Starting phenix.real_space_refine on Fri Jun 20 16:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cpo_45805/06_2025/9cpo_45805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cpo_45805/06_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_45805/06_2025/9cpo_45805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cpo_45805/06_2025/9cpo_45805.map" model { file = "/net/cci-nas-00/data/ceres_data/9cpo_45805/06_2025/9cpo_45805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cpo_45805/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.36, per 1000 atoms: 0.51 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: 6.43 Conformation dependent library (CDL) restraints added in 2.4 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: 9.80 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: 9.62 Time building geometry restraints manager: 7.84 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: 1.510 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: 0.460 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 69.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.760 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16679 ( 585) hydrogen bonds : angle 5.58144 ( 1566) metal coordination : bond 0.01860 ( 8) metal coordination : angle 2.33061 ( 6) covalent geometry : bond 0.00324 (12867) covalent geometry : angle 0.49310 (17733) *********************** 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 : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5416 time to fit residues: 101.6320 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 : 1.639 ------------------------------------------------------------------------------- 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 = 0.3095 r_free = 0.3095 target = 0.101985 restraints weight = 39268.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099717 restraints weight = 32725.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102473 restraints weight = 27346.197| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- 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 0.053 12875 Z= 0.157 Angle : 0.493 5.049 17739 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 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 585) hydrogen bonds : angle 4.10895 ( 1566) metal coordination : bond 0.01966 ( 8) metal coordination : angle 2.49911 ( 6) covalent geometry : bond 0.00369 (12867) covalent geometry : angle 0.49125 (17733) *********************** 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 : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 130 average time/residue: 0.5435 time to fit residues: 106.6085 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 : 1.801 ------------------------------------------------------------------------------- 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: 0.4980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.157979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104096 restraints weight = 38771.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102089 restraints weight = 29469.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104932 restraints weight = 24508.707| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12875 Z= 0.098 Angle : 0.442 4.585 17739 Z= 0.234 Chirality : 0.035 0.154 2023 Planarity : 0.003 0.037 2040 Dihedral : 12.709 90.687 2454 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.81 % Allowed : 13.00 % 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: 0.18 (0.24), residues: 1384 helix: 1.15 (0.22), residues: 631 sheet: -1.42 (0.44), residues: 131 loop : -0.52 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS A 318 PHE 0.005 0.001 PHE A 110 TYR 0.009 0.001 TYR C 31 ARG 0.007 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 585) hydrogen bonds : angle 3.69210 ( 1566) metal coordination : bond 0.01426 ( 8) metal coordination : angle 1.79952 ( 6) covalent geometry : bond 0.00223 (12867) covalent geometry : angle 0.44131 (17733) *********************** 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 141 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7293 (ttm110) cc_final: 0.7064 (ttm110) REVERT: C 70 GLU cc_start: 0.7345 (mp0) cc_final: 0.7114 (mp0) outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.5048 time to fit residues: 103.2148 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 : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 205 MET 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: 2.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 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 = 0.3727 r_free = 0.3727 target = 0.154874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101090 restraints weight = 39220.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.098585 restraints weight = 31899.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101828 restraints weight = 26228.709| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12875 Z= 0.189 Angle : 0.497 4.901 17739 Z= 0.267 Chirality : 0.038 0.149 2023 Planarity : 0.004 0.037 2040 Dihedral : 12.656 91.035 2454 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.30 % Allowed : 13.40 % 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: -0.07 (0.23), residues: 1384 helix: 0.97 (0.22), residues: 633 sheet: -1.36 (0.46), residues: 121 loop : -0.76 (0.25), residues: 630 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 0.012 0.001 TYR C 31 ARG 0.007 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 585) hydrogen bonds : angle 3.78409 ( 1566) metal coordination : bond 0.02285 ( 8) metal coordination : angle 2.68321 ( 6) covalent geometry : bond 0.00459 (12867) covalent geometry : angle 0.49436 (17733) *********************** 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: 16 poor density : 127 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7394 (ttm110) cc_final: 0.7111 (ttm110) REVERT: C 70 GLU cc_start: 0.7446 (mp0) cc_final: 0.6944 (mp0) outliers start: 16 outliers final: 16 residues processed: 136 average time/residue: 0.5486 time to fit residues: 111.1105 Evaluate side-chains 139 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 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 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: 0.8980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.155928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102406 restraints weight = 39337.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100268 restraints weight = 33210.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102959 restraints weight = 27088.690| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12875 Z= 0.089 Angle : 0.435 4.384 17739 Z= 0.230 Chirality : 0.035 0.153 2023 Planarity : 0.003 0.038 2040 Dihedral : 12.527 90.716 2454 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.30 % Allowed : 13.08 % 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 (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: 0.26 (0.24), residues: 1384 helix: 1.25 (0.22), residues: 629 sheet: -1.38 (0.44), residues: 131 loop : -0.53 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.000 HIS A 318 PHE 0.007 0.001 PHE A 349 TYR 0.008 0.001 TYR C 31 ARG 0.006 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 585) hydrogen bonds : angle 3.53296 ( 1566) metal coordination : bond 0.01379 ( 8) metal coordination : angle 1.73896 ( 6) covalent geometry : bond 0.00199 (12867) covalent geometry : angle 0.43424 (17733) *********************** 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 149 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7367 (ttm110) cc_final: 0.7136 (ttm110) REVERT: A 524 TYR cc_start: 0.8149 (m-80) cc_final: 0.7832 (m-80) REVERT: C 70 GLU cc_start: 0.7488 (mp0) cc_final: 0.6983 (mp0) REVERT: D 165 ASP cc_start: 0.6784 (t70) cc_final: 0.6422 (t70) outliers start: 16 outliers final: 13 residues processed: 144 average time/residue: 0.5380 time to fit residues: 116.5144 Evaluate side-chains 144 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET 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 164 THR 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: 0.9990 chunk 115 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 139 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.157198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103565 restraints weight = 39160.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101273 restraints weight = 30425.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104201 restraints weight = 25418.444| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12875 Z= 0.113 Angle : 0.442 4.467 17739 Z= 0.234 Chirality : 0.036 0.148 2023 Planarity : 0.003 0.038 2040 Dihedral : 12.458 90.574 2454 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.54 % Allowed : 12.92 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.24), residues: 1384 helix: 1.28 (0.22), residues: 630 sheet: -1.34 (0.45), residues: 131 loop : -0.54 (0.25), residues: 623 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 0.010 0.001 TYR C 31 ARG 0.010 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 585) hydrogen bonds : angle 3.50427 ( 1566) metal coordination : bond 0.01563 ( 8) metal coordination : angle 1.90685 ( 6) covalent geometry : bond 0.00267 (12867) covalent geometry : angle 0.44058 (17733) *********************** 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: 19 poor density : 134 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7278 (ttm110) cc_final: 0.7028 (ttm110) REVERT: C 70 GLU cc_start: 0.7523 (mp0) cc_final: 0.6963 (mp0) REVERT: D 165 ASP cc_start: 0.6757 (t70) cc_final: 0.6282 (t70) outliers start: 19 outliers final: 16 residues processed: 145 average time/residue: 0.5011 time to fit residues: 108.2486 Evaluate side-chains 144 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 155 THR Chi-restraints excluded: chain B residue 164 THR 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=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: 0.4980 chunk 130 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.154790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100878 restraints weight = 39423.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.098672 restraints weight = 30391.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101597 restraints weight = 25869.853| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12875 Z= 0.176 Angle : 0.487 4.798 17739 Z= 0.260 Chirality : 0.037 0.146 2023 Planarity : 0.004 0.045 2040 Dihedral : 12.489 90.863 2454 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.87 % Allowed : 13.08 % 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: 0.04 (0.23), residues: 1384 helix: 1.09 (0.22), residues: 633 sheet: -1.30 (0.46), residues: 121 loop : -0.74 (0.25), residues: 630 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 0.013 0.001 PHE A 473 TYR 0.011 0.001 TYR A 154 ARG 0.010 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 585) hydrogen bonds : angle 3.63820 ( 1566) metal coordination : bond 0.02145 ( 8) metal coordination : angle 2.49337 ( 6) covalent geometry : bond 0.00426 (12867) covalent geometry : angle 0.48464 (17733) *********************** 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: 23 poor density : 127 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7354 (ttm110) cc_final: 0.7087 (ttm110) REVERT: C 70 GLU cc_start: 0.7500 (mp0) cc_final: 0.6950 (mp0) REVERT: D 165 ASP cc_start: 0.6834 (t70) cc_final: 0.6379 (t70) outliers start: 23 outliers final: 20 residues processed: 141 average time/residue: 0.7019 time to fit residues: 149.5735 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 : 1.629 ------------------------------------------------------------------------------- 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 309 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 472 MET 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 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: 0.9980 chunk 6 optimal weight: 8.9990 chunk 138 optimal weight: 40.0000 chunk 55 optimal weight: 0.2980 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.153614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100284 restraints weight = 39481.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.098071 restraints weight = 34106.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100638 restraints weight = 28118.995| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1166 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= 0.137 Angle : 0.462 4.562 17739 Z= 0.246 Chirality : 0.036 0.148 2023 Planarity : 0.003 0.049 2040 Dihedral : 12.466 90.756 2454 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.87 % Allowed : 13.16 % 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: 0.13 (0.23), residues: 1384 helix: 1.16 (0.22), residues: 630 sheet: -1.26 (0.46), residues: 121 loop : -0.68 (0.25), residues: 633 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 0.009 0.001 PHE A 349 TYR 0.009 0.001 TYR C 31 ARG 0.011 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 585) hydrogen bonds : angle 3.57267 ( 1566) metal coordination : bond 0.01854 ( 8) metal coordination : angle 2.22861 ( 6) covalent geometry : bond 0.00327 (12867) covalent geometry : angle 0.45994 (17733) *********************** 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: 23 poor density : 129 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7337 (ttm110) cc_final: 0.7083 (ttm110) REVERT: B 79 ARG cc_start: 0.8148 (mmp80) cc_final: 0.7917 (mmp80) REVERT: C 70 GLU cc_start: 0.7454 (mp0) cc_final: 0.6894 (mp0) REVERT: D 165 ASP cc_start: 0.6821 (t70) cc_final: 0.6401 (t70) outliers start: 23 outliers final: 22 residues processed: 144 average time/residue: 0.5124 time to fit residues: 110.2837 Evaluate side-chains 152 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 112 ASP 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: 0.0470 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 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: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.154256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100800 restraints weight = 39548.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098579 restraints weight = 33377.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101079 restraints weight = 27901.510| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12875 Z= 0.125 Angle : 0.454 4.520 17739 Z= 0.241 Chirality : 0.036 0.148 2023 Planarity : 0.003 0.057 2040 Dihedral : 12.425 90.474 2454 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.79 % Allowed : 13.24 % 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: 0.18 (0.23), residues: 1384 helix: 1.25 (0.22), residues: 627 sheet: -1.28 (0.46), residues: 116 loop : -0.71 (0.25), residues: 641 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 0.009 0.001 PHE A 349 TYR 0.009 0.001 TYR C 31 ARG 0.013 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 585) hydrogen bonds : angle 3.52197 ( 1566) metal coordination : bond 0.01695 ( 8) metal coordination : angle 2.04084 ( 6) covalent geometry : bond 0.00298 (12867) covalent geometry : angle 0.45278 (17733) *********************** 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: 22 poor density : 129 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7359 (ttm110) cc_final: 0.7097 (ttm110) REVERT: B 79 ARG cc_start: 0.8182 (mmp80) cc_final: 0.7969 (mmp80) REVERT: C 70 GLU cc_start: 0.7382 (mp0) cc_final: 0.6807 (mp0) REVERT: D 165 ASP cc_start: 0.6779 (t70) cc_final: 0.6365 (t70) outliers start: 22 outliers final: 22 residues processed: 144 average time/residue: 0.4982 time to fit residues: 106.3218 Evaluate side-chains 149 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 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 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 11 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.154004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100780 restraints weight = 39374.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.098834 restraints weight = 32613.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101284 restraints weight = 28433.128| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1260 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= 0.132 Angle : 0.463 4.670 17739 Z= 0.246 Chirality : 0.036 0.148 2023 Planarity : 0.003 0.059 2040 Dihedral : 12.408 90.312 2454 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.95 % Allowed : 13.24 % Favored : 84.81 % 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: 0.18 (0.23), residues: 1384 helix: 1.26 (0.22), residues: 628 sheet: -1.41 (0.44), residues: 126 loop : -0.66 (0.25), residues: 630 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 0.009 0.001 PHE A 349 TYR 0.009 0.001 TYR C 31 ARG 0.013 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 585) hydrogen bonds : angle 3.52606 ( 1566) metal coordination : bond 0.01755 ( 8) metal coordination : angle 2.11137 ( 6) covalent geometry : bond 0.00315 (12867) covalent geometry : angle 0.46176 (17733) ********************** 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 152 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7360 (ttm110) cc_final: 0.7112 (ttm110) REVERT: A 221 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7502 (tt) REVERT: A 907 MET cc_start: 0.7730 (tpp) cc_final: 0.7494 (tpp) REVERT: B 79 ARG cc_start: 0.8163 (mmp80) cc_final: 0.7951 (mmp80) REVERT: C 70 GLU cc_start: 0.7382 (mp0) cc_final: 0.6805 (mp0) REVERT: D 165 ASP cc_start: 0.6784 (t70) cc_final: 0.6367 (t70) outliers start: 24 outliers final: 23 residues processed: 144 average time/residue: 0.4903 time to fit residues: 105.0911 Evaluate side-chains 152 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 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 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 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: 20.0000 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.158030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.103637 restraints weight = 38854.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102544 restraints weight = 29618.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104594 restraints weight = 23986.809| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12875 Z= 0.099 Angle : 0.439 4.523 17739 Z= 0.232 Chirality : 0.035 0.148 2023 Planarity : 0.003 0.059 2040 Dihedral : 12.351 89.909 2454 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 0.34 (0.24), residues: 1384 helix: 1.38 (0.22), residues: 628 sheet: -1.29 (0.45), residues: 125 loop : -0.57 (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 0.014 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 585) hydrogen bonds : angle 3.44170 ( 1566) metal coordination : bond 0.01434 ( 8) metal coordination : angle 1.80769 ( 6) covalent geometry : bond 0.00232 (12867) covalent geometry : angle 0.43802 (17733) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7350.18 seconds wall clock time: 129 minutes 4.82 seconds (7744.82 seconds total)