Starting phenix.real_space_refine on Fri Sep 19 06:45:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cpo_45805/09_2025/9cpo_45805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cpo_45805/09_2025/9cpo_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_45805/09_2025/9cpo_45805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cpo_45805/09_2025/9cpo_45805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cpo_45805/09_2025/9cpo_45805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cpo_45805/09_2025/9cpo_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-2.0-5805/lib/python3.9/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: 4.16, per 1000 atoms: 0.17 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: 2.04 Conformation dependent library (CDL) restraints added in 868.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.94 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: 5.96 Time building geometry restraints manager: 2.85 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: 43643 1.74 - 3.48: 456 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=" CA TYR A 246 " pdb=" CB TYR A 246 " pdb=" CG TYR A 246 " ideal model delta sigma weight residual 113.90 119.78 -5.88 1.80e+00 3.09e-01 1.07e+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: 1303 0.028 - 0.057: 521 0.057 - 0.085: 101 0.085 - 0.114: 78 0.114 - 0.142: 20 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: 1.550 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: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 30.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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= 0.147 Angle : 0.495 8.699 17739 Z= 0.275 Chirality : 0.036 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 aren 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 covalent geometry : bond 0.00324 (12867) covalent geometry : angle 0.49310 (17733) hydrogen bonds : bond 0.16679 ( 585) hydrogen bonds : angle 5.58144 ( 1566) metal coordination : bond 0.01860 ( 8) metal coordination : angle 2.33061 ( 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 : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2276 time to fit residues: 42.4405 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 : 0.593 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098857 restraints weight = 39753.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.096792 restraints weight = 30756.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099795 restraints weight = 26064.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100219 restraints weight = 17739.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.100746 restraints weight = 16260.395| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12875 Z= 0.257 Angle : 0.556 5.189 17739 Z= 0.302 Chirality : 0.040 0.154 2023 Planarity : 0.004 0.039 2040 Dihedral : 12.886 91.296 2454 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.06 % Allowed : 13.32 % Favored : 85.62 % 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 aren not related in a simple way. whole: -0.41 (0.23), residues: 1384 helix: 0.66 (0.22), residues: 632 sheet: -1.45 (0.46), residues: 121 loop : -0.94 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 43 TYR 0.014 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 covalent geometry : bond 0.00624 (12867) covalent geometry : angle 0.55293 (17733) hydrogen bonds : bond 0.05758 ( 585) hydrogen bonds : angle 4.32021 ( 1566) metal coordination : bond 0.02743 ( 8) metal coordination : angle 3.28133 ( 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 137 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 132 average time/residue: 0.2309 time to fit residues: 45.3338 Evaluate side-chains 131 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 20.0000 chunk 76 optimal weight: 0.5980 chunk 123 optimal weight: 0.0170 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.157376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.103422 restraints weight = 38956.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.101325 restraints weight = 28867.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104299 restraints weight = 24811.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104711 restraints weight = 17060.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106158 restraints weight = 16131.145| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12875 Z= 0.099 Angle : 0.454 4.760 17739 Z= 0.241 Chirality : 0.036 0.156 2023 Planarity : 0.003 0.036 2040 Dihedral : 12.769 91.004 2454 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.41 % Allowed : 13.48 % Favored : 86.11 % 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 aren not related in a simple way. whole: 0.01 (0.23), residues: 1384 helix: 1.02 (0.22), residues: 629 sheet: -1.49 (0.44), residues: 131 loop : -0.63 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 43 TYR 0.009 0.001 TYR A 839 PHE 0.006 0.001 PHE A 349 TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00221 (12867) covalent geometry : angle 0.45262 (17733) hydrogen bonds : bond 0.03957 ( 585) hydrogen bonds : angle 3.78503 ( 1566) metal coordination : bond 0.01559 ( 8) metal coordination : angle 1.97442 ( 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 135 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7404 (ttm110) cc_final: 0.7193 (ttm110) REVERT: A 524 TYR cc_start: 0.8241 (m-80) cc_final: 0.7717 (m-80) outliers start: 5 outliers final: 2 residues processed: 133 average time/residue: 0.2321 time to fit residues: 45.5129 Evaluate side-chains 129 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 551 ASN 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: 20.0000 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.156298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.102333 restraints weight = 39013.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100227 restraints weight = 29093.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103139 restraints weight = 24856.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103537 restraints weight = 17394.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103739 restraints weight = 16306.203| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0894 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= 0.136 Angle : 0.466 4.744 17739 Z= 0.248 Chirality : 0.036 0.151 2023 Planarity : 0.003 0.037 2040 Dihedral : 12.648 90.942 2454 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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 aren not related in a simple way. whole: -0.01 (0.23), residues: 1384 helix: 1.04 (0.22), residues: 629 sheet: -1.62 (0.41), residues: 142 loop : -0.62 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00325 (12867) covalent geometry : angle 0.46373 (17733) hydrogen bonds : bond 0.04038 ( 585) hydrogen bonds : angle 3.71719 ( 1566) metal coordination : bond 0.01898 ( 8) metal coordination : angle 2.26525 ( 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 147 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7288 (ttm110) cc_final: 0.7050 (ttm110) REVERT: C 70 GLU cc_start: 0.7054 (mp0) cc_final: 0.6543 (mp0) outliers start: 16 outliers final: 15 residues processed: 142 average time/residue: 0.2308 time to fit residues: 48.3330 Evaluate side-chains 138 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 A residue 830 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.0020 chunk 143 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.155387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101940 restraints weight = 39135.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.099854 restraints weight = 33473.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102678 restraints weight = 26807.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103447 restraints weight = 17849.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103606 restraints weight = 16253.046| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12875 Z= 0.097 Angle : 0.437 4.400 17739 Z= 0.231 Chirality : 0.035 0.151 2023 Planarity : 0.003 0.038 2040 Dihedral : 12.538 90.690 2454 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.06 % Allowed : 13.73 % Favored : 85.22 % 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 aren not related in a simple way. whole: 0.18 (0.24), residues: 1384 helix: 1.21 (0.22), residues: 629 sheet: -1.46 (0.44), residues: 131 loop : -0.58 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 43 TYR 0.009 0.001 TYR C 31 PHE 0.009 0.001 PHE A 349 TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00221 (12867) covalent geometry : angle 0.43596 (17733) hydrogen bonds : bond 0.03543 ( 585) hydrogen bonds : angle 3.55081 ( 1566) metal coordination : bond 0.01499 ( 8) metal coordination : angle 1.81348 ( 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 140 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7419 (ttm110) cc_final: 0.7177 (ttm110) REVERT: C 70 GLU cc_start: 0.7142 (mp0) cc_final: 0.6683 (mp0) outliers start: 13 outliers final: 11 residues processed: 136 average time/residue: 0.2348 time to fit residues: 46.7097 Evaluate side-chains 141 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 205 MET 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 100 LYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.150741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.096679 restraints weight = 39717.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.094387 restraints weight = 29977.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.096896 restraints weight = 26583.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097576 restraints weight = 18625.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.098785 restraints weight = 17066.561| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 12875 Z= 0.267 Angle : 0.545 5.293 17739 Z= 0.295 Chirality : 0.040 0.147 2023 Planarity : 0.004 0.038 2040 Dihedral : 12.615 91.368 2454 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.95 % Allowed : 13.00 % 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 aren not related in a simple way. whole: -0.30 (0.23), residues: 1384 helix: 0.81 (0.22), residues: 636 sheet: -1.44 (0.46), residues: 121 loop : -0.95 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 43 TYR 0.015 0.002 TYR A 154 PHE 0.017 0.002 PHE A 243 TRP 0.011 0.001 TRP A 924 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00659 (12867) covalent geometry : angle 0.54214 (17733) hydrogen bonds : bond 0.04817 ( 585) hydrogen bonds : angle 3.84894 ( 1566) metal coordination : bond 0.02730 ( 8) metal coordination : angle 3.10007 ( 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 159 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 GLU cc_start: 0.7191 (mp0) cc_final: 0.6720 (mp0) REVERT: D 138 ASP cc_start: 0.8599 (p0) cc_final: 0.8398 (p0) REVERT: D 165 ASP cc_start: 0.6789 (t70) cc_final: 0.6345 (t70) outliers start: 24 outliers final: 21 residues processed: 154 average time/residue: 0.2214 time to fit residues: 50.6231 Evaluate side-chains 152 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 98 ASP 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 324 ILE Chi-restraints excluded: chain A residue 345 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 A residue 556 ILE Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain A residue 830 VAL 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 18 THR 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: 9.9990 chunk 74 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 131 optimal weight: 0.0770 chunk 133 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.153691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.099398 restraints weight = 39455.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.096966 restraints weight = 29369.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099168 restraints weight = 24291.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100682 restraints weight = 16982.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100846 restraints weight = 15016.758| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1106 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= 0.116 Angle : 0.456 4.484 17739 Z= 0.243 Chirality : 0.036 0.148 2023 Planarity : 0.003 0.043 2040 Dihedral : 12.545 91.051 2454 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.30 % Allowed : 14.13 % Favored : 84.57 % 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 aren not related in a simple way. whole: 0.02 (0.23), residues: 1384 helix: 1.10 (0.22), residues: 629 sheet: -1.53 (0.44), residues: 131 loop : -0.70 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 43 TYR 0.009 0.001 TYR C 31 PHE 0.009 0.001 PHE A 349 TRP 0.010 0.001 TRP A 924 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00271 (12867) covalent geometry : angle 0.45457 (17733) hydrogen bonds : bond 0.03811 ( 585) hydrogen bonds : angle 3.61633 ( 1566) metal coordination : bond 0.01825 ( 8) metal coordination : angle 2.19650 ( 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 150 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7958 (mmp80) REVERT: C 70 GLU cc_start: 0.7417 (mp0) cc_final: 0.6975 (mp0) REVERT: D 165 ASP cc_start: 0.6852 (t70) cc_final: 0.6445 (t70) outliers start: 16 outliers final: 15 residues processed: 146 average time/residue: 0.2294 time to fit residues: 50.2534 Evaluate side-chains 145 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 324 ILE 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 556 ILE Chi-restraints excluded: chain A residue 830 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 95 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.156289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.102537 restraints weight = 39197.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100092 restraints weight = 30180.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102863 restraints weight = 25637.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103624 restraints weight = 17389.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105227 restraints weight = 16627.950| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12875 Z= 0.121 Angle : 0.452 4.517 17739 Z= 0.241 Chirality : 0.036 0.147 2023 Planarity : 0.003 0.051 2040 Dihedral : 12.480 90.705 2454 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.71 % Allowed : 14.13 % Favored : 84.16 % 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 aren not related in a simple way. whole: 0.10 (0.24), residues: 1384 helix: 1.18 (0.22), residues: 630 sheet: -1.50 (0.45), residues: 126 loop : -0.67 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 43 TYR 0.010 0.001 TYR C 31 PHE 0.009 0.001 PHE A 349 TRP 0.009 0.001 TRP A 924 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00288 (12867) covalent geometry : angle 0.45088 (17733) hydrogen bonds : bond 0.03712 ( 585) hydrogen bonds : angle 3.54447 ( 1566) metal coordination : bond 0.01715 ( 8) metal coordination : angle 2.08279 ( 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 152 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7526 (tt) REVERT: C 70 GLU cc_start: 0.7408 (mp0) cc_final: 0.6976 (mp0) REVERT: D 165 ASP cc_start: 0.6844 (t70) cc_final: 0.6435 (t70) outliers start: 21 outliers final: 19 residues processed: 146 average time/residue: 0.2197 time to fit residues: 48.1988 Evaluate side-chains 149 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 221 LEU 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 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain A residue 830 VAL 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 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: 0.9980 chunk 122 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099286 restraints weight = 39551.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.096709 restraints weight = 34638.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.099371 restraints weight = 28360.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100283 restraints weight = 18978.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100519 restraints weight = 17002.486| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12875 Z= 0.164 Angle : 0.482 4.725 17739 Z= 0.258 Chirality : 0.037 0.146 2023 Planarity : 0.004 0.055 2040 Dihedral : 12.489 90.747 2454 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.71 % Allowed : 13.97 % Favored : 84.32 % 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 aren not related in a simple way. whole: -0.00 (0.23), residues: 1384 helix: 1.09 (0.22), residues: 630 sheet: -1.56 (0.44), residues: 126 loop : -0.74 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 43 TYR 0.010 0.001 TYR A 154 PHE 0.011 0.001 PHE A 243 TRP 0.009 0.001 TRP A 924 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00397 (12867) covalent geometry : angle 0.47988 (17733) hydrogen bonds : bond 0.04013 ( 585) hydrogen bonds : angle 3.61399 ( 1566) metal coordination : bond 0.02087 ( 8) metal coordination : angle 2.45690 ( 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 150 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7493 (tt) REVERT: C 70 GLU cc_start: 0.7455 (mp0) cc_final: 0.6946 (mp0) REVERT: D 165 ASP cc_start: 0.6815 (t70) cc_final: 0.6378 (t70) outliers start: 21 outliers final: 20 residues processed: 144 average time/residue: 0.2162 time to fit residues: 46.6208 Evaluate side-chains 150 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 221 LEU 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 472 MET Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 100 LYS 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 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: 0.9990 chunk 142 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 143 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101048 restraints weight = 39298.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098842 restraints weight = 33401.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101550 restraints weight = 27242.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102381 restraints weight = 18215.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102627 restraints weight = 16433.104| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12875 Z= 0.105 Angle : 0.446 4.403 17739 Z= 0.236 Chirality : 0.035 0.148 2023 Planarity : 0.003 0.059 2040 Dihedral : 12.436 90.392 2454 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.62 % Allowed : 14.30 % Favored : 84.08 % 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 aren not related in a simple way. whole: 0.20 (0.24), residues: 1384 helix: 1.29 (0.22), residues: 627 sheet: -1.44 (0.44), residues: 126 loop : -0.66 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 43 TYR 0.009 0.001 TYR C 31 PHE 0.007 0.001 PHE A 349 TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00244 (12867) covalent geometry : angle 0.44439 (17733) hydrogen bonds : bond 0.03547 ( 585) hydrogen bonds : angle 3.49765 ( 1566) metal coordination : bond 0.01587 ( 8) metal coordination : angle 1.98299 ( 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 151 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7449 (tt) REVERT: C 70 GLU cc_start: 0.7447 (mp0) cc_final: 0.6946 (mp0) REVERT: D 165 ASP cc_start: 0.6814 (t70) cc_final: 0.6392 (t70) outliers start: 20 outliers final: 19 residues processed: 145 average time/residue: 0.2205 time to fit residues: 46.9350 Evaluate side-chains 150 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 221 LEU 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 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 100 LYS 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 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: 2.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.0270 chunk 115 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.154235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100567 restraints weight = 39339.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.098233 restraints weight = 32842.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101064 restraints weight = 27575.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101533 restraints weight = 19053.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101478 restraints weight = 17427.438| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1297 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= 0.127 Angle : 0.458 4.624 17739 Z= 0.244 Chirality : 0.036 0.147 2023 Planarity : 0.003 0.059 2040 Dihedral : 12.400 90.212 2454 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.71 % Allowed : 14.30 % Favored : 84.00 % 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 aren not related in a simple way. whole: 0.15 (0.24), residues: 1384 helix: 1.26 (0.22), residues: 627 sheet: -1.47 (0.44), residues: 126 loop : -0.69 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 43 TYR 0.010 0.001 TYR C 31 PHE 0.009 0.001 PHE A 349 TRP 0.009 0.001 TRP A 924 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00304 (12867) covalent geometry : angle 0.45590 (17733) hydrogen bonds : bond 0.03687 ( 585) hydrogen bonds : angle 3.51538 ( 1566) metal coordination : bond 0.01769 ( 8) metal coordination : angle 2.14637 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.23 seconds wall clock time: 59 minutes 7.44 seconds (3547.44 seconds total)