Starting phenix.real_space_refine on Thu Feb 5 00:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgj_52145/02_2026/9hgj_52145.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgj_52145/02_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_52145/02_2026/9hgj_52145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgj_52145/02_2026/9hgj_52145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgj_52145/02_2026/9hgj_52145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgj_52145/02_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-2.0-5952/lib/python3.9/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: 3.54, per 1000 atoms: 0.26 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: 1.13 Conformation dependent library (CDL) restraints added in 483.3 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: 1.95 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: 2.60 Time building geometry restraints manager: 1.55 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=" 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=" 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 bond pdb=" CA SER B 305 " pdb=" CB SER B 305 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.64e-02 3.72e+03 1.65e+01 bond pdb=" CA CYS A 249 " pdb=" C CYS A 249 " ideal model delta sigma weight residual 1.523 1.572 -0.049 1.23e-02 6.61e+03 1.60e+01 ... (remaining 13986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 17810 3.21 - 6.41: 1313 6.41 - 9.62: 97 9.62 - 12.82: 8 12.82 - 16.03: 3 Bond angle restraints: 19231 Sorted by residual: 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=" CA ASP B 377 " pdb=" CB ASP B 377 " pdb=" CG ASP B 377 " ideal model delta sigma weight residual 112.60 119.46 -6.86 1.00e+00 1.00e+00 4.70e+01 angle pdb=" CA ASP B 130 " pdb=" CB ASP B 130 " pdb=" CG ASP B 130 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA ASP A 130 " pdb=" CB ASP A 130 " pdb=" CG ASP A 130 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.00e+00 1.00e+00 4.22e+01 ... (remaining 19226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 7904 34.77 - 69.55: 326 69.55 - 104.32: 18 104.32 - 139.09: 1 139.09 - 173.87: 2 Dihedral angle restraints: 8251 sinusoidal: 3617 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 8248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1761 0.132 - 0.265: 384 0.265 - 0.397: 39 0.397 - 0.529: 3 0.529 - 0.662: 2 Chirality restraints: 2189 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 2.35 -3.01 -0.66 2.00e-01 2.50e+01 1.09e+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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.86e+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 2186 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: 7.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.300 Find NCS groups from input model: 0.240 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.011 0.074 13991 Z= 0.708 Angle : 1.779 16.026 19231 Z= 1.131 Chirality : 0.107 0.662 2189 Planarity : 0.018 0.194 2300 Dihedral : 17.119 173.866 5261 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 covalent geometry : bond 0.01131 (13991) covalent geometry : angle 1.77926 (19231) hydrogen bonds : bond 0.23020 ( 555) hydrogen bonds : angle 8.34942 ( 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 : 0.518 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: 0.1509 time to fit residues: 34.9360 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 : 0.501 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.104386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075256 restraints weight = 43990.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077929 restraints weight = 24660.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079610 restraints weight = 18148.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.080591 restraints weight = 15299.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.080982 restraints weight = 13894.140| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13991 Z= 0.167 Angle : 0.730 11.532 19231 Z= 0.389 Chirality : 0.045 0.232 2189 Planarity : 0.005 0.044 2300 Dihedral : 18.782 171.843 2339 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.03 % Allowed : 7.79 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.20), residues: 1594 helix: -1.22 (0.18), residues: 721 sheet: -0.51 (0.34), residues: 219 loop : -0.76 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 794 TYR 0.020 0.002 TYR B 461 PHE 0.030 0.002 PHE A 131 TRP 0.018 0.002 TRP B 839 HIS 0.006 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00354 (13991) covalent geometry : angle 0.72989 (19231) hydrogen bonds : bond 0.05275 ( 555) hydrogen bonds : angle 4.79613 ( 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 131 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 817 SER cc_start: 0.8966 (m) cc_final: 0.8644 (p) REVERT: B 179 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8970 (p) REVERT: B 585 TYR cc_start: 0.8815 (m-80) cc_final: 0.8533 (m-80) REVERT: B 642 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7857 (tp30) outliers start: 14 outliers final: 4 residues processed: 125 average time/residue: 0.1061 time to fit residues: 20.5992 Evaluate side-chains 88 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 B residue 179 THR Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 119 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 153 optimal weight: 30.0000 chunk 88 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.104454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075095 restraints weight = 43831.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077841 restraints weight = 24110.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.079571 restraints weight = 17597.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080567 restraints weight = 14708.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080991 restraints weight = 13310.043| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13991 Z= 0.145 Angle : 0.634 10.288 19231 Z= 0.334 Chirality : 0.042 0.175 2189 Planarity : 0.004 0.043 2300 Dihedral : 18.334 173.281 2339 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 1.62 % Allowed : 9.99 % Favored : 88.39 % 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: -0.92 (0.21), residues: 1594 helix: -0.46 (0.19), residues: 735 sheet: -0.22 (0.36), residues: 208 loop : -0.72 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 526 TYR 0.019 0.002 TYR B 786 PHE 0.024 0.001 PHE A 131 TRP 0.015 0.001 TRP B 839 HIS 0.013 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00323 (13991) covalent geometry : angle 0.63375 (19231) hydrogen bonds : bond 0.04362 ( 555) hydrogen bonds : angle 4.33767 ( 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 115 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 760 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8521 (pt) REVERT: A 817 SER cc_start: 0.8980 (m) cc_final: 0.8667 (p) REVERT: B 414 MET cc_start: 0.8354 (tpp) cc_final: 0.8152 (tpp) REVERT: B 585 TYR cc_start: 0.8784 (m-80) cc_final: 0.8388 (m-80) REVERT: B 642 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7755 (mm-30) outliers start: 22 outliers final: 11 residues processed: 110 average time/residue: 0.1021 time to fit residues: 18.2045 Evaluate side-chains 97 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 789 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 634 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 HIS B 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.103928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075225 restraints weight = 43562.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.078000 restraints weight = 24030.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079686 restraints weight = 17480.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080712 restraints weight = 14590.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.081047 restraints weight = 13165.925| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13991 Z= 0.135 Angle : 0.600 7.959 19231 Z= 0.314 Chirality : 0.040 0.169 2189 Planarity : 0.004 0.039 2300 Dihedral : 18.164 177.921 2339 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 1.69 % Allowed : 12.12 % Favored : 86.19 % 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: -0.56 (0.21), residues: 1594 helix: -0.09 (0.19), residues: 733 sheet: -0.09 (0.36), residues: 213 loop : -0.63 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 682 TYR 0.010 0.001 TYR B 585 PHE 0.019 0.001 PHE A 131 TRP 0.012 0.001 TRP B 839 HIS 0.013 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00301 (13991) covalent geometry : angle 0.60042 (19231) hydrogen bonds : bond 0.03840 ( 555) hydrogen bonds : angle 4.18790 ( 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 112 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 817 SER cc_start: 0.8996 (m) cc_final: 0.8713 (p) REVERT: B 414 MET cc_start: 0.8348 (tpp) cc_final: 0.8109 (tpp) REVERT: B 585 TYR cc_start: 0.8750 (m-80) cc_final: 0.8397 (m-80) REVERT: B 642 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 650 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8005 (mmm) REVERT: B 684 MET cc_start: 0.8684 (ptp) cc_final: 0.7579 (mmm) outliers start: 23 outliers final: 15 residues processed: 104 average time/residue: 0.0984 time to fit residues: 16.6071 Evaluate side-chains 99 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL 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 748 THR Chi-restraints excluded: chain A residue 789 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 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 650 MET Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 157 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 123 optimal weight: 1.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 782 HIS B 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.103752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074726 restraints weight = 43778.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077523 restraints weight = 24070.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079214 restraints weight = 17487.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080261 restraints weight = 14650.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080824 restraints weight = 13210.123| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13991 Z= 0.131 Angle : 0.586 8.501 19231 Z= 0.304 Chirality : 0.040 0.257 2189 Planarity : 0.004 0.040 2300 Dihedral : 18.040 177.914 2339 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 2.42 % Allowed : 12.05 % Favored : 85.53 % 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: -0.32 (0.21), residues: 1594 helix: 0.24 (0.19), residues: 736 sheet: -0.09 (0.36), residues: 209 loop : -0.63 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.011 0.001 TYR A 168 PHE 0.017 0.001 PHE A 131 TRP 0.009 0.001 TRP B 839 HIS 0.011 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00295 (13991) covalent geometry : angle 0.58602 (19231) hydrogen bonds : bond 0.03640 ( 555) hydrogen bonds : angle 4.09844 ( 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 122 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 817 SER cc_start: 0.9002 (m) cc_final: 0.8732 (p) REVERT: B 414 MET cc_start: 0.8409 (tpp) cc_final: 0.8142 (tpp) REVERT: B 585 TYR cc_start: 0.8723 (m-80) cc_final: 0.8305 (m-80) REVERT: B 642 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7780 (mm-30) outliers start: 33 outliers final: 18 residues processed: 116 average time/residue: 0.0975 time to fit residues: 18.3398 Evaluate side-chains 101 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 416 LEU 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 A residue 789 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 599 THR Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 0.0980 chunk 30 optimal weight: 0.4980 chunk 152 optimal weight: 0.0370 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.105010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075806 restraints weight = 43448.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.078554 restraints weight = 23818.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080255 restraints weight = 17373.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.081236 restraints weight = 14568.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.081640 restraints weight = 13212.025| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13991 Z= 0.111 Angle : 0.588 10.013 19231 Z= 0.298 Chirality : 0.040 0.230 2189 Planarity : 0.004 0.037 2300 Dihedral : 17.966 179.250 2339 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 1.69 % Allowed : 13.52 % Favored : 84.79 % 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: -0.06 (0.22), residues: 1594 helix: 0.45 (0.20), residues: 733 sheet: 0.14 (0.37), residues: 205 loop : -0.53 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 804 TYR 0.024 0.001 TYR A 786 PHE 0.015 0.001 PHE A 131 TRP 0.006 0.001 TRP A 94 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00244 (13991) covalent geometry : angle 0.58768 (19231) hydrogen bonds : bond 0.03223 ( 555) hydrogen bonds : angle 4.01264 ( 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 117 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 817 SER cc_start: 0.9028 (m) cc_final: 0.8748 (p) REVERT: B 414 MET cc_start: 0.8542 (tpp) cc_final: 0.8261 (tpp) REVERT: B 585 TYR cc_start: 0.8704 (m-80) cc_final: 0.8345 (m-80) REVERT: B 642 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 683 TYR cc_start: 0.8165 (m-80) cc_final: 0.7954 (m-80) REVERT: B 684 MET cc_start: 0.8241 (ptt) cc_final: 0.7156 (mmm) outliers start: 23 outliers final: 20 residues processed: 112 average time/residue: 0.1067 time to fit residues: 18.9477 Evaluate side-chains 104 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 748 THR Chi-restraints excluded: chain A residue 789 LEU 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 412 THR Chi-restraints excluded: chain B residue 517 VAL 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 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: 4.9990 chunk 143 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.0060 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.104024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.075261 restraints weight = 42890.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.077878 restraints weight = 23404.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079541 restraints weight = 17017.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.080546 restraints weight = 14215.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.080942 restraints weight = 12871.967| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13991 Z= 0.121 Angle : 0.586 9.608 19231 Z= 0.296 Chirality : 0.039 0.208 2189 Planarity : 0.004 0.041 2300 Dihedral : 17.902 179.699 2339 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 1.91 % Allowed : 13.67 % Favored : 84.42 % 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: 0.10 (0.22), residues: 1594 helix: 0.60 (0.20), residues: 735 sheet: 0.29 (0.37), residues: 205 loop : -0.48 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.009 0.001 TYR A 168 PHE 0.015 0.001 PHE B 430 TRP 0.007 0.001 TRP A 839 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00274 (13991) covalent geometry : angle 0.58638 (19231) hydrogen bonds : bond 0.03292 ( 555) hydrogen bonds : angle 3.99929 ( 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 113 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: A 686 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9071 (mm) REVERT: A 817 SER cc_start: 0.9033 (m) cc_final: 0.8757 (p) REVERT: B 408 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7545 (mm-30) REVERT: B 585 TYR cc_start: 0.8701 (m-80) cc_final: 0.8318 (m-80) REVERT: B 642 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 683 TYR cc_start: 0.8099 (m-80) cc_final: 0.7813 (m-80) REVERT: B 684 MET cc_start: 0.8108 (ptt) cc_final: 0.7005 (mtp) REVERT: B 804 ARG cc_start: 0.8624 (mtp180) cc_final: 0.8174 (tmm-80) outliers start: 26 outliers final: 17 residues processed: 108 average time/residue: 0.1105 time to fit residues: 18.6425 Evaluate side-chains 105 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 372 MET 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 686 LEU 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 223 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 5 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 50 optimal weight: 0.0010 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.103379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074488 restraints weight = 43346.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077130 restraints weight = 23979.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078808 restraints weight = 17508.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.079812 restraints weight = 14668.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080367 restraints weight = 13275.028| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13991 Z= 0.133 Angle : 0.595 10.071 19231 Z= 0.299 Chirality : 0.040 0.198 2189 Planarity : 0.004 0.039 2300 Dihedral : 17.860 179.680 2339 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.76 % Allowed : 13.67 % Favored : 84.57 % 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: 0.17 (0.22), residues: 1594 helix: 0.67 (0.20), residues: 732 sheet: 0.32 (0.37), residues: 211 loop : -0.48 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 472 TYR 0.013 0.001 TYR A 786 PHE 0.013 0.001 PHE A 732 TRP 0.008 0.001 TRP A 839 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00302 (13991) covalent geometry : angle 0.59475 (19231) hydrogen bonds : bond 0.03432 ( 555) hydrogen bonds : angle 4.02959 ( 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 115 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 TYR cc_start: 0.8757 (m-80) cc_final: 0.8334 (m-80) REVERT: B 642 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 683 TYR cc_start: 0.8128 (m-80) cc_final: 0.7806 (m-80) REVERT: B 684 MET cc_start: 0.8187 (ptt) cc_final: 0.7138 (mtp) REVERT: B 804 ARG cc_start: 0.8603 (mtp180) cc_final: 0.8187 (tmm-80) outliers start: 24 outliers final: 19 residues processed: 111 average time/residue: 0.1079 time to fit residues: 18.9184 Evaluate side-chains 103 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 748 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 15 optimal weight: 1.9990 chunk 145 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 126 optimal weight: 0.9990 chunk 4 optimal weight: 0.0030 chunk 115 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4029 r_free = 0.4029 target = 0.104352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.075948 restraints weight = 42867.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.078704 restraints weight = 23331.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.080391 restraints weight = 16823.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081393 restraints weight = 14011.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.081739 restraints weight = 12596.756| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13991 Z= 0.110 Angle : 0.591 10.339 19231 Z= 0.296 Chirality : 0.039 0.192 2189 Planarity : 0.004 0.037 2300 Dihedral : 17.806 179.381 2339 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.25 % Allowed : 14.70 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1594 helix: 0.85 (0.20), residues: 721 sheet: 0.42 (0.37), residues: 212 loop : -0.31 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 708 TYR 0.023 0.001 TYR A 786 PHE 0.013 0.001 PHE A 732 TRP 0.007 0.001 TRP B 45 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00245 (13991) covalent geometry : angle 0.59087 (19231) hydrogen bonds : bond 0.03109 ( 555) hydrogen bonds : angle 3.99390 ( 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 103 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 TYR cc_start: 0.8666 (m-80) cc_final: 0.8265 (m-80) REVERT: B 642 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 683 TYR cc_start: 0.8112 (m-80) cc_final: 0.7724 (m-80) REVERT: B 684 MET cc_start: 0.8094 (ptt) cc_final: 0.7104 (mtp) REVERT: B 804 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8214 (tmm-80) outliers start: 17 outliers final: 15 residues processed: 99 average time/residue: 0.1087 time to fit residues: 17.0391 Evaluate side-chains 100 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 686 LEU 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 412 THR Chi-restraints excluded: chain B residue 517 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 61 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** 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 = 0.4007 r_free = 0.4007 target = 0.103061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074395 restraints weight = 42789.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077055 restraints weight = 23451.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.078717 restraints weight = 17063.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079722 restraints weight = 14263.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080158 restraints weight = 12865.788| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4124 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= 0.134 Angle : 0.607 11.593 19231 Z= 0.303 Chirality : 0.040 0.202 2189 Planarity : 0.004 0.040 2300 Dihedral : 17.784 179.158 2339 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.25 % Allowed : 14.92 % Favored : 83.84 % 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: 0.46 (0.22), residues: 1594 helix: 0.90 (0.20), residues: 721 sheet: 0.38 (0.37), residues: 212 loop : -0.27 (0.26), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.056 0.001 TYR A 786 PHE 0.014 0.001 PHE B 430 TRP 0.009 0.001 TRP A 839 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00304 (13991) covalent geometry : angle 0.60686 (19231) hydrogen bonds : bond 0.03452 ( 555) hydrogen bonds : angle 4.04760 ( 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 99 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 GLU cc_start: 0.8438 (pt0) cc_final: 0.8192 (pt0) REVERT: B 585 TYR cc_start: 0.8752 (m-80) cc_final: 0.8350 (m-80) REVERT: B 642 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 683 TYR cc_start: 0.8041 (m-80) cc_final: 0.7636 (m-80) REVERT: B 684 MET cc_start: 0.8056 (ptt) cc_final: 0.7104 (mtp) REVERT: B 804 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8165 (tmm-80) outliers start: 17 outliers final: 16 residues processed: 95 average time/residue: 0.1047 time to fit residues: 15.7127 Evaluate side-chains 97 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 608 ILE Chi-restraints excluded: chain A residue 686 LEU 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 412 THR Chi-restraints excluded: chain B residue 517 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 128 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 10 optimal weight: 0.0060 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4020 r_free = 0.4020 target = 0.104108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075052 restraints weight = 42636.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.077697 restraints weight = 23394.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079387 restraints weight = 17066.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.080388 restraints weight = 14304.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.080807 restraints weight = 12922.563| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13991 Z= 0.108 Angle : 0.590 11.048 19231 Z= 0.291 Chirality : 0.039 0.187 2189 Planarity : 0.004 0.036 2300 Dihedral : 17.740 178.879 2339 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.32 % Allowed : 15.14 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1594 helix: 0.99 (0.20), residues: 719 sheet: 0.49 (0.37), residues: 211 loop : -0.27 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 472 TYR 0.025 0.001 TYR A 786 PHE 0.013 0.001 PHE A 732 TRP 0.008 0.001 TRP B 45 HIS 0.007 0.000 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00242 (13991) covalent geometry : angle 0.59049 (19231) hydrogen bonds : bond 0.02967 ( 555) hydrogen bonds : angle 3.93338 ( 1529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.85 seconds wall clock time: 46 minutes 1.95 seconds (2761.95 seconds total)