Starting phenix.real_space_refine on Thu Jul 2 16:47:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sar_54695/07_2026/9sar_54695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sar_54695/07_2026/9sar_54695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sar_54695/07_2026/9sar_54695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sar_54695/07_2026/9sar_54695.map" model { file = "/net/cci-nas-00/data/ceres_data/9sar_54695/07_2026/9sar_54695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sar_54695/07_2026/9sar_54695.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 31 5.49 5 S 63 5.16 5 C 5830 2.51 5 N 1566 2.21 5 O 1838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9330 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 7296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7296 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 875} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 897 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "C" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} 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 3055 SG CYS A 301 68.116 42.751 44.758 1.00 62.10 S ATOM 3096 SG CYS A 306 70.648 45.420 43.854 1.00 57.78 S ATOM 3128 SG CYS A 310 67.181 45.376 42.175 1.00 54.31 S ATOM 4536 SG CYS A 487 70.224 36.929 64.840 1.00 59.13 S ATOM 5789 SG CYS A 645 73.655 38.422 63.953 1.00 65.59 S ATOM 5795 SG CYS A 646 71.731 36.373 61.319 1.00 63.85 S Time building chain proxies: 1.93, per 1000 atoms: 0.21 Number of scatterers: 9330 At special positions: 0 Unit cell: (90.9, 102.6, 116.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 63 16.00 P 31 15.00 O 1838 8.00 N 1566 7.00 C 5830 6.00 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: 0.94 Conformation dependent library (CDL) restraints added in 297.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 51.8% alpha, 17.0% beta 10 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.818A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 249 Proline residue: A 243 - end of helix removed outlier: 4.248A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 removed outlier: 4.214A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 259 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.662A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.536A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.517A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.729A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.854A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.606A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.184A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.566A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 582 removed outlier: 3.874A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 780 through 790 removed outlier: 3.873A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 847 through 855 removed outlier: 5.297A pdb=" N GLY A 852 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR A 853 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 4.224A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.414A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.808A pdb=" N VAL B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.546A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.638A pdb=" N GLU B 171 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 172' Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.599A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.606A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.609A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 22 removed outlier: 3.724A pdb=" N CYS A 22 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 55 " --> pdb=" O CYS A 22 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 22 removed outlier: 3.724A pdb=" N CYS A 22 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 55 " --> pdb=" O CYS A 22 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 111 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.413A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 354 removed outlier: 3.583A pdb=" N GLY A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.636A pdb=" N SER A 363 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.675A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.675A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.660A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 758 removed outlier: 3.831A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 616 " --> pdb=" O TRP A 800 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 822 removed outlier: 4.107A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2420 1.33 - 1.45: 2007 1.45 - 1.57: 5025 1.57 - 1.69: 60 1.69 - 1.81: 93 Bond restraints: 9605 Sorted by residual: bond pdb=" CA SER A 778 " pdb=" CB SER A 778 " ideal model delta sigma weight residual 1.534 1.481 0.053 1.34e-02 5.57e+03 1.56e+01 bond pdb=" CA SER A 239 " pdb=" CB SER A 239 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.58e-02 4.01e+03 1.30e+01 bond pdb=" N ASP A 218 " pdb=" CA ASP A 218 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.21e-02 6.83e+03 1.23e+01 bond pdb=" CA SER A 784 " pdb=" CB SER A 784 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.22e+01 bond pdb=" N ILE A 757 " pdb=" CA ILE A 757 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.19e-02 7.06e+03 1.14e+01 ... (remaining 9600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 12565 2.20 - 4.41: 525 4.41 - 6.61: 76 6.61 - 8.81: 8 8.81 - 11.02: 2 Bond angle restraints: 13176 Sorted by residual: angle pdb=" CA PHE A 753 " pdb=" CB PHE A 753 " pdb=" CG PHE A 753 " ideal model delta sigma weight residual 113.80 119.98 -6.18 1.00e+00 1.00e+00 3.81e+01 angle pdb=" N PRO A 612 " pdb=" CA PRO A 612 " pdb=" C PRO A 612 " ideal model delta sigma weight residual 110.80 119.88 -9.08 1.51e+00 4.39e-01 3.62e+01 angle pdb=" N ILE A 779 " pdb=" CA ILE A 779 " pdb=" C ILE A 779 " ideal model delta sigma weight residual 112.98 106.32 6.66 1.25e+00 6.40e-01 2.84e+01 angle pdb=" N VAL A 820 " pdb=" CA VAL A 820 " pdb=" CB VAL A 820 " ideal model delta sigma weight residual 112.34 106.45 5.89 1.14e+00 7.69e-01 2.67e+01 angle pdb=" CA ILE A 333 " pdb=" C ILE A 333 " pdb=" O ILE A 333 " ideal model delta sigma weight residual 121.68 117.60 4.08 7.90e-01 1.60e+00 2.67e+01 ... (remaining 13171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 5100 16.45 - 32.90: 458 32.90 - 49.35: 108 49.35 - 65.79: 54 65.79 - 82.24: 8 Dihedral angle restraints: 5728 sinusoidal: 2511 harmonic: 3217 Sorted by residual: dihedral pdb=" N LYS A 807 " pdb=" C LYS A 807 " pdb=" CA LYS A 807 " pdb=" CB LYS A 807 " ideal model delta harmonic sigma weight residual 122.80 112.22 10.58 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" N MET A 818 " pdb=" C MET A 818 " pdb=" CA MET A 818 " pdb=" CB MET A 818 " ideal model delta harmonic sigma weight residual 122.80 114.05 8.75 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" C ASP A 618 " pdb=" N ASP A 618 " pdb=" CA ASP A 618 " pdb=" CB ASP A 618 " ideal model delta harmonic sigma weight residual -122.60 -130.85 8.25 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 5725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1342 0.102 - 0.205: 133 0.205 - 0.307: 15 0.307 - 0.410: 3 0.410 - 0.512: 8 Chirality restraints: 1501 Sorted by residual: chirality pdb=" P C T 27 " pdb=" OP1 C T 27 " pdb=" OP2 C T 27 " pdb=" O5' C T 27 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" P A P 15 " pdb=" OP1 A P 15 " pdb=" OP2 A P 15 " pdb=" O5' A P 15 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" P A P 25 " pdb=" OP1 A P 25 " pdb=" OP2 A P 25 " pdb=" O5' A P 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 1498 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 116 " -0.436 9.50e-02 1.11e+02 1.95e-01 2.34e+01 pdb=" NE ARG A 116 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 116 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 116 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 116 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 118 " -0.267 9.50e-02 1.11e+02 1.20e-01 8.81e+00 pdb=" NE ARG A 118 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 118 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 118 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 118 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 20 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO A 21 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.039 5.00e-02 4.00e+02 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2186 2.79 - 3.32: 8281 3.32 - 3.85: 15175 3.85 - 4.37: 18708 4.37 - 4.90: 31224 Nonbonded interactions: 75574 Sorted by model distance: nonbonded pdb=" OG1 THR A 462 " pdb=" OD1 ASN A 791 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 433 " pdb=" OE2 GLU A 876 " model vdw 2.272 3.040 nonbonded pdb=" O TRP A 617 " pdb=" OD1 ASP A 618 " model vdw 2.310 3.040 nonbonded pdb=" O6 G T 13 " pdb=" NZ LYS A 545 " model vdw 2.338 3.120 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASP A 208 " model vdw 2.344 3.040 ... (remaining 75569 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.530 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 : 0.007 0.057 9613 Z= 0.454 Angle : 0.933 11.019 13182 Z= 0.636 Chirality : 0.070 0.512 1501 Planarity : 0.008 0.195 1568 Dihedral : 14.582 82.243 3650 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.17 % Favored : 96.65 % Rotamer: Outliers : 0.42 % Allowed : 3.65 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.25), residues: 1074 helix: 0.30 (0.24), residues: 499 sheet: -1.35 (0.41), residues: 145 loop : -1.10 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.020 0.002 TYR A 217 PHE 0.025 0.001 PHE A 753 TRP 0.018 0.002 TRP A 916 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.45 ( 9605) covalent geometry : angle 0.93253 / 0.64 (13176) hydrogen bonds : bond 0.18258 / 16.75 ( 433) hydrogen bonds : angle 6.45505 / 7.43 ( 1226) metal coordination : bond 0.00597 / 0.31 ( 8) metal coordination : angle 1.32549 / 2.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.232 Fit side-chains REVERT: A 377 ASP cc_start: 0.7716 (t70) cc_final: 0.7224 (p0) REVERT: A 718 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7174 (ttpp) REVERT: A 761 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8254 (t0) REVERT: A 780 LYS cc_start: 0.8155 (ptpt) cc_final: 0.7708 (pttm) REVERT: A 781 ASN cc_start: 0.8664 (m110) cc_final: 0.8333 (m110) REVERT: A 825 ASP cc_start: 0.7289 (m-30) cc_final: 0.6939 (t0) REVERT: A 924 MET cc_start: 0.9119 (mmm) cc_final: 0.8512 (mmm) REVERT: C 34 GLN cc_start: 0.7417 (tp40) cc_final: 0.7198 (tm-30) outliers start: 4 outliers final: 1 residues processed: 156 average time/residue: 0.3757 time to fit residues: 63.9104 Evaluate side-chains 115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0030 chunk 106 optimal weight: 7.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 138 ASN A 404 ASN A 492 GLN A 613 HIS A 791 ASN B 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118304 restraints weight = 11616.413| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.05 r_work: 0.3403 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9613 Z= 0.127 Angle : 0.503 5.827 13182 Z= 0.282 Chirality : 0.040 0.150 1501 Planarity : 0.004 0.047 1568 Dihedral : 11.199 81.806 1646 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.88 % Allowed : 9.71 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.25), residues: 1074 helix: 0.65 (0.24), residues: 505 sheet: -0.85 (0.41), residues: 145 loop : -1.03 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.020 0.001 TYR A 38 PHE 0.025 0.001 PHE A 77 TRP 0.017 0.001 TRP A 916 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9605) covalent geometry : angle 0.50227 / 0.28 (13176) hydrogen bonds : bond 0.05681 / 5.32 ( 433) hydrogen bonds : angle 4.83244 / 5.97 ( 1226) metal coordination : bond 0.00529 / 0.27 ( 8) metal coordination : angle 1.50758 / 2.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.340 Fit side-chains REVERT: A 377 ASP cc_start: 0.7848 (t70) cc_final: 0.6910 (p0) REVERT: A 718 LYS cc_start: 0.7358 (mmtm) cc_final: 0.6814 (ttpp) REVERT: A 726 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6701 (ttp-170) REVERT: A 761 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8021 (t0) REVERT: A 780 LYS cc_start: 0.7934 (ptpt) cc_final: 0.7655 (ptpp) REVERT: A 781 ASN cc_start: 0.8534 (m110) cc_final: 0.8172 (m110) REVERT: A 790 ASN cc_start: 0.8292 (t160) cc_final: 0.8051 (t0) REVERT: A 821 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8408 (tttp) REVERT: A 825 ASP cc_start: 0.7153 (m-30) cc_final: 0.6632 (t0) REVERT: A 924 MET cc_start: 0.8972 (mmm) cc_final: 0.8305 (mmm) REVERT: B 171 GLU cc_start: 0.6738 (pm20) cc_final: 0.6342 (pm20) REVERT: C 34 GLN cc_start: 0.7558 (tp40) cc_final: 0.7165 (tm-30) outliers start: 18 outliers final: 10 residues processed: 134 average time/residue: 0.3744 time to fit residues: 54.9189 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 174 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 0.0170 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.0370 overall best weight: 1.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 81 GLN A 138 ASN A 150 ASN A 404 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118726 restraints weight = 11667.525| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.07 r_work: 0.3409 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9613 Z= 0.108 Angle : 0.457 6.698 13182 Z= 0.252 Chirality : 0.039 0.133 1501 Planarity : 0.004 0.040 1568 Dihedral : 11.049 79.810 1646 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.61 % Allowed : 11.38 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1074 helix: 0.88 (0.24), residues: 506 sheet: -0.53 (0.41), residues: 147 loop : -0.94 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.027 0.001 TYR A 80 PHE 0.017 0.001 PHE A 340 TRP 0.014 0.001 TRP A 916 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9605) covalent geometry : angle 0.45667 / 0.25 (13176) hydrogen bonds : bond 0.04504 / 4.42 ( 433) hydrogen bonds : angle 4.48858 / 5.60 ( 1226) metal coordination : bond 0.00492 / 0.26 ( 8) metal coordination : angle 1.23024 / 2.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.308 Fit side-chains REVERT: A 74 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7058 (mtt180) REVERT: A 77 PHE cc_start: 0.5547 (t80) cc_final: 0.5061 (t80) REVERT: A 81 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6962 (mp-120) REVERT: A 377 ASP cc_start: 0.7833 (t70) cc_final: 0.6835 (p0) REVERT: A 718 LYS cc_start: 0.7341 (mmtm) cc_final: 0.6805 (ttpp) REVERT: A 726 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6610 (ttp-170) REVERT: A 780 LYS cc_start: 0.7847 (ptpt) cc_final: 0.7608 (ptpp) REVERT: A 781 ASN cc_start: 0.8555 (m110) cc_final: 0.8281 (m110) REVERT: A 790 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8061 (t0) REVERT: A 811 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: A 821 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8408 (tttp) REVERT: A 825 ASP cc_start: 0.7240 (m-30) cc_final: 0.6733 (t0) REVERT: A 924 MET cc_start: 0.8888 (mmm) cc_final: 0.8219 (mmm) REVERT: B 171 GLU cc_start: 0.6880 (pm20) cc_final: 0.6275 (pm20) REVERT: C 3 MET cc_start: 0.6228 (mmm) cc_final: 0.5631 (mmm) REVERT: C 34 GLN cc_start: 0.7556 (tp40) cc_final: 0.7144 (tm-30) outliers start: 25 outliers final: 9 residues processed: 138 average time/residue: 0.3479 time to fit residues: 52.3831 Evaluate side-chains 124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 79 ASN A 138 ASN A 150 ASN A 404 ASN A 573 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112329 restraints weight = 11778.048| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.08 r_work: 0.3337 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9613 Z= 0.243 Angle : 0.578 6.920 13182 Z= 0.314 Chirality : 0.045 0.157 1501 Planarity : 0.005 0.039 1568 Dihedral : 11.016 78.067 1642 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.55 % Allowed : 11.90 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1074 helix: 0.66 (0.24), residues: 506 sheet: -0.61 (0.41), residues: 146 loop : -1.16 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 55 TYR 0.020 0.002 TYR A 80 PHE 0.024 0.002 PHE A 77 TRP 0.015 0.002 TRP A 916 HIS 0.008 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 ( 9605) covalent geometry : angle 0.57620 / 0.31 (13176) hydrogen bonds : bond 0.05996 / 5.95 ( 433) hydrogen bonds : angle 4.69797 / 5.86 ( 1226) metal coordination : bond 0.00762 / 0.42 ( 8) metal coordination : angle 2.07818 / 3.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.320 Fit side-chains REVERT: A 74 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7177 (mtt180) REVERT: A 81 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: A 138 ASN cc_start: 0.7105 (t0) cc_final: 0.6902 (t0) REVERT: A 164 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: A 377 ASP cc_start: 0.7964 (t70) cc_final: 0.7005 (p0) REVERT: A 718 LYS cc_start: 0.7618 (mmtm) cc_final: 0.7005 (ttpp) REVERT: A 780 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7618 (ptpp) REVERT: A 811 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: A 821 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8367 (tttp) REVERT: A 825 ASP cc_start: 0.7225 (m-30) cc_final: 0.6613 (t0) REVERT: A 889 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6423 (ttp-170) REVERT: A 924 MET cc_start: 0.8857 (mmm) cc_final: 0.8254 (mmm) REVERT: B 171 GLU cc_start: 0.6996 (pm20) cc_final: 0.6399 (pm20) REVERT: C 21 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6717 (mtm110) REVERT: C 34 GLN cc_start: 0.7730 (tp40) cc_final: 0.7295 (tm-30) outliers start: 34 outliers final: 13 residues processed: 128 average time/residue: 0.3905 time to fit residues: 54.6010 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 21 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 81 GLN A 150 ASN A 404 ASN A 790 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114814 restraints weight = 11680.185| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.07 r_work: 0.3360 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9613 Z= 0.145 Angle : 0.485 6.746 13182 Z= 0.265 Chirality : 0.041 0.168 1501 Planarity : 0.004 0.037 1568 Dihedral : 10.959 76.874 1642 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.13 % Allowed : 12.42 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1074 helix: 0.78 (0.24), residues: 506 sheet: -0.54 (0.41), residues: 147 loop : -1.06 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.025 0.001 TYR A 80 PHE 0.016 0.001 PHE A 741 TRP 0.015 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9605) covalent geometry : angle 0.48429 / 0.27 (13176) hydrogen bonds : bond 0.04906 / 4.90 ( 433) hydrogen bonds : angle 4.50357 / 5.63 ( 1226) metal coordination : bond 0.00577 / 0.30 ( 8) metal coordination : angle 1.57854 / 2.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.363 Fit side-chains REVERT: A 74 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7077 (mtt180) REVERT: A 77 PHE cc_start: 0.5822 (t80) cc_final: 0.5326 (t80) REVERT: A 81 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6902 (mp-120) REVERT: A 103 LYS cc_start: 0.7054 (mtmt) cc_final: 0.6518 (mtpp) REVERT: A 138 ASN cc_start: 0.7161 (t0) cc_final: 0.6808 (t0) REVERT: A 164 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: A 377 ASP cc_start: 0.7814 (t70) cc_final: 0.6901 (p0) REVERT: A 718 LYS cc_start: 0.7484 (mmtm) cc_final: 0.6905 (ttpp) REVERT: A 780 LYS cc_start: 0.7820 (ptpt) cc_final: 0.7511 (ptpp) REVERT: A 821 LYS cc_start: 0.8959 (ttpp) cc_final: 0.8610 (ttmp) REVERT: A 825 ASP cc_start: 0.7205 (m-30) cc_final: 0.6648 (t0) REVERT: A 889 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6397 (ttp-170) REVERT: A 924 MET cc_start: 0.8813 (mmm) cc_final: 0.8205 (mmm) REVERT: B 171 GLU cc_start: 0.6978 (pm20) cc_final: 0.6200 (pm20) REVERT: C 21 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6689 (mtm110) REVERT: C 34 GLN cc_start: 0.7694 (tp40) cc_final: 0.7247 (tm-30) outliers start: 30 outliers final: 14 residues processed: 128 average time/residue: 0.3830 time to fit residues: 53.5793 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain C residue 21 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 75 HIS A 81 GLN A 404 ASN A 790 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.146883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116953 restraints weight = 11723.351| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.06 r_work: 0.3414 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9613 Z= 0.117 Angle : 0.463 6.598 13182 Z= 0.254 Chirality : 0.039 0.156 1501 Planarity : 0.004 0.037 1568 Dihedral : 10.923 76.208 1642 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.03 % Allowed : 13.36 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1074 helix: 0.86 (0.24), residues: 506 sheet: -0.47 (0.41), residues: 147 loop : -0.97 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.027 0.001 TYR A 80 PHE 0.017 0.001 PHE A 340 TRP 0.015 0.001 TRP A 916 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9605) covalent geometry : angle 0.46210 / 0.25 (13176) hydrogen bonds : bond 0.04490 / 4.46 ( 433) hydrogen bonds : angle 4.38016 / 5.43 ( 1226) metal coordination : bond 0.00554 / 0.29 ( 8) metal coordination : angle 1.42561 / 2.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.336 Fit side-chains REVERT: A 74 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7113 (mtt180) REVERT: A 77 PHE cc_start: 0.5873 (t80) cc_final: 0.5357 (t80) REVERT: A 81 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6466 (mp-120) REVERT: A 103 LYS cc_start: 0.7007 (mtmt) cc_final: 0.6480 (mtpp) REVERT: A 138 ASN cc_start: 0.7164 (t0) cc_final: 0.6739 (t0) REVERT: A 377 ASP cc_start: 0.7765 (t70) cc_final: 0.6769 (p0) REVERT: A 718 LYS cc_start: 0.7389 (mmtm) cc_final: 0.6833 (ttpp) REVERT: A 780 LYS cc_start: 0.7706 (ptpt) cc_final: 0.7410 (ptpp) REVERT: A 794 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7713 (ttm) REVERT: A 821 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8599 (ttmp) REVERT: A 825 ASP cc_start: 0.7098 (m-30) cc_final: 0.6569 (t0) REVERT: A 889 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6347 (ttp-170) REVERT: A 924 MET cc_start: 0.8773 (mmm) cc_final: 0.8172 (mmm) REVERT: B 171 GLU cc_start: 0.6949 (pm20) cc_final: 0.6134 (pm20) REVERT: C 21 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6652 (mtm110) REVERT: C 34 GLN cc_start: 0.7678 (tp40) cc_final: 0.7227 (tm-30) outliers start: 29 outliers final: 15 residues processed: 127 average time/residue: 0.4180 time to fit residues: 58.0482 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 21 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 150 ASN A 404 ASN A 790 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.148771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118914 restraints weight = 11690.803| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.06 r_work: 0.3438 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9613 Z= 0.095 Angle : 0.441 6.495 13182 Z= 0.242 Chirality : 0.038 0.157 1501 Planarity : 0.004 0.035 1568 Dihedral : 10.886 75.331 1642 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.13 % Allowed : 13.57 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1074 helix: 1.02 (0.24), residues: 506 sheet: -0.40 (0.41), residues: 145 loop : -0.83 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.026 0.001 TYR A 80 PHE 0.023 0.001 PHE A 340 TRP 0.015 0.001 TRP A 916 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 ( 9605) covalent geometry : angle 0.44034 / 0.24 (13176) hydrogen bonds : bond 0.03896 / 3.92 ( 433) hydrogen bonds : angle 4.26432 / 5.29 ( 1226) metal coordination : bond 0.00503 / 0.26 ( 8) metal coordination : angle 1.25479 / 2.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.341 Fit side-chains REVERT: A 74 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7103 (mtt180) REVERT: A 81 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: A 138 ASN cc_start: 0.7156 (t0) cc_final: 0.6679 (t0) REVERT: A 377 ASP cc_start: 0.7725 (t70) cc_final: 0.6671 (p0) REVERT: A 718 LYS cc_start: 0.7333 (mmtm) cc_final: 0.6806 (ttpp) REVERT: A 780 LYS cc_start: 0.7646 (ptpt) cc_final: 0.7379 (ptpp) REVERT: A 794 MET cc_start: 0.7867 (ttm) cc_final: 0.7550 (ttm) REVERT: A 821 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8595 (ttmp) REVERT: A 825 ASP cc_start: 0.7093 (m-30) cc_final: 0.6631 (t0) REVERT: A 889 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6272 (ttp-170) REVERT: A 924 MET cc_start: 0.8763 (mmm) cc_final: 0.8185 (mmm) REVERT: B 171 GLU cc_start: 0.7019 (pm20) cc_final: 0.6237 (pm20) REVERT: C 3 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4256 (tmm) REVERT: C 34 GLN cc_start: 0.7673 (tp40) cc_final: 0.7222 (tm-30) outliers start: 30 outliers final: 15 residues processed: 130 average time/residue: 0.4141 time to fit residues: 59.0854 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116056 restraints weight = 11688.778| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.11 r_work: 0.3401 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9613 Z= 0.149 Angle : 0.481 6.490 13182 Z= 0.260 Chirality : 0.041 0.161 1501 Planarity : 0.004 0.036 1568 Dihedral : 10.866 75.175 1642 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.92 % Allowed : 14.20 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1074 helix: 0.93 (0.24), residues: 506 sheet: -0.37 (0.41), residues: 145 loop : -0.85 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 640 TYR 0.026 0.002 TYR A 80 PHE 0.017 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9605) covalent geometry : angle 0.48026 / 0.26 (13176) hydrogen bonds : bond 0.04628 / 4.61 ( 433) hydrogen bonds : angle 4.33104 / 5.42 ( 1226) metal coordination : bond 0.00562 / 0.30 ( 8) metal coordination : angle 1.56810 / 2.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.299 Fit side-chains REVERT: A 74 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7126 (mtt180) REVERT: A 77 PHE cc_start: 0.6020 (t80) cc_final: 0.5457 (t80) REVERT: A 81 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6731 (mp-120) REVERT: A 138 ASN cc_start: 0.7230 (t0) cc_final: 0.6720 (t0) REVERT: A 377 ASP cc_start: 0.7756 (t70) cc_final: 0.6715 (p0) REVERT: A 718 LYS cc_start: 0.7422 (mmtm) cc_final: 0.6850 (ttpp) REVERT: A 780 LYS cc_start: 0.7697 (ptpt) cc_final: 0.7401 (ptpp) REVERT: A 790 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8124 (t0) REVERT: A 821 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8588 (ttmp) REVERT: A 825 ASP cc_start: 0.6955 (m-30) cc_final: 0.6509 (t0) REVERT: A 889 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6298 (ttp-170) REVERT: A 924 MET cc_start: 0.8744 (mmm) cc_final: 0.8161 (mmm) REVERT: B 171 GLU cc_start: 0.7050 (pm20) cc_final: 0.6245 (pm20) REVERT: C 3 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.4812 (tmm) REVERT: C 34 GLN cc_start: 0.7668 (tp40) cc_final: 0.7229 (tm-30) outliers start: 28 outliers final: 16 residues processed: 127 average time/residue: 0.4241 time to fit residues: 59.0087 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 3 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 0.0030 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 150 ASN A 404 ASN A 892 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117340 restraints weight = 11660.691| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.10 r_work: 0.3414 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9613 Z= 0.114 Angle : 0.458 6.599 13182 Z= 0.248 Chirality : 0.039 0.167 1501 Planarity : 0.004 0.035 1568 Dihedral : 10.860 74.884 1642 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.51 % Allowed : 14.93 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1074 helix: 0.97 (0.24), residues: 506 sheet: -0.35 (0.41), residues: 145 loop : -0.79 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 640 TYR 0.027 0.001 TYR A 80 PHE 0.016 0.001 PHE A 340 TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9605) covalent geometry : angle 0.45745 / 0.25 (13176) hydrogen bonds : bond 0.04252 / 4.22 ( 433) hydrogen bonds : angle 4.28712 / 5.40 ( 1226) metal coordination : bond 0.00546 / 0.28 ( 8) metal coordination : angle 1.37816 / 2.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.285 Fit side-chains REVERT: A 74 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7080 (mtt180) REVERT: A 77 PHE cc_start: 0.6003 (t80) cc_final: 0.5430 (t80) REVERT: A 81 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6554 (mp-120) REVERT: A 138 ASN cc_start: 0.7336 (t0) cc_final: 0.6780 (t0) REVERT: A 377 ASP cc_start: 0.7703 (t70) cc_final: 0.6664 (p0) REVERT: A 718 LYS cc_start: 0.7332 (mmtm) cc_final: 0.6794 (ttpp) REVERT: A 780 LYS cc_start: 0.7590 (ptpt) cc_final: 0.7330 (ptpp) REVERT: A 790 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8122 (t0) REVERT: A 821 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8591 (ttmp) REVERT: A 825 ASP cc_start: 0.6893 (m-30) cc_final: 0.6480 (t0) REVERT: A 889 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6259 (ttp-170) REVERT: A 892 HIS cc_start: 0.5668 (OUTLIER) cc_final: 0.5352 (m90) REVERT: A 924 MET cc_start: 0.8737 (mmm) cc_final: 0.8141 (mmm) REVERT: B 171 GLU cc_start: 0.7029 (pm20) cc_final: 0.6214 (pm20) REVERT: C 3 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.4720 (tmm) REVERT: C 34 GLN cc_start: 0.7661 (tp40) cc_final: 0.7226 (tm-30) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.4176 time to fit residues: 55.9502 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain C residue 3 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 150 ASN A 404 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115952 restraints weight = 11721.715| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.10 r_work: 0.3402 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9613 Z= 0.161 Angle : 0.494 7.428 13182 Z= 0.266 Chirality : 0.041 0.160 1501 Planarity : 0.004 0.036 1568 Dihedral : 10.866 75.056 1642 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.51 % Allowed : 14.72 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1074 helix: 0.85 (0.24), residues: 506 sheet: -0.39 (0.41), residues: 147 loop : -0.88 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 640 TYR 0.029 0.002 TYR A 80 PHE 0.017 0.001 PHE A 741 TRP 0.014 0.001 TRP A 916 HIS 0.011 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 9605) covalent geometry : angle 0.49307 / 0.27 (13176) hydrogen bonds : bond 0.04717 / 4.68 ( 433) hydrogen bonds : angle 4.33833 / 5.43 ( 1226) metal coordination : bond 0.00581 / 0.31 ( 8) metal coordination : angle 1.53645 / 2.81 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.353 Fit side-chains REVERT: A 74 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7103 (mtt180) REVERT: A 81 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7308 (mm110) REVERT: A 138 ASN cc_start: 0.7344 (t0) cc_final: 0.6773 (t0) REVERT: A 377 ASP cc_start: 0.7764 (t70) cc_final: 0.6718 (p0) REVERT: A 718 LYS cc_start: 0.7412 (mmtm) cc_final: 0.6858 (ttpp) REVERT: A 780 LYS cc_start: 0.7668 (ptpt) cc_final: 0.7384 (ptpp) REVERT: A 790 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8137 (t0) REVERT: A 821 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8602 (ttmp) REVERT: A 825 ASP cc_start: 0.6954 (m-30) cc_final: 0.6526 (t0) REVERT: A 889 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6405 (ttp-170) REVERT: A 924 MET cc_start: 0.8747 (mmm) cc_final: 0.8154 (mmm) REVERT: B 171 GLU cc_start: 0.7072 (pm20) cc_final: 0.6246 (pm20) REVERT: C 3 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.4861 (tmm) REVERT: C 34 GLN cc_start: 0.7679 (tp40) cc_final: 0.7238 (tm-30) outliers start: 24 outliers final: 14 residues processed: 119 average time/residue: 0.4277 time to fit residues: 55.8089 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 3 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117908 restraints weight = 11566.646| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.10 r_work: 0.3427 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9613 Z= 0.103 Angle : 0.448 6.603 13182 Z= 0.243 Chirality : 0.039 0.155 1501 Planarity : 0.004 0.035 1568 Dihedral : 10.856 74.878 1642 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.40 % Allowed : 14.82 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1074 helix: 1.00 (0.24), residues: 507 sheet: -0.37 (0.41), residues: 145 loop : -0.77 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.027 0.001 TYR A 80 PHE 0.014 0.001 PHE A 340 TRP 0.016 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 9605) covalent geometry : angle 0.44688 / 0.24 (13176) hydrogen bonds : bond 0.04018 / 4.03 ( 433) hydrogen bonds : angle 4.25826 / 5.37 ( 1226) metal coordination : bond 0.00530 / 0.27 ( 8) metal coordination : angle 1.35857 / 2.59 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.37 seconds wall clock time: 48 minutes 53.97 seconds (2933.97 seconds total)