Starting phenix.real_space_refine on Fri Jul 3 06:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wui_32836/07_2026/7wui_32836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wui_32836/07_2026/7wui_32836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wui_32836/07_2026/7wui_32836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wui_32836/07_2026/7wui_32836.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wui_32836/07_2026/7wui_32836.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wui_32836/07_2026/7wui_32836.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wui_32836/07_2026/7wui_32836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wui_32836/07_2026/7wui_32836.cif" } resolution = 3.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3658 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6168 2.51 5 N 1652 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 9666 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1905 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1985 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 241} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1703 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 211} Chain breaks: 4 Chain: "L" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 87 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4PH:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.10, per 1000 atoms: 0.22 Number of scatterers: 9666 At special positions: 0 Unit cell: (118, 112, 97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1784 8.00 N 1652 7.00 C 6168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.95 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.58 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.52 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.89 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.34 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: 1.00 Conformation dependent library (CDL) restraints added in 354.1 milliseconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 18 sheets defined 34.0% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.943A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.771A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.103A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.002A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.514A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.132A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.863A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.872A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 21 removed outlier: 4.335A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 34 through 43 removed outlier: 3.818A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.508A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 617 through 644 removed outlier: 3.738A pdb=" N ILE R 623 " --> pdb=" O ALA R 619 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR R 624 " --> pdb=" O LEU R 620 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL R 637 " --> pdb=" O ILE R 633 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR R 638 " --> pdb=" O PHE R 634 " (cutoff:3.500A) Processing helix chain 'R' and resid 645 through 650 removed outlier: 3.697A pdb=" N ILE R 648 " --> pdb=" O PHE R 645 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG R 650 " --> pdb=" O LYS R 647 " (cutoff:3.500A) Processing helix chain 'R' and resid 651 through 680 removed outlier: 3.836A pdb=" N ILE R 670 " --> pdb=" O LEU R 666 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA R 678 " --> pdb=" O ASP R 674 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU R 679 " --> pdb=" O SER R 675 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR R 680 " --> pdb=" O TRP R 676 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 716 removed outlier: 3.781A pdb=" N ALA R 688 " --> pdb=" O GLY R 684 " (cutoff:3.500A) Processing helix chain 'R' and resid 725 through 735 removed outlier: 3.887A pdb=" N VAL R 733 " --> pdb=" O LYS R 729 " (cutoff:3.500A) Processing helix chain 'R' and resid 735 through 747 Processing helix chain 'R' and resid 749 through 751 No H-bonds generated for 'chain 'R' and resid 749 through 751' Processing helix chain 'R' and resid 774 through 782 Processing helix chain 'R' and resid 782 through 792 Processing helix chain 'R' and resid 793 through 810 removed outlier: 3.783A pdb=" N ILE R 798 " --> pdb=" O VAL R 794 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL R 799 " --> pdb=" O SER R 795 " (cutoff:3.500A) Processing helix chain 'R' and resid 824 through 834 removed outlier: 4.305A pdb=" N PHE R 832 " --> pdb=" O ALA R 828 " (cutoff:3.500A) Processing helix chain 'R' and resid 836 through 842 removed outlier: 4.123A pdb=" N ALA R 841 " --> pdb=" O TRP R 838 " (cutoff:3.500A) Processing helix chain 'R' and resid 850 through 862 removed outlier: 3.637A pdb=" N TYR R 854 " --> pdb=" O VAL R 850 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU R 862 " --> pdb=" O ILE R 858 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 883 removed outlier: 3.512A pdb=" N ARG R 879 " --> pdb=" O LYS R 875 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.609A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.504A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'L' and resid 600 through 604 removed outlier: 3.622A pdb=" N ILE L 603 " --> pdb=" O SER L 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.824A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.172A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.705A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.678A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.001A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.902A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.590A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.606A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.615A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 4.087A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 18 through 19 Processing sheet with id=AB3, first strand: chain 'R' and resid 753 through 754 removed outlier: 3.691A pdb=" N GLY R 754 " --> pdb=" O TRP R 771 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP R 771 " --> pdb=" O GLY R 754 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.499A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.499A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 68 through 73 Processing sheet with id=AB8, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB9, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.953A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR S 190 " --> pdb=" O ASN S 194 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1549 1.30 - 1.43: 2702 1.43 - 1.56: 5522 1.56 - 1.68: 6 1.68 - 1.81: 89 Bond restraints: 9868 Sorted by residual: bond pdb=" CG 4PH L 601 " pdb=" CD2 4PH L 601 " ideal model delta sigma weight residual 1.392 1.535 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" CG 4PH L 601 " pdb=" CD1 4PH L 601 " ideal model delta sigma weight residual 1.394 1.533 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" CE1 4PH L 601 " pdb=" CZ 4PH L 601 " ideal model delta sigma weight residual 1.394 1.532 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CD1 4PH L 601 " pdb=" CE1 4PH L 601 " ideal model delta sigma weight residual 1.387 1.524 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" CE2 4PH L 601 " pdb=" CZ 4PH L 601 " ideal model delta sigma weight residual 1.392 1.529 -0.137 2.00e-02 2.50e+03 4.69e+01 ... (remaining 9863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12749 2.48 - 4.97: 516 4.97 - 7.45: 59 7.45 - 9.94: 21 9.94 - 12.42: 4 Bond angle restraints: 13349 Sorted by residual: angle pdb=" N VAL R 783 " pdb=" CA VAL R 783 " pdb=" C VAL R 783 " ideal model delta sigma weight residual 110.53 122.95 -12.42 9.40e-01 1.13e+00 1.75e+02 angle pdb=" N GLY R 784 " pdb=" CA GLY R 784 " pdb=" C GLY R 784 " ideal model delta sigma weight residual 112.50 105.34 7.16 1.16e+00 7.43e-01 3.81e+01 angle pdb=" N LYS A 24 " pdb=" CA LYS A 24 " pdb=" C LYS A 24 " ideal model delta sigma weight residual 111.28 105.03 6.25 1.09e+00 8.42e-01 3.29e+01 angle pdb=" N CYS N 107 " pdb=" CA CYS N 107 " pdb=" C CYS N 107 " ideal model delta sigma weight residual 109.11 116.99 -7.88 1.42e+00 4.96e-01 3.08e+01 angle pdb=" N ALA N 92 " pdb=" CA ALA N 92 " pdb=" C ALA N 92 " ideal model delta sigma weight residual 109.96 118.06 -8.10 1.58e+00 4.01e-01 2.63e+01 ... (remaining 13344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5235 17.82 - 35.64: 491 35.64 - 53.46: 71 53.46 - 71.27: 10 71.27 - 89.09: 11 Dihedral angle restraints: 5818 sinusoidal: 2278 harmonic: 3540 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 154.76 25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LYS R 717 " pdb=" C LYS R 717 " pdb=" N VAL R 718 " pdb=" CA VAL R 718 " ideal model delta harmonic sigma weight residual 180.00 -155.60 -24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASP B 186 " pdb=" C ASP B 186 " pdb=" N VAL B 187 " pdb=" CA VAL B 187 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 5815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1205 0.080 - 0.161: 247 0.161 - 0.241: 32 0.241 - 0.322: 9 0.322 - 0.402: 1 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CA VAL R 783 " pdb=" N VAL R 783 " pdb=" C VAL R 783 " pdb=" CB VAL R 783 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB VAL R 699 " pdb=" CA VAL R 699 " pdb=" CG1 VAL R 699 " pdb=" CG2 VAL R 699 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB THR S 115 " pdb=" CA THR S 115 " pdb=" OG1 THR S 115 " pdb=" CG2 THR S 115 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1491 not shown) Planarity restraints: 1685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB 4PH L 601 " -0.020 2.00e-02 2.50e+03 2.04e-01 8.31e+02 pdb=" CG 4PH L 601 " 0.296 2.00e-02 2.50e+03 pdb=" CD1 4PH L 601 " -0.189 2.00e-02 2.50e+03 pdb=" CD2 4PH L 601 " -0.185 2.00e-02 2.50e+03 pdb=" CE1 4PH L 601 " 0.157 2.00e-02 2.50e+03 pdb=" CE2 4PH L 601 " 0.156 2.00e-02 2.50e+03 pdb=" CZ 4PH L 601 " -0.334 2.00e-02 2.50e+03 pdb=" C33 4PH L 601 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 47 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C THR B 47 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 47 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG B 48 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 283 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ARG B 283 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG B 283 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 284 " -0.019 2.00e-02 2.50e+03 ... (remaining 1682 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1307 2.76 - 3.29: 9590 3.29 - 3.83: 17744 3.83 - 4.36: 21834 4.36 - 4.90: 35386 Nonbonded interactions: 85861 Sorted by model distance: nonbonded pdb=" OH TYR R 625 " pdb=" OG SER R 675 " model vdw 2.221 3.040 nonbonded pdb=" CE MET S 93 " pdb=" OH TYR S 95 " model vdw 2.226 3.460 nonbonded pdb=" CD1 ILE R 687 " pdb=" O TYR R 753 " model vdw 2.227 3.460 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.228 3.040 nonbonded pdb=" SD MET S 93 " pdb=" OH TYR S 95 " model vdw 2.240 3.400 ... (remaining 85856 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.400 Find NCS groups from input model: 0.050 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 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 : 0.016 0.920 9873 Z= 0.827 Angle : 1.158 19.811 13359 Z= 0.655 Chirality : 0.068 0.402 1494 Planarity : 0.009 0.204 1685 Dihedral : 13.956 89.093 3523 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.29 % Allowed : 2.59 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.70 (0.22), residues: 1190 helix: -1.75 (0.24), residues: 347 sheet: -2.00 (0.28), residues: 265 loop : -1.59 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 38 TYR 0.026 0.003 TYR A 358 PHE 0.040 0.004 PHE B 241 TRP 0.043 0.004 TRP A 281 HIS 0.023 0.004 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.35 ( 9868) covalent geometry : angle 1.11457 / 0.64 (13349) SS BOND : bond 0.66642 / 34.55 ( 5) SS BOND : angle 11.54814 / 6.78 ( 10) hydrogen bonds : bond 0.16802 / 11.10 ( 404) hydrogen bonds : angle 9.24425 / 6.25 ( 1131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 392 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6649 (mm-30) REVERT: B 289 TYR cc_start: 0.6933 (m-80) cc_final: 0.6620 (m-80) REVERT: B 329 THR cc_start: 0.7459 (p) cc_final: 0.7103 (p) REVERT: R 683 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6081 (tpt90) REVERT: S 43 LYS cc_start: 0.7389 (ttmt) cc_final: 0.6909 (tptt) outliers start: 3 outliers final: 1 residues processed: 211 average time/residue: 0.0971 time to fit residues: 29.2269 Evaluate side-chains 167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 683 ARG Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 267 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 31 ASN N 35 ASN R 860 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.209015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.183119 restraints weight = 10335.051| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.65 r_work: 0.3979 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9873 Z= 0.160 Angle : 0.637 9.115 13359 Z= 0.338 Chirality : 0.044 0.204 1494 Planarity : 0.005 0.045 1685 Dihedral : 5.821 40.802 1339 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.11 % Allowed : 9.00 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.24), residues: 1190 helix: -0.44 (0.27), residues: 348 sheet: -1.57 (0.30), residues: 270 loop : -1.23 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 38 TYR 0.017 0.002 TYR B 264 PHE 0.020 0.002 PHE N 108 TRP 0.025 0.002 TRP B 339 HIS 0.008 0.002 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9868) covalent geometry : angle 0.63634 / 0.34 (13349) SS BOND : bond 0.00443 / 0.23 ( 5) SS BOND : angle 1.09150 / 0.61 ( 10) hydrogen bonds : bond 0.04524 / 2.93 ( 404) hydrogen bonds : angle 6.62116 / 4.62 ( 1131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7759 (ptpt) cc_final: 0.7393 (ptmt) REVERT: B 297 TRP cc_start: 0.8336 (m100) cc_final: 0.8007 (m100) REVERT: R 621 THR cc_start: 0.7015 (OUTLIER) cc_final: 0.6802 (m) REVERT: R 731 CYS cc_start: 0.6786 (t) cc_final: 0.6445 (t) REVERT: R 853 MET cc_start: 0.7132 (mmt) cc_final: 0.6595 (mmp) outliers start: 22 outliers final: 14 residues processed: 214 average time/residue: 0.0886 time to fit residues: 27.1718 Evaluate side-chains 195 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 621 THR Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN B 125 ASN B 156 GLN N 31 ASN R 775 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.210501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.183093 restraints weight = 10108.215| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.74 r_work: 0.3932 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9873 Z= 0.143 Angle : 0.587 10.318 13359 Z= 0.314 Chirality : 0.043 0.201 1494 Planarity : 0.004 0.044 1685 Dihedral : 5.329 33.649 1335 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.49 % Allowed : 12.74 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.24), residues: 1190 helix: -0.04 (0.27), residues: 346 sheet: -1.49 (0.30), residues: 267 loop : -1.14 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 280 TYR 0.013 0.002 TYR A 391 PHE 0.029 0.002 PHE R 778 TRP 0.018 0.002 TRP B 339 HIS 0.007 0.002 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9868) covalent geometry : angle 0.58644 / 0.31 (13349) SS BOND : bond 0.00148 / 0.08 ( 5) SS BOND : angle 0.79744 / 0.44 ( 10) hydrogen bonds : bond 0.04199 / 2.70 ( 404) hydrogen bonds : angle 6.14013 / 4.32 ( 1131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7758 (ptpt) cc_final: 0.7332 (ptmt) REVERT: A 230 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 275 SER cc_start: 0.8273 (m) cc_final: 0.7950 (p) REVERT: A 356 ARG cc_start: 0.6766 (tpp-160) cc_final: 0.6266 (ttm170) REVERT: B 134 ARG cc_start: 0.6539 (ptp-170) cc_final: 0.6149 (ptm160) REVERT: B 297 TRP cc_start: 0.8331 (m100) cc_final: 0.8045 (m100) REVERT: R 652 TYR cc_start: 0.7914 (m-10) cc_final: 0.7599 (m-10) REVERT: R 731 CYS cc_start: 0.7017 (t) cc_final: 0.6750 (t) REVERT: S 156 SER cc_start: 0.7126 (m) cc_final: 0.6722 (p) REVERT: S 192 MET cc_start: 0.3375 (mpp) cc_final: 0.2765 (mpp) outliers start: 26 outliers final: 16 residues processed: 206 average time/residue: 0.0909 time to fit residues: 26.9158 Evaluate side-chains 195 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 780 ILE Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 35 ASN ** R 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.184762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154740 restraints weight = 10183.766| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.67 r_work: 0.3657 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9873 Z= 0.252 Angle : 0.680 11.895 13359 Z= 0.357 Chirality : 0.046 0.261 1494 Planarity : 0.005 0.077 1685 Dihedral : 5.631 42.444 1335 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.45 % Allowed : 13.31 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.24), residues: 1190 helix: -0.11 (0.27), residues: 345 sheet: -1.55 (0.29), residues: 301 loop : -0.97 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 98 TYR 0.017 0.002 TYR A 358 PHE 0.021 0.002 PHE N 108 TRP 0.019 0.002 TRP A 281 HIS 0.012 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 ( 9868) covalent geometry : angle 0.67962 / 0.36 (13349) SS BOND : bond 0.00338 / 0.22 ( 5) SS BOND : angle 1.04772 / 0.59 ( 10) hydrogen bonds : bond 0.04897 / 3.15 ( 404) hydrogen bonds : angle 6.32881 / 4.44 ( 1131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.332 Fit side-chains REVERT: A 275 SER cc_start: 0.8499 (m) cc_final: 0.8139 (p) REVERT: A 356 ARG cc_start: 0.7293 (tpp-160) cc_final: 0.6575 (ttm110) REVERT: A 389 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7690 (mtt90) REVERT: B 78 LYS cc_start: 0.8158 (tppt) cc_final: 0.7763 (tptt) REVERT: B 297 TRP cc_start: 0.8847 (m100) cc_final: 0.8477 (m100) REVERT: N 38 ARG cc_start: 0.8330 (ptt-90) cc_final: 0.8104 (ptt-90) REVERT: R 652 TYR cc_start: 0.7926 (m-10) cc_final: 0.7450 (m-10) REVERT: S 156 SER cc_start: 0.7369 (m) cc_final: 0.6910 (p) REVERT: S 192 MET cc_start: 0.3474 (mpp) cc_final: 0.2932 (mpp) outliers start: 36 outliers final: 21 residues processed: 231 average time/residue: 0.0869 time to fit residues: 28.6173 Evaluate side-chains 220 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 232 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 16 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 31 ASN N 35 ASN ** R 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.194875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.166455 restraints weight = 10018.418| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.71 r_work: 0.3690 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9873 Z= 0.181 Angle : 0.622 9.365 13359 Z= 0.327 Chirality : 0.044 0.195 1494 Planarity : 0.005 0.054 1685 Dihedral : 5.495 43.849 1335 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.49 % Allowed : 16.09 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.24), residues: 1190 helix: -0.03 (0.27), residues: 347 sheet: -1.59 (0.30), residues: 281 loop : -0.91 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.015 0.002 TYR A 311 PHE 0.018 0.002 PHE A 212 TRP 0.026 0.002 TRP A 281 HIS 0.007 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 9868) covalent geometry : angle 0.62023 / 0.33 (13349) SS BOND : bond 0.00162 / 0.08 ( 5) SS BOND : angle 1.64089 / 0.98 ( 10) hydrogen bonds : bond 0.04313 / 2.78 ( 404) hydrogen bonds : angle 6.22075 / 4.40 ( 1131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.306 Fit side-chains REVERT: A 275 SER cc_start: 0.8386 (m) cc_final: 0.8119 (p) REVERT: A 356 ARG cc_start: 0.7292 (tpp-160) cc_final: 0.6678 (ttm110) REVERT: A 386 MET cc_start: 0.7649 (ptp) cc_final: 0.7342 (ptt) REVERT: A 392 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6961 (mt-10) REVERT: B 230 ASN cc_start: 0.7739 (m110) cc_final: 0.7408 (m110) REVERT: B 297 TRP cc_start: 0.8750 (m100) cc_final: 0.8366 (m100) REVERT: R 652 TYR cc_start: 0.7994 (m-10) cc_final: 0.7628 (m-10) REVERT: R 723 ILE cc_start: 0.6997 (mp) cc_final: 0.6581 (mm) REVERT: S 156 SER cc_start: 0.7548 (m) cc_final: 0.7029 (p) REVERT: S 192 MET cc_start: 0.3428 (mpp) cc_final: 0.2221 (mtm) REVERT: S 214 LEU cc_start: 0.6262 (tp) cc_final: 0.4897 (tp) REVERT: S 231 GLN cc_start: 0.8178 (pm20) cc_final: 0.7586 (pm20) outliers start: 26 outliers final: 18 residues processed: 216 average time/residue: 0.0825 time to fit residues: 26.0567 Evaluate side-chains 207 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 15 optimal weight: 0.0010 chunk 67 optimal weight: 0.0870 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 35 ASN ** R 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.198599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.170938 restraints weight = 10082.922| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.71 r_work: 0.3808 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9873 Z= 0.149 Angle : 0.595 9.805 13359 Z= 0.314 Chirality : 0.044 0.235 1494 Planarity : 0.004 0.044 1685 Dihedral : 5.333 43.490 1335 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.68 % Allowed : 16.28 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.25), residues: 1190 helix: 0.18 (0.27), residues: 346 sheet: -1.58 (0.29), residues: 289 loop : -0.89 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 180 TYR 0.014 0.002 TYR A 391 PHE 0.017 0.002 PHE R 778 TRP 0.025 0.002 TRP A 281 HIS 0.006 0.002 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9868) covalent geometry : angle 0.59434 / 0.31 (13349) SS BOND : bond 0.00208 / 0.15 ( 5) SS BOND : angle 1.09898 / 0.64 ( 10) hydrogen bonds : bond 0.03965 / 2.55 ( 404) hydrogen bonds : angle 6.06111 / 4.30 ( 1131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.358 Fit side-chains REVERT: A 216 LYS cc_start: 0.8130 (ptpt) cc_final: 0.7741 (ptmt) REVERT: A 280 ARG cc_start: 0.7585 (tpt170) cc_final: 0.7310 (ttt-90) REVERT: A 356 ARG cc_start: 0.7137 (tpp-160) cc_final: 0.6709 (ttm110) REVERT: A 371 ASN cc_start: 0.7274 (m-40) cc_final: 0.7072 (m-40) REVERT: A 392 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6938 (mt-10) REVERT: B 217 MET cc_start: 0.7230 (pmm) cc_final: 0.6715 (pmm) REVERT: B 230 ASN cc_start: 0.7691 (m110) cc_final: 0.7426 (m110) REVERT: B 297 TRP cc_start: 0.8627 (m100) cc_final: 0.8223 (m100) REVERT: B 325 MET cc_start: 0.8038 (tpp) cc_final: 0.7667 (mmm) REVERT: N 38 ARG cc_start: 0.8152 (ptt-90) cc_final: 0.7651 (ptt90) REVERT: N 65 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7739 (tptm) REVERT: N 95 TYR cc_start: 0.8381 (m-80) cc_final: 0.7546 (m-80) REVERT: R 652 TYR cc_start: 0.7873 (m-10) cc_final: 0.7543 (m-10) REVERT: S 156 SER cc_start: 0.7451 (m) cc_final: 0.6907 (p) REVERT: S 173 TYR cc_start: 0.7357 (m-80) cc_final: 0.7151 (m-80) REVERT: S 192 MET cc_start: 0.3408 (mpp) cc_final: 0.2199 (mtm) outliers start: 28 outliers final: 24 residues processed: 205 average time/residue: 0.0902 time to fit residues: 26.7020 Evaluate side-chains 214 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 15 optimal weight: 0.0070 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 118 optimal weight: 0.0570 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 266 HIS N 35 ASN ** R 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.203259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.176409 restraints weight = 10101.163| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.69 r_work: 0.3793 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9873 Z= 0.129 Angle : 0.569 8.342 13359 Z= 0.301 Chirality : 0.043 0.208 1494 Planarity : 0.004 0.042 1685 Dihedral : 5.163 42.949 1335 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.07 % Allowed : 16.57 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.25), residues: 1190 helix: 0.41 (0.27), residues: 346 sheet: -1.51 (0.30), residues: 275 loop : -0.85 (0.28), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 649 TYR 0.014 0.001 TYR A 391 PHE 0.016 0.002 PHE A 212 TRP 0.023 0.002 TRP A 281 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9868) covalent geometry : angle 0.56866 / 0.30 (13349) SS BOND : bond 0.00226 / 0.16 ( 5) SS BOND : angle 0.85195 / 0.50 ( 10) hydrogen bonds : bond 0.03723 / 2.39 ( 404) hydrogen bonds : angle 5.90931 / 4.19 ( 1131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.398 Fit side-chains REVERT: A 209 GLU cc_start: 0.6207 (mp0) cc_final: 0.5940 (mp0) REVERT: A 216 LYS cc_start: 0.8065 (ptpt) cc_final: 0.7709 (ptmt) REVERT: A 280 ARG cc_start: 0.7594 (tpt170) cc_final: 0.7352 (ttt-90) REVERT: A 356 ARG cc_start: 0.7190 (tpp-160) cc_final: 0.6762 (ttm110) REVERT: A 392 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6944 (mt-10) REVERT: B 159 THR cc_start: 0.8241 (p) cc_final: 0.7914 (p) REVERT: B 217 MET cc_start: 0.7157 (pmm) cc_final: 0.6750 (pmm) REVERT: B 230 ASN cc_start: 0.7661 (m110) cc_final: 0.7382 (m110) REVERT: B 297 TRP cc_start: 0.8520 (m100) cc_final: 0.8211 (m100) REVERT: N 38 ARG cc_start: 0.8122 (ptt-90) cc_final: 0.7627 (ptt90) REVERT: N 65 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7732 (tptm) REVERT: N 80 TYR cc_start: 0.7806 (m-80) cc_final: 0.7222 (m-80) REVERT: N 95 TYR cc_start: 0.8354 (m-80) cc_final: 0.7444 (m-80) REVERT: R 652 TYR cc_start: 0.7903 (m-10) cc_final: 0.7596 (m-10) REVERT: R 685 PHE cc_start: 0.5997 (OUTLIER) cc_final: 0.5625 (t80) REVERT: S 100 ILE cc_start: 0.8249 (tt) cc_final: 0.7818 (tt) REVERT: S 156 SER cc_start: 0.7520 (m) cc_final: 0.7054 (p) REVERT: S 173 TYR cc_start: 0.7207 (m-80) cc_final: 0.6946 (m-80) REVERT: S 192 MET cc_start: 0.3407 (mpp) cc_final: 0.2165 (mtp) outliers start: 32 outliers final: 24 residues processed: 206 average time/residue: 0.0958 time to fit residues: 28.3350 Evaluate side-chains 208 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 685 PHE Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 16 ASN B 266 HIS N 35 ASN ** R 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.195497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.167008 restraints weight = 10037.403| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.72 r_work: 0.3704 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9873 Z= 0.182 Angle : 0.617 8.269 13359 Z= 0.324 Chirality : 0.044 0.222 1494 Planarity : 0.004 0.047 1685 Dihedral : 5.314 43.962 1335 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.97 % Allowed : 17.05 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.25), residues: 1190 helix: 0.38 (0.27), residues: 347 sheet: -1.47 (0.30), residues: 280 loop : -0.82 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.013 0.002 TYR A 391 PHE 0.031 0.002 PHE R 769 TRP 0.025 0.002 TRP A 281 HIS 0.006 0.002 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 9868) covalent geometry : angle 0.61713 / 0.32 (13349) SS BOND : bond 0.00116 / 0.06 ( 5) SS BOND : angle 0.94651 / 0.55 ( 10) hydrogen bonds : bond 0.04131 / 2.64 ( 404) hydrogen bonds : angle 6.01587 / 4.24 ( 1131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.361 Fit side-chains REVERT: A 15 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: A 209 GLU cc_start: 0.6479 (mp0) cc_final: 0.6255 (mp0) REVERT: A 275 SER cc_start: 0.8398 (m) cc_final: 0.8113 (p) REVERT: A 356 ARG cc_start: 0.7281 (tpp-160) cc_final: 0.6852 (ttp-170) REVERT: A 392 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6927 (mt-10) REVERT: B 217 MET cc_start: 0.7282 (pmm) cc_final: 0.6920 (pmm) REVERT: B 230 ASN cc_start: 0.7701 (m110) cc_final: 0.7430 (m110) REVERT: B 297 TRP cc_start: 0.8596 (m100) cc_final: 0.8393 (m100) REVERT: N 38 ARG cc_start: 0.8162 (ptt-90) cc_final: 0.7674 (ptt90) REVERT: N 65 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7790 (tptm) REVERT: N 80 TYR cc_start: 0.7910 (m-80) cc_final: 0.7417 (m-80) REVERT: N 95 TYR cc_start: 0.8424 (m-80) cc_final: 0.7530 (m-80) REVERT: R 618 MET cc_start: 0.4971 (mtm) cc_final: 0.4213 (pmm) REVERT: R 866 PHE cc_start: 0.7897 (m-80) cc_final: 0.7691 (m-80) REVERT: S 100 ILE cc_start: 0.8283 (tt) cc_final: 0.7847 (tt) REVERT: S 156 SER cc_start: 0.7566 (m) cc_final: 0.7051 (p) REVERT: S 192 MET cc_start: 0.3263 (mpp) cc_final: 0.2041 (mtp) outliers start: 31 outliers final: 25 residues processed: 211 average time/residue: 0.0900 time to fit residues: 27.3906 Evaluate side-chains 216 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 125 ASN B 266 HIS N 35 ASN ** R 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.200226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.172006 restraints weight = 10019.553| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.75 r_work: 0.3743 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9873 Z= 0.148 Angle : 0.602 8.378 13359 Z= 0.317 Chirality : 0.043 0.202 1494 Planarity : 0.004 0.042 1685 Dihedral : 5.228 42.943 1335 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.68 % Allowed : 18.39 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.25), residues: 1190 helix: 0.42 (0.27), residues: 347 sheet: -1.39 (0.30), residues: 280 loop : -0.75 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.015 0.002 TYR A 358 PHE 0.029 0.002 PHE R 769 TRP 0.026 0.002 TRP A 281 HIS 0.011 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9868) covalent geometry : angle 0.60224 / 0.32 (13349) SS BOND : bond 0.00439 / 0.32 ( 5) SS BOND : angle 0.80763 / 0.44 ( 10) hydrogen bonds : bond 0.03879 / 2.48 ( 404) hydrogen bonds : angle 5.93751 / 4.20 ( 1131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.285 Fit side-chains REVERT: A 209 GLU cc_start: 0.6350 (mp0) cc_final: 0.6118 (mp0) REVERT: A 216 LYS cc_start: 0.7948 (ptpt) cc_final: 0.7577 (ptmt) REVERT: A 280 ARG cc_start: 0.7680 (tpt170) cc_final: 0.7374 (ttt-90) REVERT: A 356 ARG cc_start: 0.7203 (tpp-160) cc_final: 0.6820 (ttm110) REVERT: A 392 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6997 (mt-10) REVERT: B 30 LEU cc_start: 0.6057 (tp) cc_final: 0.5755 (tt) REVERT: B 159 THR cc_start: 0.8282 (p) cc_final: 0.7936 (p) REVERT: B 217 MET cc_start: 0.7228 (pmm) cc_final: 0.6900 (pmm) REVERT: B 230 ASN cc_start: 0.7686 (m110) cc_final: 0.7417 (m110) REVERT: B 284 LEU cc_start: 0.7559 (tt) cc_final: 0.7159 (tt) REVERT: B 297 TRP cc_start: 0.8493 (m100) cc_final: 0.8260 (m100) REVERT: N 38 ARG cc_start: 0.8137 (ptt-90) cc_final: 0.7660 (ptt90) REVERT: N 65 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7763 (tptm) REVERT: N 80 TYR cc_start: 0.7939 (m-80) cc_final: 0.7465 (m-80) REVERT: N 95 TYR cc_start: 0.8436 (m-80) cc_final: 0.7469 (m-80) REVERT: R 618 MET cc_start: 0.4969 (mtm) cc_final: 0.4187 (pmm) REVERT: R 733 VAL cc_start: 0.8984 (t) cc_final: 0.8774 (t) REVERT: R 866 PHE cc_start: 0.7837 (m-80) cc_final: 0.7623 (m-80) REVERT: S 100 ILE cc_start: 0.8206 (tt) cc_final: 0.7789 (tt) REVERT: S 156 SER cc_start: 0.7428 (m) cc_final: 0.6948 (p) REVERT: S 192 MET cc_start: 0.3229 (mpp) cc_final: 0.2711 (mpp) outliers start: 28 outliers final: 24 residues processed: 202 average time/residue: 0.0850 time to fit residues: 24.6764 Evaluate side-chains 213 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 111 optimal weight: 0.2980 chunk 114 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 266 HIS N 35 ASN ** R 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.197570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.169817 restraints weight = 10140.037| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.72 r_work: 0.3722 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9873 Z= 0.163 Angle : 0.620 8.580 13359 Z= 0.326 Chirality : 0.044 0.208 1494 Planarity : 0.004 0.043 1685 Dihedral : 5.270 43.838 1335 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.59 % Allowed : 18.97 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.25), residues: 1190 helix: 0.34 (0.27), residues: 353 sheet: -1.43 (0.30), residues: 278 loop : -0.78 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 180 TYR 0.014 0.002 TYR B 111 PHE 0.030 0.002 PHE R 769 TRP 0.027 0.002 TRP A 281 HIS 0.017 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9868) covalent geometry : angle 0.61933 / 0.33 (13349) SS BOND : bond 0.00220 / 0.15 ( 5) SS BOND : angle 0.87184 / 0.47 ( 10) hydrogen bonds : bond 0.03989 / 2.55 ( 404) hydrogen bonds : angle 5.96800 / 4.22 ( 1131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.383 Fit side-chains REVERT: A 15 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: A 209 GLU cc_start: 0.6397 (mp0) cc_final: 0.6161 (mp0) REVERT: A 280 ARG cc_start: 0.7672 (tpt170) cc_final: 0.7376 (ttt-90) REVERT: A 356 ARG cc_start: 0.7212 (tpp-160) cc_final: 0.6868 (ttp-170) REVERT: A 392 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6956 (mt-10) REVERT: B 217 MET cc_start: 0.7229 (pmm) cc_final: 0.6898 (pmm) REVERT: B 230 ASN cc_start: 0.7681 (m110) cc_final: 0.7416 (m110) REVERT: B 284 LEU cc_start: 0.7561 (tt) cc_final: 0.7192 (tt) REVERT: N 38 ARG cc_start: 0.8167 (ptt-90) cc_final: 0.7686 (ptt90) REVERT: N 65 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7740 (tptm) REVERT: N 80 TYR cc_start: 0.7954 (m-80) cc_final: 0.7477 (m-80) REVERT: N 95 TYR cc_start: 0.8454 (m-80) cc_final: 0.7501 (m-80) REVERT: R 618 MET cc_start: 0.4973 (mtm) cc_final: 0.4190 (pmm) REVERT: R 733 VAL cc_start: 0.8995 (t) cc_final: 0.8788 (t) REVERT: R 866 PHE cc_start: 0.7859 (m-80) cc_final: 0.7650 (m-80) REVERT: S 100 ILE cc_start: 0.8226 (tt) cc_final: 0.7784 (tt) REVERT: S 156 SER cc_start: 0.7453 (m) cc_final: 0.6964 (p) REVERT: S 192 MET cc_start: 0.3254 (mpp) cc_final: 0.1961 (mtp) outliers start: 27 outliers final: 24 residues processed: 207 average time/residue: 0.0913 time to fit residues: 27.2306 Evaluate side-chains 216 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 266 HIS N 35 ASN ** R 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.192947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164086 restraints weight = 10078.606| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.74 r_work: 0.3692 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9873 Z= 0.201 Angle : 0.656 10.558 13359 Z= 0.345 Chirality : 0.046 0.235 1494 Planarity : 0.005 0.050 1685 Dihedral : 5.443 45.046 1335 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.49 % Allowed : 18.87 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.25), residues: 1190 helix: 0.21 (0.27), residues: 353 sheet: -1.46 (0.30), residues: 280 loop : -0.78 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 180 TYR 0.014 0.002 TYR A 391 PHE 0.026 0.002 PHE R 769 TRP 0.027 0.002 TRP A 281 HIS 0.010 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 9868) covalent geometry : angle 0.65554 / 0.34 (13349) SS BOND : bond 0.00213 / 0.14 ( 5) SS BOND : angle 0.89115 / 0.50 ( 10) hydrogen bonds : bond 0.04287 / 2.74 ( 404) hydrogen bonds : angle 6.12883 / 4.33 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.76 seconds wall clock time: 47 minutes 49.10 seconds (2869.10 seconds total)