Starting phenix.real_space_refine on Sun Apr 5 18:01:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uyo_64620/04_2026/9uyo_64620.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uyo_64620/04_2026/9uyo_64620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uyo_64620/04_2026/9uyo_64620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uyo_64620/04_2026/9uyo_64620.map" model { file = "/net/cci-nas-00/data/ceres_data/9uyo_64620/04_2026/9uyo_64620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uyo_64620/04_2026/9uyo_64620.cif" } resolution = 3.39 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= -0.001 sd= 0.035 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 76 5.16 5 C 7608 2.51 5 N 2055 2.21 5 O 2219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11960 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5964 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 42, 'TRANS': 734} Chain breaks: 3 Chain: "A" Number of atoms: 5974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5974 Classifications: {'peptide': 778} Link IDs: {'PTRANS': 42, 'TRANS': 735} Chain breaks: 3 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.45, per 1000 atoms: 0.20 Number of scatterers: 11960 At special positions: 0 Unit cell: (93.28, 99.216, 184.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 2 15.00 O 2219 8.00 N 2055 7.00 C 7608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 522 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 522 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.04 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 744 " distance=2.03 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: 1.02 Conformation dependent library (CDL) restraints added in 717.7 milliseconds 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 19 sheets defined 48.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 61 through 81 removed outlier: 3.772A pdb=" N HIS B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.873A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 165 removed outlier: 3.650A pdb=" N MET B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.617A pdb=" N SER B 182 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 183 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 258 through 268 removed outlier: 3.867A pdb=" N LYS B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 264 " --> pdb=" O PHE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.760A pdb=" N ARG B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.724A pdb=" N GLN B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 Processing helix chain 'B' and resid 400 through 423 removed outlier: 3.647A pdb=" N VAL B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 586 through 610 removed outlier: 3.781A pdb=" N LEU B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 620 Processing helix chain 'B' and resid 622 through 642 removed outlier: 4.135A pdb=" N VAL B 642 " --> pdb=" O THR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 658 removed outlier: 3.920A pdb=" N ALA B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG B 654 " --> pdb=" O CYS B 650 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 678 Processing helix chain 'B' and resid 693 through 717 Processing helix chain 'B' and resid 734 through 738 removed outlier: 3.634A pdb=" N ALA B 738 " --> pdb=" O PRO B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 775 removed outlier: 3.889A pdb=" N SER B 750 " --> pdb=" O MET B 746 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 806 removed outlier: 3.794A pdb=" N THR B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 789 " --> pdb=" O ILE B 785 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 790 " --> pdb=" O GLY B 786 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 800 " --> pdb=" O TRP B 796 " (cutoff:3.500A) Proline residue: B 801 - end of helix Processing helix chain 'B' and resid 807 through 809 No H-bonds generated for 'chain 'B' and resid 807 through 809' Processing helix chain 'B' and resid 811 through 834 removed outlier: 3.928A pdb=" N THR B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 845 removed outlier: 3.868A pdb=" N VAL B 842 " --> pdb=" O PRO B 838 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 843 " --> pdb=" O LYS B 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.552A pdb=" N VAL A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ARG A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.579A pdb=" N LEU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 removed outlier: 4.051A pdb=" N MET A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.590A pdb=" N ILE A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.607A pdb=" N ASP A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.597A pdb=" N PHE A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 423 removed outlier: 3.554A pdb=" N ILE A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.521A pdb=" N GLN A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 586 through 610 removed outlier: 3.682A pdb=" N LEU A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 620 removed outlier: 3.947A pdb=" N SER A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 642 removed outlier: 4.012A pdb=" N THR A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 639 " --> pdb=" O TYR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 680 removed outlier: 4.092A pdb=" N CYS A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 719 removed outlier: 3.524A pdb=" N GLN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 749 through 772 Processing helix chain 'A' and resid 781 through 807 removed outlier: 4.141A pdb=" N ILE A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 791 " --> pdb=" O PHE A 787 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 800 " --> pdb=" O TRP A 796 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 811 through 836 removed outlier: 4.098A pdb=" N THR A 818 " --> pdb=" O TYR A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 846 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.726A pdb=" N PHE B 45 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.566A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ARG B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 41 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR B 40 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.057A pdb=" N GLN B 171 " --> pdb=" O SER B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 245 through 251 removed outlier: 7.883A pdb=" N VAL B 216 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER B 248 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 218 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS B 250 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 220 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE B 276 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 331 removed outlier: 3.876A pdb=" N ILE B 472 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 491 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 449 through 451 removed outlier: 3.575A pdb=" N PHE B 450 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AA8, first strand: chain 'B' and resid 547 through 549 Processing sheet with id=AA9, first strand: chain 'B' and resid 562 through 564 Processing sheet with id=AB1, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AB2, first strand: chain 'A' and resid 33 through 34 removed outlier: 7.000A pdb=" N LEU A 39 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ARG A 94 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 41 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 96 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY A 43 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 40 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA A 147 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 149 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ILE A 172 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 148 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 48 through 50 removed outlier: 4.739A pdb=" N GLN A 59 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 245 through 251 removed outlier: 8.073A pdb=" N VAL A 216 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N SER A 248 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR A 218 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS A 250 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 220 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 328 through 331 removed outlier: 3.606A pdb=" N GLY A 491 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN A 474 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA A 489 " --> pdb=" O GLN A 474 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN A 476 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR A 487 " --> pdb=" O GLN A 476 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 450 through 451 removed outlier: 3.747A pdb=" N PHE A 450 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB8, first strand: chain 'A' and resid 547 through 551 removed outlier: 3.653A pdb=" N VAL A 550 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 562 through 564 Processing sheet with id=AC1, first strand: chain 'A' and resid 723 through 726 removed outlier: 3.510A pdb=" N VAL A 724 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 743 " --> pdb=" O VAL A 724 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1569 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3919 1.34 - 1.46: 2857 1.46 - 1.58: 5337 1.58 - 1.70: 2 1.70 - 1.82: 110 Bond restraints: 12225 Sorted by residual: bond pdb=" O2P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O1P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O1P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O2P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O3P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.57e+01 ... (remaining 12220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 16471 2.11 - 4.22: 124 4.22 - 6.33: 24 6.33 - 8.45: 8 8.45 - 10.56: 2 Bond angle restraints: 16629 Sorted by residual: angle pdb=" CB MET B 641 " pdb=" CG MET B 641 " pdb=" SD MET B 641 " ideal model delta sigma weight residual 112.70 123.26 -10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CA PRO A 589 " pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 112.00 107.36 4.64 1.40e+00 5.10e-01 1.10e+01 angle pdb=" CA GLN B 235 " pdb=" CB GLN B 235 " pdb=" CG GLN B 235 " ideal model delta sigma weight residual 114.10 119.56 -5.46 2.00e+00 2.50e-01 7.46e+00 angle pdb=" CA LYS A 256 " pdb=" CB LYS A 256 " pdb=" CG LYS A 256 " ideal model delta sigma weight residual 114.10 119.53 -5.43 2.00e+00 2.50e-01 7.36e+00 angle pdb=" CB SEP A1001 " pdb=" OG SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 110.00 118.11 -8.11 3.00e+00 1.11e-01 7.30e+00 ... (remaining 16624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6181 16.96 - 33.91: 835 33.91 - 50.87: 247 50.87 - 67.83: 45 67.83 - 84.79: 19 Dihedral angle restraints: 7327 sinusoidal: 2856 harmonic: 4471 Sorted by residual: dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 24.93 68.07 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS B 558 " pdb=" SG CYS B 558 " pdb=" SG CYS B 571 " pdb=" CB CYS B 571 " ideal model delta sinusoidal sigma weight residual 93.00 147.07 -54.07 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual -86.00 -34.02 -51.98 1 1.00e+01 1.00e-02 3.69e+01 ... (remaining 7324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1110 0.026 - 0.052: 487 0.052 - 0.079: 199 0.079 - 0.105: 79 0.105 - 0.131: 22 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL A 304 " pdb=" N VAL A 304 " pdb=" C VAL A 304 " pdb=" CB VAL A 304 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1894 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 588 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 589 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 644 " 0.063 5.00e-02 4.00e+02 9.50e-02 1.44e+01 pdb=" N PRO A 645 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 645 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 645 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 693 " -0.059 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO B 694 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " -0.049 5.00e-02 4.00e+02 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.98: 5637 2.98 - 3.46: 11691 3.46 - 3.94: 17861 3.94 - 4.42: 20026 4.42 - 4.90: 33906 Nonbonded interactions: 89121 Sorted by model distance: nonbonded pdb=" N SEP A1001 " pdb=" OG SEP A1001 " model vdw 2.495 2.496 nonbonded pdb=" N SEP B1001 " pdb=" OG SEP B1001 " model vdw 2.522 2.496 nonbonded pdb=" C SER B 221 " pdb=" OG SER B 221 " model vdw 2.619 2.616 nonbonded pdb=" C SER A 237 " pdb=" OG SER A 237 " model vdw 2.630 2.616 nonbonded pdb=" C SER A 825 " pdb=" OG SER A 825 " model vdw 2.635 2.616 ... (remaining 89116 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 29 through 845 or resid 1001)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.240 Find NCS groups from input model: 0.210 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 12241 Z= 0.148 Angle : 0.498 10.558 16661 Z= 0.240 Chirality : 0.037 0.131 1897 Planarity : 0.005 0.104 2134 Dihedral : 16.896 84.787 4409 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.16 % Allowed : 28.54 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1539 helix: 0.33 (0.19), residues: 678 sheet: -1.00 (0.40), residues: 201 loop : -1.38 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.008 0.001 TYR A 727 PHE 0.026 0.001 PHE A 799 TRP 0.006 0.000 TRP A 303 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00314 (12225) covalent geometry : angle 0.49802 (16629) SS BOND : bond 0.00212 ( 16) SS BOND : angle 0.69662 ( 32) hydrogen bonds : bond 0.27002 ( 537) hydrogen bonds : angle 7.24453 ( 1569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.328 Fit side-chains REVERT: B 235 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8346 (tt0) REVERT: A 70 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8251 (mm-30) outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.0915 time to fit residues: 12.8144 Evaluate side-chains 90 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.163232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104786 restraints weight = 17515.658| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.10 r_work: 0.3041 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12241 Z= 0.130 Angle : 0.533 11.302 16661 Z= 0.268 Chirality : 0.040 0.142 1897 Planarity : 0.005 0.078 2134 Dihedral : 4.378 76.898 1707 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.74 % Allowed : 26.27 % Favored : 70.99 % 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: -0.25 (0.21), residues: 1539 helix: 1.17 (0.20), residues: 691 sheet: -1.04 (0.38), residues: 201 loop : -1.33 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.011 0.001 TYR A 225 PHE 0.014 0.001 PHE A 799 TRP 0.010 0.001 TRP B 361 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00268 (12225) covalent geometry : angle 0.53225 (16629) SS BOND : bond 0.00210 ( 16) SS BOND : angle 0.75115 ( 32) hydrogen bonds : bond 0.06032 ( 537) hydrogen bonds : angle 4.43628 ( 1569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.526 Fit side-chains REVERT: B 565 THR cc_start: 0.5962 (OUTLIER) cc_final: 0.5689 (p) REVERT: A 716 LEU cc_start: 0.7668 (pp) cc_final: 0.7452 (pt) outliers start: 35 outliers final: 16 residues processed: 125 average time/residue: 0.0927 time to fit residues: 18.0748 Evaluate side-chains 106 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 102 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 78 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 14 optimal weight: 0.0980 chunk 133 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 121 optimal weight: 0.0070 chunk 49 optimal weight: 0.7980 overall best weight: 0.3336 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.164912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106849 restraints weight = 17715.443| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.92 r_work: 0.3042 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12241 Z= 0.101 Angle : 0.500 10.744 16661 Z= 0.244 Chirality : 0.039 0.174 1897 Planarity : 0.005 0.071 2134 Dihedral : 4.133 70.746 1707 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.50 % Allowed : 26.82 % Favored : 70.68 % 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: 0.08 (0.22), residues: 1539 helix: 1.54 (0.20), residues: 688 sheet: -0.99 (0.38), residues: 197 loop : -1.22 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 653 TYR 0.005 0.001 TYR A 727 PHE 0.006 0.001 PHE A 260 TRP 0.008 0.001 TRP B 361 HIS 0.001 0.000 HIS A 419 Details of bonding type rmsd covalent geometry : bond 0.00201 (12225) covalent geometry : angle 0.49980 (16629) SS BOND : bond 0.00204 ( 16) SS BOND : angle 0.70603 ( 32) hydrogen bonds : bond 0.04650 ( 537) hydrogen bonds : angle 3.94994 ( 1569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.481 Fit side-chains REVERT: B 565 THR cc_start: 0.5689 (OUTLIER) cc_final: 0.5430 (p) REVERT: B 804 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6386 (t80) REVERT: A 268 MET cc_start: 0.9215 (mmm) cc_final: 0.8907 (mmp) REVERT: A 697 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7601 (pm20) outliers start: 32 outliers final: 14 residues processed: 122 average time/residue: 0.0874 time to fit residues: 16.7361 Evaluate side-chains 105 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 69 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN A 808 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.160352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103590 restraints weight = 17720.609| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.51 r_work: 0.2979 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12241 Z= 0.248 Angle : 0.583 10.322 16661 Z= 0.292 Chirality : 0.042 0.136 1897 Planarity : 0.005 0.067 2134 Dihedral : 4.602 73.363 1707 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.21 % Allowed : 26.58 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1539 helix: 1.37 (0.20), residues: 698 sheet: -1.14 (0.37), residues: 202 loop : -1.52 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.012 0.001 TYR A 104 PHE 0.016 0.001 PHE B 279 TRP 0.009 0.001 TRP B 303 HIS 0.005 0.001 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00606 (12225) covalent geometry : angle 0.58175 (16629) SS BOND : bond 0.00237 ( 16) SS BOND : angle 0.89208 ( 32) hydrogen bonds : bond 0.05241 ( 537) hydrogen bonds : angle 4.06394 ( 1569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 0.441 Fit side-chains REVERT: B 369 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 565 THR cc_start: 0.6097 (OUTLIER) cc_final: 0.5797 (p) REVERT: B 804 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6549 (t80) REVERT: A 716 LEU cc_start: 0.7490 (pp) cc_final: 0.7274 (pt) outliers start: 41 outliers final: 26 residues processed: 125 average time/residue: 0.0851 time to fit residues: 16.7422 Evaluate side-chains 113 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 803 PHE Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 148 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.162550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103487 restraints weight = 17693.774| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.77 r_work: 0.2999 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12241 Z= 0.128 Angle : 0.525 10.528 16661 Z= 0.256 Chirality : 0.040 0.139 1897 Planarity : 0.004 0.064 2134 Dihedral : 4.349 68.176 1707 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.19 % Allowed : 27.52 % Favored : 70.29 % 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: 0.00 (0.22), residues: 1539 helix: 1.60 (0.20), residues: 678 sheet: -1.07 (0.37), residues: 201 loop : -1.37 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 527 TYR 0.007 0.001 TYR A 225 PHE 0.011 0.001 PHE A 260 TRP 0.008 0.001 TRP B 361 HIS 0.002 0.000 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00295 (12225) covalent geometry : angle 0.52397 (16629) SS BOND : bond 0.00206 ( 16) SS BOND : angle 0.78393 ( 32) hydrogen bonds : bond 0.04219 ( 537) hydrogen bonds : angle 3.84844 ( 1569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.418 Fit side-chains REVERT: B 565 THR cc_start: 0.5656 (OUTLIER) cc_final: 0.5374 (p) REVERT: B 804 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6452 (t80) REVERT: A 697 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7608 (pm20) outliers start: 28 outliers final: 19 residues processed: 114 average time/residue: 0.0832 time to fit residues: 14.8860 Evaluate side-chains 110 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 803 PHE Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 145 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN B 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.161919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103864 restraints weight = 17703.369| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.79 r_work: 0.3025 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12241 Z= 0.158 Angle : 0.553 13.374 16661 Z= 0.268 Chirality : 0.040 0.133 1897 Planarity : 0.004 0.063 2134 Dihedral : 4.409 68.728 1707 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.81 % Allowed : 26.66 % Favored : 70.52 % 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: -0.04 (0.22), residues: 1539 helix: 1.53 (0.20), residues: 682 sheet: -1.06 (0.38), residues: 197 loop : -1.39 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 653 TYR 0.009 0.001 TYR A 225 PHE 0.012 0.001 PHE B 279 TRP 0.007 0.001 TRP A 303 HIS 0.003 0.001 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00376 (12225) covalent geometry : angle 0.55263 (16629) SS BOND : bond 0.00201 ( 16) SS BOND : angle 0.78882 ( 32) hydrogen bonds : bond 0.04345 ( 537) hydrogen bonds : angle 3.87055 ( 1569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 565 THR cc_start: 0.5924 (OUTLIER) cc_final: 0.5628 (p) REVERT: B 804 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6479 (t80) REVERT: A 641 MET cc_start: 0.6094 (tpp) cc_final: 0.5526 (tpt) outliers start: 36 outliers final: 25 residues processed: 122 average time/residue: 0.0880 time to fit residues: 16.7037 Evaluate side-chains 114 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 803 PHE Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 151 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103960 restraints weight = 17645.147| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.76 r_work: 0.3039 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12241 Z= 0.123 Angle : 0.530 11.005 16661 Z= 0.255 Chirality : 0.040 0.144 1897 Planarity : 0.004 0.063 2134 Dihedral : 4.307 66.639 1707 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.58 % Allowed : 27.13 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1539 helix: 1.64 (0.20), residues: 678 sheet: -1.00 (0.38), residues: 197 loop : -1.36 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.007 0.001 TYR A 104 PHE 0.023 0.001 PHE A 799 TRP 0.008 0.001 TRP B 361 HIS 0.002 0.000 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00285 (12225) covalent geometry : angle 0.52933 (16629) SS BOND : bond 0.00200 ( 16) SS BOND : angle 0.74054 ( 32) hydrogen bonds : bond 0.03976 ( 537) hydrogen bonds : angle 3.76070 ( 1569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 565 THR cc_start: 0.5931 (OUTLIER) cc_final: 0.5638 (p) REVERT: B 804 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6486 (t80) REVERT: A 639 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8290 (m-10) REVERT: A 716 LEU cc_start: 0.6935 (pp) cc_final: 0.6453 (pt) outliers start: 33 outliers final: 23 residues processed: 117 average time/residue: 0.0863 time to fit residues: 15.9516 Evaluate side-chains 110 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 9 optimal weight: 0.4980 chunk 120 optimal weight: 0.8980 chunk 49 optimal weight: 0.0370 chunk 146 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.163727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105541 restraints weight = 17503.735| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.18 r_work: 0.3046 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12241 Z= 0.107 Angle : 0.531 11.482 16661 Z= 0.253 Chirality : 0.039 0.157 1897 Planarity : 0.004 0.062 2134 Dihedral : 4.179 64.254 1707 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.58 % Allowed : 27.44 % Favored : 69.98 % 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: 0.18 (0.22), residues: 1539 helix: 1.78 (0.20), residues: 672 sheet: -0.97 (0.38), residues: 197 loop : -1.28 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 653 TYR 0.006 0.001 TYR A 104 PHE 0.008 0.001 PHE A 279 TRP 0.008 0.001 TRP B 361 HIS 0.002 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00242 (12225) covalent geometry : angle 0.53051 (16629) SS BOND : bond 0.00210 ( 16) SS BOND : angle 0.71638 ( 32) hydrogen bonds : bond 0.03683 ( 537) hydrogen bonds : angle 3.67334 ( 1569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.337 Fit side-chains REVERT: B 235 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8064 (tt0) REVERT: B 565 THR cc_start: 0.5760 (OUTLIER) cc_final: 0.5473 (p) REVERT: B 641 MET cc_start: 0.7295 (tpp) cc_final: 0.6623 (mmm) REVERT: B 804 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6498 (t80) REVERT: A 641 MET cc_start: 0.5844 (tpt) cc_final: 0.5464 (tpt) REVERT: A 697 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7545 (pm20) outliers start: 33 outliers final: 26 residues processed: 120 average time/residue: 0.0825 time to fit residues: 15.5655 Evaluate side-chains 116 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.163442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104599 restraints weight = 17540.519| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.58 r_work: 0.3061 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12241 Z= 0.114 Angle : 0.532 10.740 16661 Z= 0.254 Chirality : 0.039 0.141 1897 Planarity : 0.004 0.062 2134 Dihedral : 4.161 63.906 1707 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.58 % Allowed : 27.83 % Favored : 69.59 % 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: 0.18 (0.22), residues: 1539 helix: 1.79 (0.20), residues: 675 sheet: -0.95 (0.38), residues: 201 loop : -1.31 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 653 TYR 0.006 0.001 TYR A 225 PHE 0.024 0.001 PHE A 799 TRP 0.007 0.001 TRP B 361 HIS 0.002 0.000 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00263 (12225) covalent geometry : angle 0.53186 (16629) SS BOND : bond 0.00196 ( 16) SS BOND : angle 0.69696 ( 32) hydrogen bonds : bond 0.03702 ( 537) hydrogen bonds : angle 3.65264 ( 1569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.545 Fit side-chains REVERT: B 565 THR cc_start: 0.5825 (OUTLIER) cc_final: 0.5536 (p) REVERT: B 641 MET cc_start: 0.7317 (tpp) cc_final: 0.6665 (mmm) REVERT: B 804 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6561 (t80) REVERT: A 639 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8334 (m-10) REVERT: A 697 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7617 (pm20) outliers start: 33 outliers final: 27 residues processed: 117 average time/residue: 0.0889 time to fit residues: 16.1321 Evaluate side-chains 117 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 chunk 122 optimal weight: 0.0870 chunk 144 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.163989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105677 restraints weight = 17631.113| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.18 r_work: 0.3048 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12241 Z= 0.106 Angle : 0.532 10.481 16661 Z= 0.254 Chirality : 0.039 0.141 1897 Planarity : 0.004 0.063 2134 Dihedral : 4.094 62.276 1707 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.58 % Allowed : 27.76 % Favored : 69.66 % 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: 0.25 (0.22), residues: 1539 helix: 1.84 (0.20), residues: 675 sheet: -0.93 (0.38), residues: 201 loop : -1.27 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 653 TYR 0.005 0.001 TYR B 187 PHE 0.023 0.001 PHE A 799 TRP 0.008 0.001 TRP B 361 HIS 0.002 0.000 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00240 (12225) covalent geometry : angle 0.53135 (16629) SS BOND : bond 0.00192 ( 16) SS BOND : angle 0.64616 ( 32) hydrogen bonds : bond 0.03563 ( 537) hydrogen bonds : angle 3.61571 ( 1569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.413 Fit side-chains REVERT: B 235 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8061 (tt0) REVERT: B 565 THR cc_start: 0.5886 (OUTLIER) cc_final: 0.5601 (p) REVERT: B 804 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6537 (t80) REVERT: A 381 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7007 (ttp-110) REVERT: A 639 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8298 (m-10) REVERT: A 641 MET cc_start: 0.5793 (tpp) cc_final: 0.5321 (tpt) REVERT: A 697 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7567 (pm20) outliers start: 33 outliers final: 27 residues processed: 116 average time/residue: 0.0920 time to fit residues: 16.5820 Evaluate side-chains 115 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 150 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.161954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102559 restraints weight = 17543.586| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.88 r_work: 0.2978 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12241 Z= 0.180 Angle : 0.569 10.499 16661 Z= 0.276 Chirality : 0.041 0.140 1897 Planarity : 0.004 0.064 2134 Dihedral : 4.336 66.615 1707 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.74 % Allowed : 27.60 % Favored : 69.66 % 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: -0.03 (0.22), residues: 1539 helix: 1.57 (0.20), residues: 692 sheet: -1.06 (0.38), residues: 197 loop : -1.46 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.009 0.001 TYR A 225 PHE 0.022 0.001 PHE A 799 TRP 0.007 0.001 TRP B 303 HIS 0.004 0.001 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00432 (12225) covalent geometry : angle 0.56823 (16629) SS BOND : bond 0.00222 ( 16) SS BOND : angle 0.82700 ( 32) hydrogen bonds : bond 0.04171 ( 537) hydrogen bonds : angle 3.73472 ( 1569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.31 seconds wall clock time: 53 minutes 9.34 seconds (3189.34 seconds total)