Starting phenix.real_space_refine on Sat Jan 25 21:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cpo_45805/01_2025/9cpo_45805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cpo_45805/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cpo_45805/01_2025/9cpo_45805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cpo_45805/01_2025/9cpo_45805.map" model { file = "/net/cci-nas-00/data/ceres_data/9cpo_45805/01_2025/9cpo_45805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cpo_45805/01_2025/9cpo_45805.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.02, per 1000 atoms: 0.46 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: 6.79 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 11.60 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: 11.04 Time building geometry restraints manager: 7.52 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.390 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 69.530 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.950 ------------------------------------------------------------------------------- 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 0.045 12867 Z= 0.210 Angle : 0.493 8.699 17733 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 924 HIS 0.004 0.001 HIS C 36 PHE 0.019 0.001 PHE A 473 TYR 0.019 0.001 TYR A 246 ARG 0.013 0.000 ARG D 43 *********************** 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 : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5616 time to fit residues: 105.3894 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 : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 30.0000 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.155237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.101995 restraints weight = 39268.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099737 restraints weight = 32716.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102506 restraints weight = 27388.415| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12867 Z= 0.240 Angle : 0.491 5.049 17733 Z= 0.265 Chirality : 0.037 0.157 2023 Planarity : 0.003 0.035 2040 Dihedral : 12.858 90.821 2454 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.57 % Allowed : 12.92 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1384 helix: 0.93 (0.22), residues: 625 sheet: -1.32 (0.46), residues: 121 loop : -0.66 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 924 HIS 0.005 0.001 HIS C 36 PHE 0.011 0.001 PHE A 473 TYR 0.011 0.001 TYR C 31 ARG 0.004 0.000 ARG D 43 *********************** 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 134 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 130 average time/residue: 0.5205 time to fit residues: 100.2221 Evaluate side-chains 131 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 155 THR 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 46 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 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 = 0.3753 r_free = 0.3753 target = 0.157478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104707 restraints weight = 38772.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.102568 restraints weight = 33183.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105699 restraints weight = 27312.279| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12867 Z= 0.158 Angle : 0.447 4.676 17733 Z= 0.238 Chirality : 0.036 0.153 2023 Planarity : 0.003 0.037 2040 Dihedral : 12.715 90.756 2454 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.89 % Allowed : 12.92 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1384 helix: 1.13 (0.22), residues: 629 sheet: -1.45 (0.44), residues: 131 loop : -0.55 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS C 36 PHE 0.006 0.001 PHE A 243 TYR 0.009 0.001 TYR C 31 ARG 0.007 0.000 ARG D 43 *********************** 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 140 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7349 (ttm110) cc_final: 0.7127 (ttm110) REVERT: C 70 GLU cc_start: 0.7208 (mp0) cc_final: 0.6988 (mp0) outliers start: 11 outliers final: 7 residues processed: 136 average time/residue: 0.5361 time to fit residues: 107.4884 Evaluate side-chains 130 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 454 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain D residue 113 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.155337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.101530 restraints weight = 39120.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099257 restraints weight = 30679.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102302 restraints weight = 25778.837| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12867 Z= 0.291 Angle : 0.493 4.868 17733 Z= 0.265 Chirality : 0.038 0.149 2023 Planarity : 0.003 0.037 2040 Dihedral : 12.668 91.045 2454 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.38 % Allowed : 13.32 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1384 helix: 0.96 (0.22), residues: 632 sheet: -1.39 (0.46), residues: 121 loop : -0.76 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 924 HIS 0.007 0.001 HIS C 36 PHE 0.013 0.001 PHE A 473 TYR 0.011 0.001 TYR C 31 ARG 0.007 0.000 ARG D 43 *********************** 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 143 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7374 (ttm110) cc_final: 0.7094 (ttm110) REVERT: C 70 GLU cc_start: 0.7444 (mp0) cc_final: 0.6947 (mp0) outliers start: 17 outliers final: 16 residues processed: 136 average time/residue: 0.5671 time to fit residues: 114.3297 Evaluate side-chains 138 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 113 GLN 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 48 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.154584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101204 restraints weight = 39440.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.098903 restraints weight = 33951.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101446 restraints weight = 27296.402| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12867 Z= 0.159 Angle : 0.443 4.467 17733 Z= 0.235 Chirality : 0.036 0.150 2023 Planarity : 0.003 0.038 2040 Dihedral : 12.550 90.851 2454 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.54 % Allowed : 13.16 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1384 helix: 1.16 (0.22), residues: 629 sheet: -1.44 (0.44), residues: 131 loop : -0.58 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS C 36 PHE 0.009 0.001 PHE A 349 TYR 0.008 0.001 TYR C 31 ARG 0.006 0.000 ARG D 43 *********************** 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 150 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7398 (ttm110) cc_final: 0.7153 (ttm110) REVERT: C 70 GLU cc_start: 0.7464 (mp0) cc_final: 0.6959 (mp0) REVERT: D 165 ASP cc_start: 0.6835 (t70) cc_final: 0.6460 (t70) outliers start: 19 outliers final: 17 residues processed: 144 average time/residue: 0.5311 time to fit residues: 113.2191 Evaluate side-chains 144 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 102 ILE 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 113 GLN 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 141 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.154178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100779 restraints weight = 39355.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.098233 restraints weight = 34092.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.101113 restraints weight = 27960.513| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12867 Z= 0.194 Angle : 0.450 4.540 17733 Z= 0.240 Chirality : 0.036 0.148 2023 Planarity : 0.003 0.037 2040 Dihedral : 12.494 90.773 2454 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.79 % Allowed : 13.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1384 helix: 1.17 (0.22), residues: 630 sheet: -1.43 (0.44), residues: 131 loop : -0.60 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.004 0.001 HIS C 36 PHE 0.011 0.001 PHE A 349 TYR 0.010 0.001 TYR C 31 ARG 0.009 0.000 ARG D 43 *********************** 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 153 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7388 (ttm110) cc_final: 0.7146 (ttm110) REVERT: C 70 GLU cc_start: 0.7511 (mp0) cc_final: 0.6994 (mp0) REVERT: D 165 ASP cc_start: 0.6794 (t70) cc_final: 0.6356 (t70) outliers start: 22 outliers final: 20 residues processed: 144 average time/residue: 0.5174 time to fit residues: 111.0419 Evaluate side-chains 147 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE 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 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 112 ASP 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 140 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 18 optimal weight: 0.1980 chunk 130 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.152222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098024 restraints weight = 39691.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095815 restraints weight = 29744.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.098804 restraints weight = 26000.590| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12867 Z= 0.305 Angle : 0.495 4.892 17733 Z= 0.267 Chirality : 0.038 0.146 2023 Planarity : 0.004 0.044 2040 Dihedral : 12.532 91.069 2454 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.03 % Allowed : 13.24 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1384 helix: 0.97 (0.22), residues: 636 sheet: -1.38 (0.46), residues: 121 loop : -0.83 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 924 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE A 349 TYR 0.012 0.001 TYR A 154 ARG 0.011 0.000 ARG D 43 *********************** 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 152 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7422 (ttm110) cc_final: 0.7140 (ttm110) REVERT: C 70 GLU cc_start: 0.7355 (mp0) cc_final: 0.6817 (mp0) REVERT: D 165 ASP cc_start: 0.6785 (t70) cc_final: 0.6339 (t70) outliers start: 25 outliers final: 21 residues processed: 143 average time/residue: 0.5116 time to fit residues: 108.8306 Evaluate side-chains 149 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR 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 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 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 B residue 189 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 138 optimal weight: 40.0000 chunk 55 optimal weight: 0.1980 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 0.0050 chunk 96 optimal weight: 8.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.154598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101119 restraints weight = 39381.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098832 restraints weight = 32882.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101410 restraints weight = 27418.325| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12867 Z= 0.156 Angle : 0.445 4.401 17733 Z= 0.237 Chirality : 0.036 0.150 2023 Planarity : 0.003 0.049 2040 Dihedral : 12.465 90.748 2454 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.62 % Allowed : 13.48 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1384 helix: 1.19 (0.22), residues: 630 sheet: -1.27 (0.46), residues: 121 loop : -0.66 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS C 36 PHE 0.009 0.001 PHE A 349 TYR 0.008 0.001 TYR C 31 ARG 0.012 0.000 ARG D 43 *********************** 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: 20 poor density : 132 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7395 (ttm110) cc_final: 0.7158 (ttm110) REVERT: C 70 GLU cc_start: 0.7353 (mp0) cc_final: 0.6802 (mp0) REVERT: D 165 ASP cc_start: 0.6831 (t70) cc_final: 0.6418 (t70) outliers start: 20 outliers final: 20 residues processed: 146 average time/residue: 0.5273 time to fit residues: 114.8397 Evaluate side-chains 148 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 102 ILE 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 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 58 optimal weight: 0.0170 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 121 optimal weight: 30.0000 chunk 55 optimal weight: 0.0670 chunk 86 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.156575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103031 restraints weight = 39383.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101060 restraints weight = 34437.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103778 restraints weight = 28269.530| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12867 Z= 0.130 Angle : 0.428 4.310 17733 Z= 0.226 Chirality : 0.035 0.151 2023 Planarity : 0.003 0.056 2040 Dihedral : 12.360 90.129 2454 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.54 % Allowed : 13.48 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1384 helix: 1.38 (0.22), residues: 634 sheet: -1.29 (0.45), residues: 125 loop : -0.52 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 924 HIS 0.003 0.000 HIS A 318 PHE 0.005 0.001 PHE D 96 TYR 0.008 0.001 TYR C 31 ARG 0.013 0.000 ARG D 43 *********************** 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 151 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7366 (ttm110) cc_final: 0.7157 (ttm110) REVERT: A 173 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: A 221 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7394 (tt) REVERT: C 70 GLU cc_start: 0.7380 (mp0) cc_final: 0.6818 (mp0) REVERT: D 165 ASP cc_start: 0.6796 (t70) cc_final: 0.6380 (t70) outliers start: 19 outliers final: 15 residues processed: 145 average time/residue: 0.5660 time to fit residues: 119.2380 Evaluate side-chains 149 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 217 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 100 LYS 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 11 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.153257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.099713 restraints weight = 39511.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.097215 restraints weight = 33990.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100017 restraints weight = 28156.659| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12867 Z= 0.265 Angle : 0.482 4.746 17733 Z= 0.259 Chirality : 0.037 0.145 2023 Planarity : 0.004 0.059 2040 Dihedral : 12.394 90.320 2454 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.62 % Allowed : 13.73 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1384 helix: 1.24 (0.22), residues: 628 sheet: -1.28 (0.46), residues: 116 loop : -0.73 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 924 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE A 349 TYR 0.011 0.001 TYR A 154 ARG 0.013 0.000 ARG D 43 ********************** 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 148 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7569 (tt) REVERT: A 907 MET cc_start: 0.7731 (tpp) cc_final: 0.7494 (tpp) REVERT: C 70 GLU cc_start: 0.7404 (mp0) cc_final: 0.6829 (mp0) REVERT: D 165 ASP cc_start: 0.6825 (t70) cc_final: 0.6376 (t70) outliers start: 20 outliers final: 19 residues processed: 142 average time/residue: 0.5559 time to fit residues: 116.5282 Evaluate side-chains 147 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 217 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 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 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 112 ASP 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 97 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.158180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.103716 restraints weight = 38860.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.102426 restraints weight = 30476.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104503 restraints weight = 24369.611| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12867 Z= 0.150 Angle : 0.443 4.571 17733 Z= 0.234 Chirality : 0.035 0.148 2023 Planarity : 0.003 0.059 2040 Dihedral : 12.350 89.991 2454 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.46 % Allowed : 14.05 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1384 helix: 1.39 (0.22), residues: 628 sheet: -1.27 (0.45), residues: 125 loop : -0.56 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS C 36 PHE 0.006 0.001 PHE A 349 TYR 0.009 0.001 TYR C 31 ARG 0.013 0.000 ARG D 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6632.86 seconds wall clock time: 119 minutes 15.47 seconds (7155.47 seconds total)