Starting phenix.real_space_refine on Mon Sep 30 00:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cpo_45805/09_2024/9cpo_45805.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cpo_45805/09_2024/9cpo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cpo_45805/09_2024/9cpo_45805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cpo_45805/09_2024/9cpo_45805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cpo_45805/09_2024/9cpo_45805.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cpo_45805/09_2024/9cpo_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-5461/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: 11.69, per 1000 atoms: 0.49 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: 6.84 Conformation dependent library (CDL) restraints added in 2.0 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: 10.25 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: 9.73 Time building geometry restraints manager: 8.22 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: 6.770 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: 0.000 Extract box with map and model: 4.570 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 67.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.520 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5273 time to fit residues: 98.3828 Evaluate side-chains 120 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 GLU cc_start: 0.7189 (mp0) cc_final: 0.6983 (mp0) outliers start: 7 outliers final: 7 residues processed: 130 average time/residue: 0.4887 time to fit residues: 94.5139 Evaluate side-chains 131 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.0050 chunk 141 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.0846 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= 0.160 Angle : 0.447 4.657 17733 Z= 0.237 Chirality : 0.036 0.154 2023 Planarity : 0.003 0.037 2040 Dihedral : 12.716 90.785 2454 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.91 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: 0.14 (0.23), residues: 1384 helix: 1.13 (0.22), residues: 629 sheet: -1.45 (0.44), residues: 131 loop : -0.56 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.001 HIS C 36 PHE 0.006 0.001 PHE A 473 TYR 0.009 0.001 TYR C 31 ARG 0.006 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 141 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7279 (ttm110) cc_final: 0.7044 (ttm110) REVERT: C 70 GLU cc_start: 0.7311 (mp0) cc_final: 0.6797 (mp0) outliers start: 11 outliers final: 7 residues processed: 137 average time/residue: 0.4967 time to fit residues: 100.5337 Evaluate side-chains 135 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 129 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12867 Z= 0.229 Angle : 0.468 4.707 17733 Z= 0.251 Chirality : 0.037 0.155 2023 Planarity : 0.003 0.037 2040 Dihedral : 12.608 90.863 2454 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.22 % Allowed : 13.48 % 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: 0.05 (0.23), residues: 1384 helix: 1.08 (0.22), residues: 629 sheet: -1.62 (0.41), residues: 142 loop : -0.58 (0.26), residues: 613 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 0.010 0.001 PHE A 473 TYR 0.010 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 fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7286 (ttm110) cc_final: 0.7004 (ttm110) REVERT: C 70 GLU cc_start: 0.7365 (mp0) cc_final: 0.6781 (mp0) outliers start: 15 outliers final: 14 residues processed: 136 average time/residue: 0.5064 time to fit residues: 101.6829 Evaluate side-chains 138 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 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 115 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12867 Z= 0.355 Angle : 0.524 5.123 17733 Z= 0.284 Chirality : 0.039 0.146 2023 Planarity : 0.004 0.038 2040 Dihedral : 12.669 91.511 2454 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.60 % Allowed : 12.75 % 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: -0.27 (0.23), residues: 1384 helix: 0.82 (0.22), residues: 636 sheet: -1.44 (0.46), residues: 121 loop : -0.91 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 924 HIS 0.008 0.001 HIS C 36 PHE 0.017 0.002 PHE A 349 TYR 0.014 0.002 TYR A 154 ARG 0.008 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 167 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7273 (ttm110) cc_final: 0.6969 (ttm110) REVERT: C 70 GLU cc_start: 0.7373 (mp0) cc_final: 0.6728 (mp0) REVERT: D 138 ASP cc_start: 0.8642 (p0) cc_final: 0.8392 (p0) REVERT: D 165 ASP cc_start: 0.6800 (t70) cc_final: 0.6328 (t70) outliers start: 32 outliers final: 25 residues processed: 159 average time/residue: 0.4755 time to fit residues: 113.0392 Evaluate side-chains 157 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 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 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 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 123 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12867 Z= 0.173 Angle : 0.453 4.453 17733 Z= 0.241 Chirality : 0.036 0.148 2023 Planarity : 0.003 0.037 2040 Dihedral : 12.570 91.117 2454 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.54 % Allowed : 13.73 % 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: 0.04 (0.23), residues: 1384 helix: 1.10 (0.22), residues: 629 sheet: -1.51 (0.44), residues: 131 loop : -0.67 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.001 HIS C 36 PHE 0.010 0.001 PHE A 349 TYR 0.009 0.001 TYR C 31 ARG 0.008 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 154 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6977 (ttm110) REVERT: B 79 ARG cc_start: 0.8141 (mmp80) cc_final: 0.7929 (mmp80) REVERT: C 70 GLU cc_start: 0.7417 (mp0) cc_final: 0.6750 (mp0) REVERT: D 138 ASP cc_start: 0.8597 (p0) cc_final: 0.8355 (p0) REVERT: D 165 ASP cc_start: 0.6719 (t70) cc_final: 0.6266 (t70) outliers start: 19 outliers final: 18 residues processed: 147 average time/residue: 0.4871 time to fit residues: 106.7762 Evaluate side-chains 150 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 138 optimal weight: 40.0000 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12867 Z= 0.173 Angle : 0.445 4.460 17733 Z= 0.236 Chirality : 0.036 0.147 2023 Planarity : 0.003 0.046 2040 Dihedral : 12.469 90.703 2454 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.87 % Allowed : 13.65 % 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: 0.16 (0.24), residues: 1384 helix: 1.19 (0.22), residues: 630 sheet: -1.24 (0.47), residues: 116 loop : -0.69 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 924 HIS 0.003 0.001 HIS C 36 PHE 0.010 0.001 PHE A 349 TYR 0.009 0.001 TYR C 31 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 161 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7227 (ttm110) cc_final: 0.6983 (ttm110) REVERT: A 221 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7424 (tt) REVERT: C 70 GLU cc_start: 0.7435 (mp0) cc_final: 0.6817 (mp0) REVERT: D 138 ASP cc_start: 0.8634 (p0) cc_final: 0.8406 (p0) REVERT: D 165 ASP cc_start: 0.6760 (t70) cc_final: 0.6334 (t70) outliers start: 23 outliers final: 21 residues processed: 153 average time/residue: 0.4993 time to fit residues: 113.3396 Evaluate side-chains 154 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 68 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1277 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= 0.153 Angle : 0.441 4.431 17733 Z= 0.233 Chirality : 0.035 0.148 2023 Planarity : 0.003 0.049 2040 Dihedral : 12.407 90.393 2454 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.62 % Allowed : 14.05 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.22), residues: 624 sheet: -1.31 (0.45), residues: 126 loop : -0.60 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 924 HIS 0.003 0.000 HIS C 36 PHE 0.006 0.001 PHE A 480 TYR 0.009 0.001 TYR C 31 ARG 0.011 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 153 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7250 (ttm110) cc_final: 0.7014 (ttm110) REVERT: C 70 GLU cc_start: 0.7443 (mp0) cc_final: 0.6813 (mp0) REVERT: D 138 ASP cc_start: 0.8632 (p0) cc_final: 0.8406 (p0) REVERT: D 165 ASP cc_start: 0.6748 (t70) cc_final: 0.6312 (t70) outliers start: 20 outliers final: 20 residues processed: 145 average time/residue: 0.5265 time to fit residues: 113.1416 Evaluate side-chains 152 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 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 132 optimal weight: 0.9990 chunk 121 optimal weight: 30.0000 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12867 Z= 0.228 Angle : 0.466 4.632 17733 Z= 0.249 Chirality : 0.036 0.149 2023 Planarity : 0.003 0.056 2040 Dihedral : 12.410 90.446 2454 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.03 % Allowed : 14.05 % Favored : 83.92 % 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: 0.12 (0.23), residues: 1384 helix: 1.16 (0.22), residues: 633 sheet: -1.23 (0.47), residues: 116 loop : -0.72 (0.25), residues: 635 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 0.010 0.001 PHE A 473 TYR 0.010 0.001 TYR A 154 ARG 0.012 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 160 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7256 (ttm110) cc_final: 0.7005 (ttm110) REVERT: A 221 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7436 (tt) REVERT: A 907 MET cc_start: 0.7724 (tpp) cc_final: 0.7504 (tpp) REVERT: C 70 GLU cc_start: 0.7423 (mp0) cc_final: 0.6737 (mp0) REVERT: D 113 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: D 138 ASP cc_start: 0.8651 (p0) cc_final: 0.8406 (p0) REVERT: D 165 ASP cc_start: 0.6714 (t70) cc_final: 0.6287 (t70) outliers start: 25 outliers final: 23 residues processed: 151 average time/residue: 0.5074 time to fit residues: 113.2890 Evaluate side-chains 158 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 655 THR 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 113 GLN 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 136 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 143 optimal weight: 30.0000 chunk 132 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12867 Z= 0.227 Angle : 0.469 4.684 17733 Z= 0.250 Chirality : 0.036 0.147 2023 Planarity : 0.003 0.059 2040 Dihedral : 12.412 90.362 2454 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.95 % Allowed : 14.13 % Favored : 83.92 % 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: 0.11 (0.24), residues: 1384 helix: 1.15 (0.22), residues: 633 sheet: -1.24 (0.47), residues: 116 loop : -0.72 (0.25), residues: 635 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 0.010 0.001 PHE A 243 TYR 0.010 0.001 TYR C 31 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 157 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7261 (ttm110) cc_final: 0.7006 (ttm110) REVERT: A 221 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7449 (tt) REVERT: C 70 GLU cc_start: 0.7432 (mp0) cc_final: 0.6762 (mp0) REVERT: D 113 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: D 138 ASP cc_start: 0.8622 (p0) cc_final: 0.8364 (p0) REVERT: D 165 ASP cc_start: 0.6780 (t70) cc_final: 0.6367 (t70) outliers start: 24 outliers final: 22 residues processed: 149 average time/residue: 0.5092 time to fit residues: 112.0308 Evaluate side-chains 157 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 655 THR 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 113 GLN 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 121 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.152841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099176 restraints weight = 39368.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.096949 restraints weight = 34976.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100277 restraints weight = 29243.102| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12867 Z= 0.260 Angle : 0.481 4.883 17733 Z= 0.258 Chirality : 0.037 0.147 2023 Planarity : 0.004 0.059 2040 Dihedral : 12.432 90.326 2454 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.11 % Allowed : 14.13 % Favored : 83.75 % 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: 0.01 (0.23), residues: 1384 helix: 1.11 (0.22), residues: 633 sheet: -1.30 (0.46), residues: 116 loop : -0.82 (0.25), residues: 635 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 243 TYR 0.011 0.001 TYR A 154 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: 4609.80 seconds wall clock time: 81 minutes 50.14 seconds (4910.14 seconds total)