (0.37), residues: 214 loop : -0.65 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.011 0.001 TYR A 786 PHE 0.016 0.001 PHE A 131 TRP 0.008 0.001 TRP A 839 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (13991) covalent geometry : angle 0.61455 / 0.31 (19231) hydrogen bonds : bond 0.03459 / 2.32 ( 555) hydrogen bonds : angle 4.12812 / 2.93 ( 1529) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 SER cc_start: 0.9043 (t) cc_final: 0.8812 (t) REVERT: B 414 MET cc_start: 0.8474 (tpp) cc_final: 0.8232 (tpp) REVERT: B 585 TYR cc_start: 0.8632 (m-80) cc_final: 0.8391 (m-80) REVERT: B 642 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 684 MET cc_start: 0.8244 (ptt) cc_final: 0.7116 (mtp) outliers start: 28 outliers final: 22 residues processed: 107 average time/residue: 0.0792 time to fit residues: 13.7841 Evaluate side-chains 104 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 15 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN B 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.102566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.073138 restraints weight = 44833.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075787 restraints weight = 25319.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077408 restraints weight = 18680.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.078351 restraints weight = 15786.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.078789 restraints weight = 14359.081| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13991 Z= 0.113 Angle : 0.608 10.778 19231 Z= 0.306 Chirality : 0.042 0.348 2185 Planarity : 0.004 0.038 2300 Dihedral : 17.939 179.297 2375 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.13 % Allowed : 14.18 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1594 helix: 0.64 (0.20), residues: 728 sheet: 0.25 (0.38), residues: 207 loop : -0.55 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 600 TYR 0.023 0.001 TYR A 786 PHE 0.015 0.001 PHE A 131 TRP 0.007 0.001 TRP A 839 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (13991) covalent geometry : angle 0.60803 / 0.31 (19231) hydrogen bonds : bond 0.03442 / 2.30 ( 555) hydrogen bonds : angle 4.09038 / 2.90 ( 1529) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 SER cc_start: 0.9022 (t) cc_final: 0.8793 (t) REVERT: B 414 MET cc_start: 0.8501 (tpp) cc_final: 0.8294 (tpp) REVERT: B 585 TYR cc_start: 0.8594 (m-80) cc_final: 0.8392 (m-80) REVERT: B 642 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7899 (mm-30) REVERT: B 684 MET cc_start: 0.8241 (ptt) cc_final: 0.7152 (mtp) REVERT: B 804 ARG cc_start: 0.8639 (mtp180) cc_final: 0.8135 (tmm-80) outliers start: 29 outliers final: 25 residues processed: 112 average time/residue: 0.0858 time to fit residues: 15.2945 Evaluate side-chains 109 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 61 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 98 optimal weight: 0.0040 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.102933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074151 restraints weight = 43617.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076873 restraints weight = 23829.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.078572 restraints weight = 17351.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079601 restraints weight = 14534.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080161 restraints weight = 13122.667| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13991 Z= 0.109 Angle : 0.607 10.315 19231 Z= 0.305 Chirality : 0.041 0.350 2185 Planarity : 0.004 0.037 2300 Dihedral : 17.863 178.430 2375 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.76 % Allowed : 14.55 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.22), residues: 1594 helix: 0.76 (0.20), residues: 726 sheet: 0.34 (0.38), residues: 207 loop : -0.52 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 708 TYR 0.024 0.001 TYR A 786 PHE 0.015 0.001 PHE A 131 TRP 0.007 0.001 TRP B 45 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (13991) covalent geometry : angle 0.60707 / 0.31 (19231) hydrogen bonds : bond 0.03277 / 2.19 ( 555) hydrogen bonds : angle 4.07113 / 2.87 ( 1529) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 SER cc_start: 0.9058 (t) cc_final: 0.8811 (t) REVERT: B 585 TYR cc_start: 0.8595 (m-80) cc_final: 0.8389 (m-80) REVERT: B 642 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7925 (mm-30) REVERT: B 684 MET cc_start: 0.8171 (ptt) cc_final: 0.7174 (mtp) REVERT: B 804 ARG cc_start: 0.8611 (mtp180) cc_final: 0.8171 (tmm-80) outliers start: 24 outliers final: 21 residues processed: 107 average time/residue: 0.0879 time to fit residues: 15.0257 Evaluate side-chains 107 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 0.0770 chunk 80 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.102520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.073933 restraints weight = 43633.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076626 restraints weight = 24150.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078302 restraints weight = 17557.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.079276 restraints weight = 14675.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079724 restraints weight = 13263.744| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13991 Z= 0.120 Angle : 0.615 12.029 19231 Z= 0.307 Chirality : 0.042 0.349 2185 Planarity : 0.004 0.039 2300 Dihedral : 17.824 177.854 2375 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.84 % Allowed : 14.99 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1594 helix: 0.83 (0.20), residues: 722 sheet: 0.39 (0.38), residues: 207 loop : -0.47 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.023 0.001 TYR A 786 PHE 0.014 0.001 PHE A 131 TRP 0.007 0.001 TRP A 839 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13991) covalent geometry : angle 0.61498 / 0.31 (19231) hydrogen bonds : bond 0.03418 / 2.28 ( 555) hydrogen bonds : angle 4.06585 / 2.87 ( 1529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.56 seconds wall clock time: 38 minutes 16.38 seconds (2296.38 seconds total)