Starting phenix.real_space_refine on Wed Feb 4 06:51:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sar_54695/02_2026/9sar_54695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sar_54695/02_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_54695/02_2026/9sar_54695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sar_54695/02_2026/9sar_54695.map" model { file = "/net/cci-nas-00/data/ceres_data/9sar_54695/02_2026/9sar_54695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sar_54695/02_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-2.0-5952/lib/python3.9/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: 1.62, per 1000 atoms: 0.17 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: 0.70 Conformation dependent library (CDL) restraints added in 320.6 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: 1.06 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: 1.42 Time building geometry restraints manager: 0.97 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: 0.230 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.530 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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= 0.451 Angle : 0.933 11.019 13182 Z= 0.631 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 covalent geometry : bond 0.00667 ( 9605) covalent geometry : angle 0.93253 (13176) hydrogen bonds : bond 0.18258 ( 433) hydrogen bonds : angle 6.45505 ( 1226) metal coordination : bond 0.00597 ( 8) metal coordination : angle 1.32549 ( 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 : 0.255 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: 0.4081 time to fit residues: 69.1386 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 : 0.257 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 81 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.148493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118571 restraints weight = 11643.488| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.06 r_work: 0.3409 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9613 Z= 0.118 Angle : 0.495 6.398 13182 Z= 0.270 Chirality : 0.040 0.161 1501 Planarity : 0.004 0.046 1568 Dihedral : 11.161 79.572 1646 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.67 % Allowed : 9.92 % 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: -0.35 (0.25), residues: 1074 helix: 0.67 (0.24), residues: 506 sheet: -0.84 (0.41), residues: 147 loop : -1.02 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.023 0.001 TYR A 38 PHE 0.029 0.001 PHE A 77 TRP 0.017 0.001 TRP A 916 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9605) covalent geometry : angle 0.49446 (13176) hydrogen bonds : bond 0.04814 ( 433) hydrogen bonds : angle 4.69206 ( 1226) metal coordination : bond 0.00561 ( 8) metal coordination : angle 1.29426 ( 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 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.226 Fit side-chains REVERT: A 74 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7056 (mtt180) REVERT: A 138 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6985 (t0) REVERT: A 377 ASP cc_start: 0.7824 (t70) cc_final: 0.6860 (p0) REVERT: A 665 GLU cc_start: 0.7988 (pm20) cc_final: 0.7781 (pm20) REVERT: A 718 LYS cc_start: 0.7352 (mmtm) cc_final: 0.6810 (ttpp) REVERT: A 726 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6657 (ttp-170) REVERT: A 780 LYS cc_start: 0.7907 (ptpt) cc_final: 0.7644 (ptpp) REVERT: A 781 ASN cc_start: 0.8567 (m110) cc_final: 0.8271 (m110) REVERT: A 821 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8433 (tttp) REVERT: A 825 ASP cc_start: 0.7201 (m-30) cc_final: 0.6640 (t0) REVERT: A 826 TYR cc_start: 0.8575 (m-80) cc_final: 0.8312 (m-80) REVERT: A 924 MET cc_start: 0.8916 (mmm) cc_final: 0.8261 (mmm) REVERT: B 171 GLU cc_start: 0.6810 (pm20) cc_final: 0.6435 (pm20) REVERT: C 34 GLN cc_start: 0.7566 (tp40) cc_final: 0.7168 (tm-30) outliers start: 16 outliers final: 9 residues processed: 133 average time/residue: 0.3940 time to fit residues: 57.1296 Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 138 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE 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: 3.9990 chunk 90 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 79 ASN 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 = 0.3808 r_free = 0.3808 target = 0.147932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117956 restraints weight = 11672.106| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.01 r_work: 0.3393 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9613 Z= 0.115 Angle : 0.468 8.039 13182 Z= 0.252 Chirality : 0.039 0.153 1501 Planarity : 0.004 0.042 1568 Dihedral : 10.995 76.458 1644 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.51 % Allowed : 11.17 % Favored : 86.33 % 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: -0.09 (0.26), residues: 1074 helix: 0.86 (0.24), residues: 506 sheet: -0.51 (0.41), residues: 150 loop : -0.95 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.028 0.001 TYR A 80 PHE 0.027 0.001 PHE A 77 TRP 0.014 0.001 TRP A 916 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9605) covalent geometry : angle 0.46775 (13176) hydrogen bonds : bond 0.04344 ( 433) hydrogen bonds : angle 4.43392 ( 1226) metal coordination : bond 0.00486 ( 8) metal coordination : angle 1.27802 ( 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 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.372 Fit side-chains REVERT: A 74 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7304 (mtt180) REVERT: A 377 ASP cc_start: 0.7836 (t70) cc_final: 0.6890 (p0) REVERT: A 665 GLU cc_start: 0.8045 (pm20) cc_final: 0.7726 (pm20) REVERT: A 718 LYS cc_start: 0.7433 (mmtm) cc_final: 0.6890 (ttpp) REVERT: A 761 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 780 LYS cc_start: 0.7918 (ptpt) cc_final: 0.7649 (ptpp) REVERT: A 821 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8437 (tttp) REVERT: A 825 ASP cc_start: 0.7232 (m-30) cc_final: 0.6714 (t0) REVERT: A 924 MET cc_start: 0.8888 (mmm) cc_final: 0.8213 (mmm) REVERT: B 171 GLU cc_start: 0.6918 (pm20) cc_final: 0.6344 (pm20) REVERT: C 3 MET cc_start: 0.6055 (mmm) cc_final: 0.5704 (mmm) REVERT: C 21 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6537 (mtm110) REVERT: C 34 GLN cc_start: 0.7665 (tp40) cc_final: 0.7250 (tm-30) outliers start: 24 outliers final: 12 residues processed: 128 average time/residue: 0.4449 time to fit residues: 61.9483 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 196 MET 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 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 21 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 0.0670 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 138 ASN A 150 ASN A 404 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114008 restraints weight = 11774.863| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.07 r_work: 0.3350 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9613 Z= 0.180 Angle : 0.519 6.838 13182 Z= 0.279 Chirality : 0.042 0.163 1501 Planarity : 0.004 0.040 1568 Dihedral : 10.985 74.363 1642 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.24 % Allowed : 11.90 % Favored : 84.86 % 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: -0.20 (0.25), residues: 1074 helix: 0.78 (0.24), residues: 507 sheet: -0.54 (0.41), residues: 147 loop : -1.03 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 640 TYR 0.027 0.002 TYR A 80 PHE 0.019 0.002 PHE A 77 TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9605) covalent geometry : angle 0.51835 (13176) hydrogen bonds : bond 0.05193 ( 433) hydrogen bonds : angle 4.52303 ( 1226) metal coordination : bond 0.00651 ( 8) metal coordination : angle 1.68799 ( 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 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.209 Fit side-chains REVERT: A 74 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7189 (mtt180) REVERT: A 138 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.7073 (t0) REVERT: A 164 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: A 377 ASP cc_start: 0.7893 (t70) cc_final: 0.6946 (p0) REVERT: A 718 LYS cc_start: 0.7502 (mmtm) cc_final: 0.6929 (ttpp) REVERT: A 780 LYS cc_start: 0.7874 (ptpt) cc_final: 0.7601 (ptpp) REVERT: A 811 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7915 (tp30) REVERT: A 821 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8631 (ttmp) REVERT: A 825 ASP cc_start: 0.7170 (m-30) cc_final: 0.6575 (t0) REVERT: A 889 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6388 (ttp-170) REVERT: A 924 MET cc_start: 0.8809 (mmm) cc_final: 0.8249 (mmm) REVERT: B 171 GLU cc_start: 0.7006 (pm20) cc_final: 0.6232 (pm20) REVERT: C 21 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6712 (mtm110) REVERT: C 34 GLN cc_start: 0.7708 (tp40) cc_final: 0.7253 (tm-30) outliers start: 31 outliers final: 13 residues processed: 125 average time/residue: 0.4141 time to fit residues: 56.3490 Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 138 ASN 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 643 THR Chi-restraints excluded: chain A residue 658 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 95 optimal weight: 0.0270 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS 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 = 0.3799 r_free = 0.3799 target = 0.147086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116917 restraints weight = 11690.849| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.07 r_work: 0.3387 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9613 Z= 0.111 Angle : 0.456 6.587 13182 Z= 0.245 Chirality : 0.039 0.155 1501 Planarity : 0.004 0.038 1568 Dihedral : 10.899 73.032 1642 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.03 % Allowed : 12.73 % Favored : 84.24 % 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: 0.00 (0.26), residues: 1074 helix: 0.93 (0.24), residues: 507 sheet: -0.39 (0.42), residues: 145 loop : -0.91 (0.28), 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 0.013 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9605) covalent geometry : angle 0.45528 (13176) hydrogen bonds : bond 0.04125 ( 433) hydrogen bonds : angle 4.31441 ( 1226) metal coordination : bond 0.00560 ( 8) metal coordination : angle 1.32015 ( 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 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.367 Fit side-chains REVERT: A 74 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7169 (mtt180) REVERT: A 77 PHE cc_start: 0.5973 (t80) cc_final: 0.5728 (t80) REVERT: A 81 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7062 (mp10) REVERT: A 377 ASP cc_start: 0.7777 (t70) cc_final: 0.6780 (p0) REVERT: A 718 LYS cc_start: 0.7382 (mmtm) cc_final: 0.6837 (ttpp) REVERT: A 780 LYS cc_start: 0.7767 (ptpt) cc_final: 0.7535 (ptpp) REVERT: A 811 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: A 821 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8667 (ttmp) REVERT: A 825 ASP cc_start: 0.7121 (m-30) cc_final: 0.6597 (t0) REVERT: A 889 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6328 (ttp-170) REVERT: A 924 MET cc_start: 0.8760 (mmm) cc_final: 0.8228 (mmm) REVERT: B 171 GLU cc_start: 0.7023 (pm20) cc_final: 0.6236 (pm20) REVERT: C 34 GLN cc_start: 0.7688 (tp40) cc_final: 0.7244 (tm-30) outliers start: 29 outliers final: 16 residues processed: 126 average time/residue: 0.4373 time to fit residues: 60.0716 Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 196 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 380 MET 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 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 811 GLU 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 B residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 138 ASN A 404 ASN A 573 GLN A 892 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117507 restraints weight = 11742.306| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.07 r_work: 0.3412 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9613 Z= 0.124 Angle : 0.463 6.472 13182 Z= 0.248 Chirality : 0.039 0.163 1501 Planarity : 0.004 0.037 1568 Dihedral : 10.844 73.001 1642 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.92 % Allowed : 13.57 % Favored : 83.51 % 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: 0.06 (0.26), residues: 1074 helix: 0.93 (0.24), residues: 508 sheet: -0.35 (0.41), residues: 145 loop : -0.83 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 640 TYR 0.029 0.001 TYR A 80 PHE 0.016 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9605) covalent geometry : angle 0.46244 (13176) hydrogen bonds : bond 0.04219 ( 433) hydrogen bonds : angle 4.28299 ( 1226) metal coordination : bond 0.00541 ( 8) metal coordination : angle 1.40912 ( 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 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.352 Fit side-chains REVERT: A 74 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7092 (mtt180) REVERT: A 77 PHE cc_start: 0.5887 (t80) cc_final: 0.5591 (t80) REVERT: A 81 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7043 (mp10) REVERT: A 377 ASP cc_start: 0.7747 (t70) cc_final: 0.6696 (p0) REVERT: A 718 LYS cc_start: 0.7399 (mmtm) cc_final: 0.6852 (ttpp) REVERT: A 780 LYS cc_start: 0.7682 (ptpt) cc_final: 0.7451 (ptpp) REVERT: A 821 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8603 (ttmp) REVERT: A 825 ASP cc_start: 0.6990 (m-30) cc_final: 0.6561 (t0) REVERT: A 889 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6270 (ttp-170) REVERT: A 892 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.5352 (m90) REVERT: A 924 MET cc_start: 0.8738 (mmm) cc_final: 0.8193 (mmm) REVERT: B 171 GLU cc_start: 0.6888 (pm20) cc_final: 0.6100 (pm20) REVERT: B 174 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7447 (mtp) REVERT: C 2 LYS cc_start: 0.7582 (mmmt) cc_final: 0.6946 (mmmm) REVERT: C 34 GLN cc_start: 0.7679 (tp40) cc_final: 0.7237 (tm-30) outliers start: 28 outliers final: 17 residues processed: 122 average time/residue: 0.4120 time to fit residues: 54.9136 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 196 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 380 MET 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 779 ILE 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 174 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN 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 = 0.3815 r_free = 0.3815 target = 0.147835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117732 restraints weight = 11746.506| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.12 r_work: 0.3413 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1790 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= 0.122 Angle : 0.463 6.422 13182 Z= 0.246 Chirality : 0.039 0.167 1501 Planarity : 0.004 0.036 1568 Dihedral : 10.831 73.005 1642 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.92 % Allowed : 13.78 % 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: 0.08 (0.26), residues: 1074 helix: 0.93 (0.24), residues: 508 sheet: -0.32 (0.41), residues: 145 loop : -0.79 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.027 0.001 TYR A 80 PHE 0.015 0.001 PHE A 741 TRP 0.015 0.001 TRP A 916 HIS 0.005 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9605) covalent geometry : angle 0.46238 (13176) hydrogen bonds : bond 0.04165 ( 433) hydrogen bonds : angle 4.26346 ( 1226) metal coordination : bond 0.00547 ( 8) metal coordination : angle 1.38173 ( 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 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.215 Fit side-chains REVERT: A 74 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7085 (mtt180) REVERT: A 77 PHE cc_start: 0.5841 (t80) cc_final: 0.5567 (t80) REVERT: A 81 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: A 370 GLU cc_start: 0.6935 (mp0) cc_final: 0.6492 (mp0) REVERT: A 377 ASP cc_start: 0.7739 (t70) cc_final: 0.6680 (p0) REVERT: A 718 LYS cc_start: 0.7339 (mmtm) cc_final: 0.6801 (ttpp) REVERT: A 780 LYS cc_start: 0.7664 (ptpt) cc_final: 0.7440 (ptpp) REVERT: A 821 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8609 (ttmp) REVERT: A 825 ASP cc_start: 0.6909 (m-30) cc_final: 0.6504 (t0) REVERT: A 889 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.6328 (ttp-170) REVERT: A 924 MET cc_start: 0.8733 (mmm) cc_final: 0.8165 (mmm) REVERT: B 171 GLU cc_start: 0.6850 (pm20) cc_final: 0.6046 (pm20) REVERT: B 174 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7415 (mtp) REVERT: C 2 LYS cc_start: 0.7516 (mmmt) cc_final: 0.6870 (mmmm) REVERT: C 34 GLN cc_start: 0.7669 (tp40) cc_final: 0.7221 (tm-30) outliers start: 28 outliers final: 17 residues processed: 123 average time/residue: 0.3825 time to fit residues: 51.1497 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 : 0.349 ------------------------------------------------------------------------------- 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 196 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 380 MET 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 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL 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 174 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 404 ASN A 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118824 restraints weight = 11684.290| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.07 r_work: 0.3429 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9613 Z= 0.103 Angle : 0.447 6.497 13182 Z= 0.238 Chirality : 0.039 0.157 1501 Planarity : 0.003 0.035 1568 Dihedral : 10.812 73.010 1642 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.92 % Allowed : 13.78 % 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: 0.20 (0.26), residues: 1074 helix: 1.04 (0.24), residues: 506 sheet: -0.28 (0.41), residues: 145 loop : -0.75 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.030 0.001 TYR A 80 PHE 0.012 0.001 PHE A 741 TRP 0.014 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9605) covalent geometry : angle 0.44674 (13176) hydrogen bonds : bond 0.03809 ( 433) hydrogen bonds : angle 4.18956 ( 1226) metal coordination : bond 0.00543 ( 8) metal coordination : angle 1.30035 ( 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 137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.233 Fit side-chains REVERT: A 74 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7180 (mtt180) REVERT: A 77 PHE cc_start: 0.5819 (t80) cc_final: 0.5555 (t80) REVERT: A 81 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7052 (mp10) REVERT: A 370 GLU cc_start: 0.6994 (mp0) cc_final: 0.6578 (mp0) REVERT: A 377 ASP cc_start: 0.7721 (t70) cc_final: 0.6648 (p0) REVERT: A 718 LYS cc_start: 0.7318 (mmtm) cc_final: 0.6789 (ttpp) REVERT: A 780 LYS cc_start: 0.7652 (ptpt) cc_final: 0.7425 (ptpp) REVERT: A 821 LYS cc_start: 0.8901 (ttpp) cc_final: 0.8619 (ttmp) REVERT: A 825 ASP cc_start: 0.6895 (m-30) cc_final: 0.6511 (t0) REVERT: A 889 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6306 (ttp-170) REVERT: A 892 HIS cc_start: 0.5653 (OUTLIER) cc_final: 0.5362 (m90) REVERT: A 924 MET cc_start: 0.8733 (mmm) cc_final: 0.8181 (mmm) REVERT: B 171 GLU cc_start: 0.6848 (pm20) cc_final: 0.6028 (pm20) REVERT: B 174 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7398 (mtp) REVERT: C 3 MET cc_start: 0.5209 (mmm) cc_final: 0.4934 (tmm) REVERT: C 34 GLN cc_start: 0.7675 (tp40) cc_final: 0.7234 (tm-30) outliers start: 28 outliers final: 17 residues processed: 122 average time/residue: 0.4272 time to fit residues: 56.7690 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 196 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 380 MET 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 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 779 ILE 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 A residue 926 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 386 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 = 0.3775 r_free = 0.3775 target = 0.144210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113883 restraints weight = 11737.612| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.10 r_work: 0.3365 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9613 Z= 0.217 Angle : 0.557 6.881 13182 Z= 0.296 Chirality : 0.043 0.175 1501 Planarity : 0.004 0.038 1568 Dihedral : 10.882 73.027 1642 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -0.14 (0.25), residues: 1074 helix: 0.77 (0.24), residues: 505 sheet: -0.40 (0.40), residues: 145 loop : -0.96 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 640 TYR 0.031 0.002 TYR A 80 PHE 0.020 0.002 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.010 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 9605) covalent geometry : angle 0.55553 (13176) hydrogen bonds : bond 0.05433 ( 433) hydrogen bonds : angle 4.45019 ( 1226) metal coordination : bond 0.00701 ( 8) metal coordination : angle 1.96163 ( 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 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.344 Fit side-chains REVERT: A 74 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7380 (mtt180) REVERT: A 77 PHE cc_start: 0.5873 (t80) cc_final: 0.5565 (t80) REVERT: A 81 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: A 377 ASP cc_start: 0.7817 (t70) cc_final: 0.6789 (p0) REVERT: A 718 LYS cc_start: 0.7526 (mmtm) cc_final: 0.6949 (ttpp) REVERT: A 780 LYS cc_start: 0.7802 (ptpt) cc_final: 0.7560 (ptpp) REVERT: A 821 LYS cc_start: 0.8899 (ttpp) cc_final: 0.8597 (ttmp) REVERT: A 825 ASP cc_start: 0.6947 (m-30) cc_final: 0.6496 (t0) REVERT: A 889 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6386 (ttp-170) REVERT: A 924 MET cc_start: 0.8771 (mmm) cc_final: 0.8160 (mmm) REVERT: B 171 GLU cc_start: 0.6939 (pm20) cc_final: 0.6109 (pm20) REVERT: B 174 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7518 (mtp) REVERT: C 21 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6725 (mtm110) REVERT: C 34 GLN cc_start: 0.7626 (tp40) cc_final: 0.7173 (tm-30) outliers start: 28 outliers final: 16 residues processed: 122 average time/residue: 0.3998 time to fit residues: 53.3450 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 196 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 380 MET 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 779 ILE Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 21 ARG 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: 7.9990 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN 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 = 0.3806 r_free = 0.3806 target = 0.146948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116829 restraints weight = 11686.106| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.09 r_work: 0.3404 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9613 Z= 0.123 Angle : 0.481 6.629 13182 Z= 0.256 Chirality : 0.039 0.164 1501 Planarity : 0.004 0.036 1568 Dihedral : 10.850 73.049 1642 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.61 % Allowed : 14.41 % Favored : 82.99 % 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: 0.03 (0.26), residues: 1074 helix: 0.92 (0.24), residues: 505 sheet: -0.36 (0.40), residues: 145 loop : -0.86 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.030 0.001 TYR A 80 PHE 0.014 0.001 PHE A 741 TRP 0.016 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9605) covalent geometry : angle 0.47994 (13176) hydrogen bonds : bond 0.04323 ( 433) hydrogen bonds : angle 4.30358 ( 1226) metal coordination : bond 0.00585 ( 8) metal coordination : angle 1.44040 ( 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: 25 poor density : 108 time to evaluate : 0.396 Fit side-chains REVERT: A 74 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7111 (mtt180) REVERT: A 77 PHE cc_start: 0.5817 (t80) cc_final: 0.5533 (t80) REVERT: A 81 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: A 370 GLU cc_start: 0.6960 (mp0) cc_final: 0.6528 (mp0) REVERT: A 377 ASP cc_start: 0.7734 (t70) cc_final: 0.6691 (p0) REVERT: A 718 LYS cc_start: 0.7352 (mmtm) cc_final: 0.6808 (ttpp) REVERT: A 780 LYS cc_start: 0.7690 (ptpt) cc_final: 0.7448 (ptpp) REVERT: A 821 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8598 (ttmp) REVERT: A 825 ASP cc_start: 0.6911 (m-30) cc_final: 0.6526 (t0) REVERT: A 889 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6326 (ttp-170) REVERT: A 924 MET cc_start: 0.8752 (mmm) cc_final: 0.8137 (mmm) REVERT: B 171 GLU cc_start: 0.6894 (pm20) cc_final: 0.6064 (pm20) REVERT: B 174 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7474 (mtp) REVERT: C 3 MET cc_start: 0.5167 (mmm) cc_final: 0.4898 (tmm) REVERT: C 34 GLN cc_start: 0.7651 (tp40) cc_final: 0.7201 (tm-30) outliers start: 25 outliers final: 18 residues processed: 119 average time/residue: 0.3952 time to fit residues: 51.4613 Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 196 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 380 MET 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 779 ILE 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 A residue 926 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 404 ASN A 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119989 restraints weight = 11528.370| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.10 r_work: 0.3433 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9613 Z= 0.095 Angle : 0.445 6.581 13182 Z= 0.236 Chirality : 0.038 0.159 1501 Planarity : 0.003 0.034 1568 Dihedral : 10.786 73.051 1642 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.19 % Allowed : 15.03 % 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: 0.27 (0.26), residues: 1074 helix: 1.08 (0.24), residues: 505 sheet: -0.37 (0.40), residues: 141 loop : -0.64 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.030 0.001 TYR A 80 PHE 0.013 0.001 PHE A 741 TRP 0.014 0.001 TRP A 916 HIS 0.002 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9605) covalent geometry : angle 0.44406 (13176) hydrogen bonds : bond 0.03465 ( 433) hydrogen bonds : angle 4.08983 ( 1226) metal coordination : bond 0.00417 ( 8) metal coordination : angle 1.07024 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2857.72 seconds wall clock time: 49 minutes 25.17 seconds (2965.17 seconds total)