Starting phenix.real_space_refine on Fri Aug 7 20:39:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cpo_45805/08_2026/9cpo_45805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cpo_45805/08_2026/9cpo_45805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cpo_45805/08_2026/9cpo_45805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cpo_45805/08_2026/9cpo_45805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cpo_45805/08_2026/9cpo_45805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cpo_45805/08_2026/9cpo_45805.map" } resolution = 3.5 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= 0.002 sd= 0.046 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 63 5.49 5 S 82 5.16 5 C 7694 2.51 5 N 2078 2.21 5 O 2546 1.98 5 H 11624 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24089 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 14865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 14865 Classifications: {'peptide': 930} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 892} Chain: "B" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3045 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 187} Chain: "C" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1122 Classifications: {'peptide': 72} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3046 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 187} Chain: "P" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 955 Classifications: {'RNA': 30} Modifications used: {'3*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 15} Link IDs: {'rna3p': 29} Chain: "T" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1054 Classifications: {'RNA': 33} Modifications used: {'3*END': 1, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4911 SG CYS A 310 78.231 71.813 54.225 1.00 47.32 S ATOM 4981 SG CYS A 315 77.614 75.003 52.310 1.00 45.19 S ATOM 5048 SG CYS A 319 76.028 71.710 51.179 1.00 51.10 S ATOM 7798 SG CYS A 496 81.883 74.727 74.874 1.00 50.75 S ATOM 10322 SG CYS A 653 82.665 78.021 73.129 1.00 59.20 S ATOM 10333 SG CYS A 654 83.499 74.717 71.433 1.00 54.97 S Time building chain proxies: 3.63, per 1000 atoms: 0.15 Number of scatterers: 24089 At special positions: 0 Unit cell: (108.528, 125.552, 168.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 63 15.00 O 2546 8.00 N 2078 7.00 C 7694 6.00 H 11624 1.00 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: 2.10 Conformation dependent library (CDL) restraints added in 444.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 304 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 319 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 315 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 650 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 496 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 654 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 653 " Number of angles added : 6 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 17 sheets defined 54.3% alpha, 11.6% beta 30 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 4.256A pdb=" N LEU A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.849A pdb=" N ASP A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.617A pdb=" N PHE A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.893A pdb=" N ILE A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.924A pdb=" N GLU A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.557A pdb=" N VAL A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.774A pdb=" N SER A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 4.005A pdb=" N ALA A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 284 through 296 removed outlier: 4.129A pdb=" N GLN A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 3.696A pdb=" N PHE A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.825A pdb=" N PHE A 335 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 Processing helix chain 'A' and resid 387 through 394 removed outlier: 4.775A pdb=" N VAL A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 392 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.012A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 removed outlier: 4.022A pdb=" N TYR A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.692A pdb=" N TYR A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.572A pdb=" N GLN A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 589 removed outlier: 3.561A pdb=" N THR A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LYS A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.656A pdb=" N LEU A 663 " --> pdb=" O ARG A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 717 removed outlier: 3.538A pdb=" N ASN A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.921A pdb=" N ILE A 723 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 removed outlier: 4.026A pdb=" N TYR A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 736 " --> pdb=" O GLN A 732 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 760 removed outlier: 3.847A pdb=" N LYS A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.706A pdb=" N GLN A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 798 removed outlier: 3.846A pdb=" N ARG A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 807 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 841 through 850 removed outlier: 3.541A pdb=" N ILE A 845 " --> pdb=" O ASP A 841 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 removed outlier: 4.296A pdb=" N SER A 860 " --> pdb=" O LYS A 857 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 861 " --> pdb=" O THR A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 874 removed outlier: 4.290A pdb=" N TYR A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 868 " --> pdb=" O MET A 864 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 872 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP A 873 " --> pdb=" O ALA A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 879 Processing helix chain 'A' and resid 886 through 907 removed outlier: 4.354A pdb=" N LEU A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 911 Processing helix chain 'A' and resid 914 through 920 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.611A pdb=" N ASN A 931 " --> pdb=" O GLU A 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.291A pdb=" N ALA B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 35 through 99 removed outlier: 3.674A pdb=" N ALA B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N MET B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.544A pdb=" N VAL B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.997A pdb=" N LYS B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.193A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 42 Processing helix chain 'C' and resid 44 through 63 removed outlier: 3.534A pdb=" N ASP C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.827A pdb=" N GLY C 69 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 29 Processing helix chain 'D' and resid 30 through 34 removed outlier: 4.102A pdb=" N GLY D 33 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 86 removed outlier: 4.489A pdb=" N LEU D 39 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 102 Processing helix chain 'D' and resid 104 through 117 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 182 through 188 removed outlier: 3.562A pdb=" N ASP D 187 " --> pdb=" O ILE D 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 removed outlier: 4.171A pdb=" N ARG A 23 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 62 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 4.171A pdb=" N ARG A 23 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 62 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TYR A 78 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 39 removed outlier: 3.648A pdb=" N VAL A 36 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 38 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.609A pdb=" N ASP A 269 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 344 Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 396 through 399 removed outlier: 4.155A pdb=" N LEU B 132 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 162 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR B 198 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE B 160 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 153 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 406 through 409 Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'A' and resid 564 through 566 removed outlier: 6.605A pdb=" N THR A 548 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 764 through 766 removed outlier: 3.541A pdb=" N LEU A 766 " --> pdb=" O ASP A 769 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 772 " --> pdb=" O MET A 623 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 622 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 810 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 824 through 830 Processing sheet with id=AB6, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB7, first strand: chain 'D' and resid 119 through 120 removed outlier: 4.018A pdb=" N VAL D 119 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 132 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 197 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS D 194 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL D 163 " --> pdb=" O LYS D 194 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 196 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 119 through 120 removed outlier: 4.018A pdb=" N VAL D 119 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 132 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 197 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS D 194 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL D 163 " --> pdb=" O LYS D 194 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 196 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL D 163 " --> pdb=" O LEU D 171 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11583 1.03 - 1.23: 88 1.23 - 1.42: 5630 1.42 - 1.62: 7067 1.62 - 1.81: 123 Bond restraints: 24491 Sorted by residual: bond pdb=" C TYR A 246 " pdb=" O TYR A 246 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.15e-02 7.56e+03 1.52e+01 bond pdb=" CA TYR A 246 " pdb=" C TYR A 246 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.24e-02 6.50e+03 1.04e+01 bond pdb=" N TYR A 664 " pdb=" CA TYR A 664 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.28e-02 6.10e+03 7.59e+00 bond pdb=" N TYR A 664 " pdb=" H TYR A 664 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" N TYR A 246 " pdb=" H TYR A 246 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.49e+00 ... (remaining 24486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 43476 1.74 - 3.48: 623 3.48 - 5.22: 35 5.22 - 6.96: 1 6.96 - 8.70: 2 Bond angle restraints: 44137 Sorted by residual: angle pdb=" N TYR A 664 " pdb=" CA TYR A 664 " pdb=" CB TYR A 664 " ideal model delta sigma weight residual 110.28 118.98 -8.70 1.55e+00 4.16e-01 3.15e+01 angle pdb=" N TYR A 246 " pdb=" CA TYR A 246 " pdb=" C TYR A 246 " ideal model delta sigma weight residual 110.97 105.93 5.04 1.09e+00 8.42e-01 2.13e+01 angle pdb=" CA TYR A 664 " pdb=" C TYR A 664 " pdb=" O TYR A 664 " ideal model delta sigma weight residual 119.97 114.94 5.03 1.15e+00 7.56e-01 1.91e+01 angle pdb=" C TYR A 664 " pdb=" CA TYR A 664 " pdb=" CB TYR A 664 " ideal model delta sigma weight residual 110.67 102.83 7.84 1.92e+00 2.71e-01 1.67e+01 angle pdb=" O5' G T 34 " pdb=" C5' G T 34 " pdb=" C4' G T 34 " ideal model delta sigma weight residual 109.40 112.22 -2.82 8.00e-01 1.56e+00 1.24e+01 ... (remaining 44132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 10396 18.11 - 36.21: 835 36.21 - 54.32: 287 54.32 - 72.42: 103 72.42 - 90.53: 24 Dihedral angle restraints: 11645 sinusoidal: 6712 harmonic: 4933 Sorted by residual: dihedral pdb=" CA ASP A 474 " pdb=" C ASP A 474 " pdb=" N ILE A 475 " pdb=" CA ILE A 475 " ideal model delta harmonic sigma weight residual 180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG A 466 " pdb=" CD ARG A 466 " pdb=" NE ARG A 466 " pdb=" CZ ARG A 466 " ideal model delta sinusoidal sigma weight residual -90.00 -134.90 44.90 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 934 " pdb=" CD ARG A 934 " pdb=" NE ARG A 934 " pdb=" CZ ARG A 934 " ideal model delta sinusoidal sigma weight residual 90.00 134.52 -44.52 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 11642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1274 0.028 - 0.057: 482 0.057 - 0.085: 105 0.085 - 0.114: 140 0.114 - 0.142: 22 Chirality restraints: 2023 Sorted by residual: chirality pdb=" CA ILE B 184 " pdb=" N ILE B 184 " pdb=" C ILE B 184 " pdb=" CB ILE B 184 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE B 136 " pdb=" N ILE B 136 " pdb=" C ILE B 136 " pdb=" CB ILE B 136 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL A 771 " pdb=" N VAL A 771 " pdb=" C VAL A 771 " pdb=" CB VAL A 771 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2020 not shown) Planarity restraints: 3419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 664 " 0.009 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" N ASN A 665 " -0.028 2.00e-02 2.50e+03 pdb=" CA ASN A 665 " 0.007 2.00e-02 2.50e+03 pdb=" H ASN A 665 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 43 " -0.132 9.50e-02 1.11e+02 4.44e-02 2.66e+00 pdb=" NE ARG D 43 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 43 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 43 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 43 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG D 43 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG D 43 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 43 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 43 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 664 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.51e+00 pdb=" C TYR A 664 " -0.027 2.00e-02 2.50e+03 pdb=" O TYR A 664 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 665 " 0.010 2.00e-02 2.50e+03 ... (remaining 3416 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2107 2.23 - 2.82: 50509 2.82 - 3.42: 58630 3.42 - 4.01: 80230 4.01 - 4.60: 124313 Nonbonded interactions: 315789 Sorted by model distance: nonbonded pdb=" O TYR D 182 " pdb=" HG SER D 185 " model vdw 1.640 2.450 nonbonded pdb=" O PHE A 923 " pdb=" HH TYR A 929 " model vdw 1.660 2.450 nonbonded pdb=" OD2 ASP A 367 " pdb="HD22 ASN A 542 " model vdw 1.664 2.450 nonbonded pdb=" OD1 ASN A 906 " pdb=" HH TYR D 75 " model vdw 1.666 2.450 nonbonded pdb="HO2' A T 24 " pdb=" O5' A T 25 " model vdw 1.671 2.450 ... (remaining 315784 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 'B' selection = (chain 'D' and (resid 6 through 149 or (resid 150 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 151 through 200)) } 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: 1.310 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: 0.110 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.400 Find NCS groups from input model: 0.120 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 0.051 12875 Z= 0.163 Angle : 0.538 8.699 17739 Z= 0.362 Chirality : 0.040 0.142 2023 Planarity : 0.003 0.058 2040 Dihedral : 15.915 90.525 5108 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.24), residues: 1384 helix: 1.05 (0.23), residues: 606 sheet: -1.51 (0.44), residues: 144 loop : -0.45 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 43 TYR 0.019 0.001 TYR A 246 PHE 0.019 0.001 PHE A 473 TRP 0.010 0.001 TRP A 924 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (12867) covalent geometry : angle 0.53637 / 0.36 (17733) hydrogen bonds : bond 0.16679 / 10.75 ( 585) hydrogen bonds : angle 5.58144 / 3.94 ( 1566) metal coordination : bond 0.01860 / 0.89 ( 8) metal coordination : angle 2.33061 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2192 time to fit residues: 40.9799 Evaluate side-chains 120 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.099809 restraints weight = 39675.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.097621 restraints weight = 31847.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.100340 restraints weight = 25837.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.100886 restraints weight = 18486.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101431 restraints weight = 17337.313| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12875 Z= 0.267 Angle : 0.562 5.119 17739 Z= 0.312 Chirality : 0.041 0.153 2023 Planarity : 0.004 0.040 2040 Dihedral : 12.836 88.054 2454 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.89 % Allowed : 13.65 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.43 (0.23), residues: 1384 helix: 0.63 (0.22), residues: 630 sheet: -1.48 (0.45), residues: 121 loop : -0.92 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 43 TYR 0.013 0.002 TYR C 31 PHE 0.016 0.002 PHE A 243 TRP 0.011 0.002 TRP A 924 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 (12867) covalent geometry : angle 0.55914 / 0.31 (17733) hydrogen bonds : bond 0.05871 / 3.72 ( 585) hydrogen bonds : angle 4.37318 / 3.05 ( 1566) metal coordination : bond 0.02565 / 1.23 ( 8) metal coordination : angle 3.02838 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 127 average time/residue: 0.1879 time to fit residues: 36.3263 Evaluate side-chains 127 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 40.0000 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN D 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101789 restraints weight = 39146.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099787 restraints weight = 28367.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102591 restraints weight = 24614.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103060 restraints weight = 17187.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105624 restraints weight = 16144.537| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12875 Z= 0.120 Angle : 0.460 5.023 17739 Z= 0.253 Chirality : 0.036 0.160 2023 Planarity : 0.003 0.044 2040 Dihedral : 12.832 88.251 2454 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.65 % Allowed : 13.57 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.15 (0.23), residues: 1384 helix: 0.92 (0.22), residues: 625 sheet: -1.59 (0.43), residues: 131 loop : -0.74 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 43 TYR 0.010 0.001 TYR C 31 PHE 0.008 0.001 PHE A 243 TRP 0.010 0.001 TRP A 924 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12867) covalent geometry : angle 0.45779 / 0.25 (17733) hydrogen bonds : bond 0.04890 / 3.10 ( 585) hydrogen bonds : angle 4.03973 / 2.81 ( 1566) metal coordination : bond 0.02005 / 0.95 ( 8) metal coordination : angle 2.53386 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.7479 (mt0) cc_final: 0.7260 (mt0) REVERT: C 70 GLU cc_start: 0.6999 (mp0) cc_final: 0.6583 (mp0) outliers start: 8 outliers final: 5 residues processed: 130 average time/residue: 0.1969 time to fit residues: 38.6576 Evaluate side-chains 128 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 189 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 9.9990 chunk 139 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.102993 restraints weight = 39049.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102575 restraints weight = 26448.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104477 restraints weight = 22075.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105222 restraints weight = 16325.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.105362 restraints weight = 14570.132| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12875 Z= 0.095 Angle : 0.436 4.714 17739 Z= 0.238 Chirality : 0.035 0.154 2023 Planarity : 0.003 0.041 2040 Dihedral : 12.752 88.101 2454 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.06 % Allowed : 13.08 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.23), residues: 1384 helix: 1.11 (0.22), residues: 626 sheet: -1.44 (0.43), residues: 131 loop : -0.66 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 43 TYR 0.009 0.001 TYR A 839 PHE 0.007 0.001 PHE A 480 TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (12867) covalent geometry : angle 0.43475 / 0.24 (17733) hydrogen bonds : bond 0.04167 / 2.63 ( 585) hydrogen bonds : angle 3.79676 / 2.63 ( 1566) metal coordination : bond 0.01514 / 0.72 ( 8) metal coordination : angle 1.99383 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7354 (ttm110) cc_final: 0.7111 (ttm110) REVERT: C 70 GLU cc_start: 0.7179 (mp0) cc_final: 0.6682 (mp0) outliers start: 13 outliers final: 10 residues processed: 136 average time/residue: 0.1911 time to fit residues: 39.0087 Evaluate side-chains 133 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 143 optimal weight: 50.0000 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.156661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103062 restraints weight = 38857.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.100432 restraints weight = 31300.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103353 restraints weight = 26191.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104156 restraints weight = 17767.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104324 restraints weight = 16597.147| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12875 Z= 0.136 Angle : 0.450 4.679 17739 Z= 0.246 Chirality : 0.036 0.150 2023 Planarity : 0.003 0.035 2040 Dihedral : 12.691 88.188 2454 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.06 % Allowed : 13.40 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.01 (0.23), residues: 1384 helix: 1.08 (0.22), residues: 629 sheet: -1.50 (0.43), residues: 131 loop : -0.71 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 43 TYR 0.010 0.001 TYR C 31 PHE 0.009 0.001 PHE A 473 TRP 0.010 0.001 TRP A 924 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12867) covalent geometry : angle 0.44826 / 0.25 (17733) hydrogen bonds : bond 0.04291 / 2.69 ( 585) hydrogen bonds : angle 3.78503 / 2.62 ( 1566) metal coordination : bond 0.01827 / 0.87 ( 8) metal coordination : angle 2.16425 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 GLU cc_start: 0.7296 (mp0) cc_final: 0.6762 (mp0) outliers start: 13 outliers final: 10 residues processed: 135 average time/residue: 0.1951 time to fit residues: 39.3270 Evaluate side-chains 130 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.0270 chunk 122 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN D 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.154321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.100841 restraints weight = 39313.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098526 restraints weight = 33113.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102218 restraints weight = 26886.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.102367 restraints weight = 17423.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102579 restraints weight = 16327.636| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12875 Z= 0.123 Angle : 0.440 4.657 17739 Z= 0.241 Chirality : 0.036 0.153 2023 Planarity : 0.003 0.035 2040 Dihedral : 12.665 88.095 2454 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.30 % Allowed : 13.32 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.23), residues: 1384 helix: 1.12 (0.22), residues: 629 sheet: -1.48 (0.43), residues: 131 loop : -0.69 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.010 0.001 TYR C 31 PHE 0.008 0.001 PHE A 243 TRP 0.010 0.001 TRP A 924 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (12867) covalent geometry : angle 0.43882 / 0.24 (17733) hydrogen bonds : bond 0.04134 / 2.59 ( 585) hydrogen bonds : angle 3.71143 / 2.57 ( 1566) metal coordination : bond 0.01764 / 0.84 ( 8) metal coordination : angle 2.12089 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 GLU cc_start: 0.7397 (mp0) cc_final: 0.6880 (mp0) outliers start: 16 outliers final: 16 residues processed: 136 average time/residue: 0.1750 time to fit residues: 36.5318 Evaluate side-chains 137 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN D 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.155690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102064 restraints weight = 39158.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099487 restraints weight = 32330.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102447 restraints weight = 25982.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103162 restraints weight = 17736.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104208 restraints weight = 16750.583| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12875 Z= 0.142 Angle : 0.456 4.665 17739 Z= 0.251 Chirality : 0.036 0.150 2023 Planarity : 0.003 0.036 2040 Dihedral : 12.638 88.132 2454 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.46 % Allowed : 13.48 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.23), residues: 1384 helix: 1.04 (0.22), residues: 629 sheet: -1.50 (0.43), residues: 131 loop : -0.72 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 43 TYR 0.010 0.001 TYR C 31 PHE 0.009 0.001 PHE A 243 TRP 0.010 0.001 TRP A 924 HIS 0.036 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (12867) covalent geometry : angle 0.45400 / 0.25 (17733) hydrogen bonds : bond 0.04260 / 2.69 ( 585) hydrogen bonds : angle 3.71337 / 2.57 ( 1566) metal coordination : bond 0.01867 / 0.89 ( 8) metal coordination : angle 2.18987 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 907 MET cc_start: 0.7712 (tpp) cc_final: 0.7489 (tpp) REVERT: C 70 GLU cc_start: 0.7413 (mp0) cc_final: 0.6897 (mp0) outliers start: 18 outliers final: 16 residues processed: 137 average time/residue: 0.1834 time to fit residues: 38.2050 Evaluate side-chains 139 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.101969 restraints weight = 39252.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.099260 restraints weight = 34764.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101968 restraints weight = 28448.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102619 restraints weight = 20083.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.103104 restraints weight = 18776.714| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12875 Z= 0.147 Angle : 0.455 4.774 17739 Z= 0.249 Chirality : 0.036 0.148 2023 Planarity : 0.003 0.036 2040 Dihedral : 12.618 88.131 2454 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.46 % Allowed : 13.65 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.23), residues: 1384 helix: 1.06 (0.22), residues: 629 sheet: -1.53 (0.43), residues: 131 loop : -0.73 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 43 TYR 0.010 0.001 TYR C 31 PHE 0.020 0.001 PHE A 349 TRP 0.010 0.001 TRP A 924 HIS 0.007 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (12867) covalent geometry : angle 0.45352 / 0.25 (17733) hydrogen bonds : bond 0.04200 / 2.63 ( 585) hydrogen bonds : angle 3.69946 / 2.56 ( 1566) metal coordination : bond 0.01970 / 0.94 ( 8) metal coordination : angle 2.26762 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 907 MET cc_start: 0.7769 (tpp) cc_final: 0.7555 (tpp) REVERT: C 70 GLU cc_start: 0.7413 (mp0) cc_final: 0.6875 (mp0) outliers start: 18 outliers final: 18 residues processed: 137 average time/residue: 0.1884 time to fit residues: 38.9036 Evaluate side-chains 139 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.154840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.100949 restraints weight = 39136.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.098928 restraints weight = 29062.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101621 restraints weight = 25450.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102246 restraints weight = 17596.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103961 restraints weight = 16501.225| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12875 Z= 0.178 Angle : 0.477 4.858 17739 Z= 0.261 Chirality : 0.037 0.147 2023 Planarity : 0.003 0.036 2040 Dihedral : 12.613 88.229 2454 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.46 % Allowed : 13.65 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.14 (0.23), residues: 1384 helix: 0.98 (0.22), residues: 632 sheet: -1.40 (0.45), residues: 121 loop : -0.89 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 43 TYR 0.012 0.001 TYR A 154 PHE 0.012 0.001 PHE A 243 TRP 0.010 0.001 TRP A 924 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (12867) covalent geometry : angle 0.47486 / 0.26 (17733) hydrogen bonds : bond 0.04391 / 2.74 ( 585) hydrogen bonds : angle 3.73650 / 2.58 ( 1566) metal coordination : bond 0.02192 / 1.05 ( 8) metal coordination : angle 2.51426 / 1.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.8048 (mmp80) cc_final: 0.7836 (mmp80) REVERT: C 70 GLU cc_start: 0.7394 (mp0) cc_final: 0.6876 (mp0) outliers start: 18 outliers final: 18 residues processed: 138 average time/residue: 0.1901 time to fit residues: 39.6432 Evaluate side-chains 143 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 50.0000 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103074 restraints weight = 38953.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100571 restraints weight = 31324.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.103907 restraints weight = 25740.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104298 restraints weight = 17132.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104523 restraints weight = 16306.851| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12875 Z= 0.113 Angle : 0.442 5.014 17739 Z= 0.240 Chirality : 0.036 0.150 2023 Planarity : 0.003 0.036 2040 Dihedral : 12.602 88.052 2454 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.30 % Allowed : 13.81 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.23), residues: 1384 helix: 1.13 (0.22), residues: 629 sheet: -1.48 (0.44), residues: 131 loop : -0.71 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 43 TYR 0.009 0.001 TYR C 31 PHE 0.012 0.001 PHE A 349 TRP 0.009 0.001 TRP A 924 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (12867) covalent geometry : angle 0.44007 / 0.24 (17733) hydrogen bonds : bond 0.03988 / 2.51 ( 585) hydrogen bonds : angle 3.62818 / 2.50 ( 1566) metal coordination : bond 0.01808 / 0.86 ( 8) metal coordination : angle 2.24295 / 1.40 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 TYR cc_start: 0.8135 (m-80) cc_final: 0.7719 (m-80) REVERT: B 79 ARG cc_start: 0.8062 (mmp80) cc_final: 0.7838 (mmp80) REVERT: C 70 GLU cc_start: 0.7421 (mp0) cc_final: 0.6822 (mp0) outliers start: 16 outliers final: 16 residues processed: 135 average time/residue: 0.2075 time to fit residues: 42.1140 Evaluate side-chains 140 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102052 restraints weight = 39051.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.099524 restraints weight = 31732.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102625 restraints weight = 26017.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103152 restraints weight = 17633.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103352 restraints weight = 16633.051| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12875 Z= 0.144 Angle : 0.455 4.839 17739 Z= 0.248 Chirality : 0.036 0.146 2023 Planarity : 0.003 0.036 2040 Dihedral : 12.573 88.090 2454 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.46 % Allowed : 13.81 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.01 (0.23), residues: 1384 helix: 1.11 (0.22), residues: 629 sheet: -1.48 (0.44), residues: 131 loop : -0.75 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 43 TYR 0.010 0.001 TYR C 31 PHE 0.010 0.001 PHE A 349 TRP 0.009 0.001 TRP A 924 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (12867) covalent geometry : angle 0.45330 / 0.25 (17733) hydrogen bonds : bond 0.04098 / 2.56 ( 585) hydrogen bonds : angle 3.64507 / 2.51 ( 1566) metal coordination : bond 0.01920 / 0.92 ( 8) metal coordination : angle 2.27383 / 1.44 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2914.37 seconds wall clock time: 50 minutes 27.55 seconds (3027.55 seconds total)