Starting phenix.real_space_refine on Sun Apr 5 18:35:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wui_32836/04_2026/7wui_32836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wui_32836/04_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_32836/04_2026/7wui_32836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wui_32836/04_2026/7wui_32836.map" model { file = "/net/cci-nas-00/data/ceres_data/7wui_32836/04_2026/7wui_32836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wui_32836/04_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-2.1rc1-6017/lib/python3.9/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: 2.14, 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: 0.72 Conformation dependent library (CDL) restraints added in 466.1 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: 0.34 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: 1.59 Time building geometry restraints manager: 1.00 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: 1.080 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 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 covalent geometry : bond 0.00674 ( 9868) covalent geometry : angle 1.11457 (13349) SS BOND : bond 0.66642 ( 5) SS BOND : angle 11.54814 ( 10) hydrogen bonds : bond 0.16802 ( 404) hydrogen bonds : angle 9.24425 ( 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 : 0.334 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: 0.7104 (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: 0.0949 time to fit residues: 28.2240 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 : 0.329 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 267 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.208119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.182249 restraints weight = 10372.069| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.65 r_work: 0.3979 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9873 Z= 0.168 Angle : 0.636 8.873 13359 Z= 0.339 Chirality : 0.045 0.206 1494 Planarity : 0.005 0.046 1685 Dihedral : 5.804 38.003 1339 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.82 % Allowed : 9.10 % Favored : 89.08 % 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: -1.71 (0.24), residues: 1190 helix: -0.46 (0.27), residues: 348 sheet: -1.54 (0.30), residues: 268 loop : -1.25 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 38 TYR 0.018 0.002 TYR B 264 PHE 0.017 0.002 PHE R 786 TRP 0.025 0.002 TRP B 339 HIS 0.007 0.002 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9868) covalent geometry : angle 0.63496 (13349) SS BOND : bond 0.00438 ( 5) SS BOND : angle 1.34145 ( 10) hydrogen bonds : bond 0.04544 ( 404) hydrogen bonds : angle 6.63741 ( 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 221 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7760 (ptpt) cc_final: 0.7387 (ptmt) REVERT: B 297 TRP cc_start: 0.8315 (m100) cc_final: 0.8030 (m100) REVERT: R 621 THR cc_start: 0.7012 (OUTLIER) cc_final: 0.6797 (m) REVERT: R 652 TYR cc_start: 0.7964 (m-10) cc_final: 0.7665 (m-10) REVERT: R 731 CYS cc_start: 0.6685 (t) cc_final: 0.6323 (t) REVERT: R 853 MET cc_start: 0.7127 (mmt) cc_final: 0.6588 (mmp) REVERT: S 34 MET cc_start: 0.8023 (mmm) cc_final: 0.7782 (mmm) REVERT: S 140 MET cc_start: 0.7986 (mmt) cc_final: 0.7774 (mmt) outliers start: 19 outliers final: 14 residues processed: 209 average time/residue: 0.0945 time to fit residues: 27.9188 Evaluate side-chains 188 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 49 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 125 ASN N 31 ASN ** 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 = 0.4374 r_free = 0.4374 target = 0.217506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.191662 restraints weight = 10190.086| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.72 r_work: 0.4026 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3887 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9873 Z= 0.120 Angle : 0.568 10.013 13359 Z= 0.304 Chirality : 0.042 0.188 1494 Planarity : 0.004 0.044 1685 Dihedral : 5.228 32.241 1335 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.30 % Allowed : 12.16 % Favored : 85.54 % 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: -1.40 (0.24), residues: 1190 helix: 0.01 (0.27), residues: 345 sheet: -1.39 (0.31), residues: 267 loop : -1.20 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 38 TYR 0.015 0.001 TYR A 391 PHE 0.014 0.002 PHE R 786 TRP 0.020 0.002 TRP B 339 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9868) covalent geometry : angle 0.56817 (13349) SS BOND : bond 0.00333 ( 5) SS BOND : angle 0.74345 ( 10) hydrogen bonds : bond 0.03971 ( 404) hydrogen bonds : angle 6.06173 ( 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 216 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7646 (ptpt) cc_final: 0.7241 (ptmt) REVERT: B 134 ARG cc_start: 0.6335 (ptp-170) cc_final: 0.5956 (ptm160) REVERT: B 247 ASP cc_start: 0.8223 (p0) cc_final: 0.7866 (p0) REVERT: B 266 HIS cc_start: 0.6150 (t-170) cc_final: 0.5945 (t-170) REVERT: B 297 TRP cc_start: 0.8143 (m100) cc_final: 0.7831 (m100) REVERT: B 325 MET cc_start: 0.7605 (tpp) cc_final: 0.7402 (tpp) REVERT: R 731 CYS cc_start: 0.6825 (t) cc_final: 0.6534 (t) REVERT: R 778 PHE cc_start: 0.7384 (t80) cc_final: 0.7016 (t80) REVERT: S 192 MET cc_start: 0.3417 (mpp) cc_final: 0.2809 (mpp) outliers start: 24 outliers final: 15 residues processed: 202 average time/residue: 0.0929 time to fit residues: 26.3774 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 225 HIS Chi-restraints excluded: chain B residue 243 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 654 SER Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 780 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.0770 chunk 29 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 0.0970 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN N 31 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 = 0.4315 r_free = 0.4315 target = 0.210437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.184120 restraints weight = 10264.531| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.66 r_work: 0.3970 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9873 Z= 0.123 Angle : 0.559 10.458 13359 Z= 0.296 Chirality : 0.042 0.198 1494 Planarity : 0.004 0.042 1685 Dihedral : 4.999 30.628 1335 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.87 % Allowed : 12.74 % Favored : 84.39 % 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: -1.14 (0.24), residues: 1190 helix: 0.37 (0.28), residues: 345 sheet: -1.28 (0.31), residues: 270 loop : -1.11 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.015 0.002 TYR A 391 PHE 0.014 0.001 PHE N 108 TRP 0.019 0.001 TRP B 339 HIS 0.012 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9868) covalent geometry : angle 0.55885 (13349) SS BOND : bond 0.00397 ( 5) SS BOND : angle 0.61337 ( 10) hydrogen bonds : bond 0.03811 ( 404) hydrogen bonds : angle 5.75797 ( 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 214 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7609 (ptpt) cc_final: 0.7264 (pttt) REVERT: A 356 ARG cc_start: 0.6727 (tpp-160) cc_final: 0.6253 (ttp80) REVERT: A 392 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 125 ASN cc_start: 0.7873 (t0) cc_final: 0.7502 (t0) REVERT: B 230 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7637 (m110) REVERT: B 247 ASP cc_start: 0.8247 (p0) cc_final: 0.7963 (p0) REVERT: B 297 TRP cc_start: 0.8128 (m100) cc_final: 0.7818 (m100) REVERT: R 717 LYS cc_start: 0.7126 (tmtt) cc_final: 0.6880 (tmtt) REVERT: R 729 LYS cc_start: 0.7148 (mtpt) cc_final: 0.6831 (ptpt) REVERT: S 192 MET cc_start: 0.3213 (mpp) cc_final: 0.2865 (mpp) outliers start: 30 outliers final: 17 residues processed: 196 average time/residue: 0.0884 time to fit residues: 24.9394 Evaluate side-chains 193 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 780 ILE Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 97 VAL 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: 1.9990 chunk 2 optimal weight: 0.0980 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN N 31 ASN R 720 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.215693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188557 restraints weight = 10155.733| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.74 r_work: 0.3977 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9873 Z= 0.124 Angle : 0.553 10.509 13359 Z= 0.291 Chirality : 0.042 0.221 1494 Planarity : 0.004 0.042 1685 Dihedral : 4.938 32.598 1335 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.78 % Allowed : 14.46 % Favored : 82.76 % 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: -1.02 (0.24), residues: 1190 helix: 0.52 (0.28), residues: 345 sheet: -1.31 (0.30), residues: 276 loop : -1.00 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.013 0.001 TYR A 391 PHE 0.014 0.001 PHE A 212 TRP 0.019 0.001 TRP A 281 HIS 0.008 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9868) covalent geometry : angle 0.55308 (13349) SS BOND : bond 0.00341 ( 5) SS BOND : angle 0.62928 ( 10) hydrogen bonds : bond 0.03713 ( 404) hydrogen bonds : angle 5.70191 ( 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 213 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7680 (ptpt) cc_final: 0.7313 (ptmt) REVERT: A 280 ARG cc_start: 0.7575 (tpt90) cc_final: 0.7108 (ttt-90) REVERT: A 392 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6666 (mt-10) REVERT: B 125 ASN cc_start: 0.8050 (t0) cc_final: 0.7850 (t0) REVERT: B 217 MET cc_start: 0.6647 (ppp) cc_final: 0.5806 (pmm) REVERT: B 297 TRP cc_start: 0.8200 (m100) cc_final: 0.7965 (m100) REVERT: N 38 ARG cc_start: 0.8225 (ptt-90) cc_final: 0.7894 (ptt90) REVERT: N 80 TYR cc_start: 0.7281 (m-80) cc_final: 0.6555 (m-80) REVERT: R 717 LYS cc_start: 0.7079 (tmtt) cc_final: 0.6776 (tmtt) REVERT: S 140 MET cc_start: 0.7920 (mmm) cc_final: 0.7689 (mmm) REVERT: S 156 SER cc_start: 0.7060 (m) cc_final: 0.6660 (p) REVERT: S 192 MET cc_start: 0.3100 (mpp) cc_final: 0.2740 (mpp) outliers start: 29 outliers final: 20 residues processed: 197 average time/residue: 0.0869 time to fit residues: 24.5510 Evaluate side-chains 190 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 225 HIS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 780 ILE 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 232 HIS 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: 0.0870 chunk 20 optimal weight: 0.0020 chunk 117 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 230 ASN N 31 ASN N 35 ASN ** 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 = 0.4307 r_free = 0.4307 target = 0.209294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.181581 restraints weight = 10384.272| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.72 r_work: 0.3993 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9873 Z= 0.123 Angle : 0.540 6.312 13359 Z= 0.287 Chirality : 0.042 0.189 1494 Planarity : 0.004 0.041 1685 Dihedral : 4.873 34.571 1335 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.16 % Allowed : 15.13 % Favored : 81.70 % 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: -0.90 (0.25), residues: 1190 helix: 0.63 (0.28), residues: 346 sheet: -1.27 (0.30), residues: 283 loop : -0.92 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.014 0.001 TYR B 111 PHE 0.015 0.001 PHE R 778 TRP 0.019 0.001 TRP B 339 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9868) covalent geometry : angle 0.53980 (13349) SS BOND : bond 0.00303 ( 5) SS BOND : angle 0.78759 ( 10) hydrogen bonds : bond 0.03608 ( 404) hydrogen bonds : angle 5.59597 ( 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 212 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7676 (ptpt) cc_final: 0.7310 (ptmt) REVERT: A 280 ARG cc_start: 0.7502 (tpt90) cc_final: 0.7183 (ttt-90) REVERT: A 356 ARG cc_start: 0.6653 (tpp-160) cc_final: 0.6289 (ttp80) REVERT: A 392 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6691 (mt-10) REVERT: B 134 ARG cc_start: 0.7011 (ptp-170) cc_final: 0.6788 (ptm160) REVERT: B 217 MET cc_start: 0.6749 (ppp) cc_final: 0.6523 (ppp) REVERT: B 230 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7589 (m-40) REVERT: B 247 ASP cc_start: 0.8400 (p0) cc_final: 0.7949 (p0) REVERT: G 50 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8286 (mt) REVERT: N 38 ARG cc_start: 0.8162 (ptt-90) cc_final: 0.7844 (ptt90) REVERT: N 80 TYR cc_start: 0.7325 (m-80) cc_final: 0.6498 (m-80) REVERT: R 717 LYS cc_start: 0.7031 (tmtt) cc_final: 0.6819 (tmtt) REVERT: S 140 MET cc_start: 0.7954 (mmm) cc_final: 0.7747 (mmm) REVERT: S 156 SER cc_start: 0.7087 (m) cc_final: 0.6711 (p) REVERT: S 192 MET cc_start: 0.3026 (mpp) cc_final: 0.2006 (mtp) outliers start: 33 outliers final: 22 residues processed: 193 average time/residue: 0.0905 time to fit residues: 24.7150 Evaluate side-chains 191 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 50 LEU 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 R residue 635 LEU Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 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 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: 0.2980 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 16 ASN N 31 ASN ** 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 = 0.4240 r_free = 0.4240 target = 0.202718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.173426 restraints weight = 10179.137| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.79 r_work: 0.3798 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9873 Z= 0.175 Angle : 0.590 9.911 13359 Z= 0.311 Chirality : 0.044 0.215 1494 Planarity : 0.004 0.055 1685 Dihedral : 5.044 34.869 1335 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.68 % Allowed : 16.57 % Favored : 80.75 % 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: -0.89 (0.25), residues: 1190 helix: 0.56 (0.28), residues: 346 sheet: -1.24 (0.30), residues: 297 loop : -0.85 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 98 TYR 0.015 0.002 TYR N 32 PHE 0.042 0.002 PHE R 769 TRP 0.021 0.002 TRP A 281 HIS 0.009 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9868) covalent geometry : angle 0.58975 (13349) SS BOND : bond 0.00325 ( 5) SS BOND : angle 0.88595 ( 10) hydrogen bonds : bond 0.03976 ( 404) hydrogen bonds : angle 5.72798 ( 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 215 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7864 (ptpt) cc_final: 0.7486 (ptmt) REVERT: A 275 SER cc_start: 0.8439 (m) cc_final: 0.8140 (p) REVERT: A 280 ARG cc_start: 0.7667 (tpt90) cc_final: 0.7321 (ttt-90) REVERT: A 356 ARG cc_start: 0.6962 (tpp-160) cc_final: 0.6401 (ttm110) REVERT: A 371 ASN cc_start: 0.7068 (t0) cc_final: 0.6858 (m-40) REVERT: A 392 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7150 (mm-30) REVERT: B 122 SER cc_start: 0.8110 (OUTLIER) cc_final: 0.7862 (t) REVERT: B 134 ARG cc_start: 0.7286 (ptp-170) cc_final: 0.7067 (ptm160) REVERT: B 217 MET cc_start: 0.6908 (ppp) cc_final: 0.6518 (ppp) REVERT: B 230 ASN cc_start: 0.7883 (m110) cc_final: 0.7556 (m110) REVERT: N 38 ARG cc_start: 0.8238 (ptt-90) cc_final: 0.7707 (ptt90) REVERT: N 74 ASN cc_start: 0.6763 (m-40) cc_final: 0.6300 (m110) REVERT: N 80 TYR cc_start: 0.7701 (m-80) cc_final: 0.6940 (m-80) REVERT: R 717 LYS cc_start: 0.7291 (tmtt) cc_final: 0.7015 (tmtt) REVERT: S 156 SER cc_start: 0.7195 (m) cc_final: 0.6738 (p) REVERT: S 192 MET cc_start: 0.3058 (mpp) cc_final: 0.2088 (mtp) outliers start: 28 outliers final: 21 residues processed: 202 average time/residue: 0.0905 time to fit residues: 26.1541 Evaluate side-chains 200 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 122 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 661 CYS Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 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 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: 0.4980 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.0060 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 230 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.198080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.170427 restraints weight = 10242.722| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.64 r_work: 0.3831 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9873 Z= 0.160 Angle : 0.598 10.311 13359 Z= 0.312 Chirality : 0.044 0.221 1494 Planarity : 0.004 0.053 1685 Dihedral : 5.100 39.740 1335 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.16 % Allowed : 16.57 % Favored : 80.27 % 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: -0.87 (0.25), residues: 1190 helix: 0.53 (0.27), residues: 347 sheet: -1.26 (0.29), residues: 302 loop : -0.77 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.014 0.002 TYR A 391 PHE 0.034 0.002 PHE R 769 TRP 0.020 0.002 TRP A 281 HIS 0.008 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9868) covalent geometry : angle 0.59809 (13349) SS BOND : bond 0.00145 ( 5) SS BOND : angle 0.89682 ( 10) hydrogen bonds : bond 0.03901 ( 404) hydrogen bonds : angle 5.79271 ( 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 214 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7571 (ptmt) REVERT: A 275 SER cc_start: 0.8277 (m) cc_final: 0.8013 (p) REVERT: A 280 ARG cc_start: 0.7820 (tpt90) cc_final: 0.7589 (tpt170) REVERT: A 356 ARG cc_start: 0.6954 (tpp-160) cc_final: 0.6625 (ttm110) REVERT: A 392 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6917 (mt-10) REVERT: B 134 ARG cc_start: 0.7411 (ptp-170) cc_final: 0.7194 (ptm160) REVERT: B 230 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7318 (m110) REVERT: G 50 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8402 (mt) REVERT: N 38 ARG cc_start: 0.8200 (ptt-90) cc_final: 0.7659 (ptt90) REVERT: N 80 TYR cc_start: 0.7803 (m-80) cc_final: 0.7149 (m-80) REVERT: R 618 MET cc_start: 0.5004 (mtm) cc_final: 0.4277 (pmm) REVERT: R 717 LYS cc_start: 0.7262 (tmtt) cc_final: 0.7002 (tmtt) REVERT: S 156 SER cc_start: 0.7193 (m) cc_final: 0.6814 (p) REVERT: S 192 MET cc_start: 0.3010 (mpp) cc_final: 0.2093 (mtp) outliers start: 33 outliers final: 23 residues processed: 201 average time/residue: 0.0967 time to fit residues: 27.8327 Evaluate side-chains 202 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 370 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 682 THR 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 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: 0.0970 chunk 76 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.204178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.176538 restraints weight = 10023.859| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.71 r_work: 0.3797 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9873 Z= 0.157 Angle : 0.604 10.535 13359 Z= 0.314 Chirality : 0.045 0.222 1494 Planarity : 0.004 0.050 1685 Dihedral : 5.171 40.178 1335 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.59 % Allowed : 17.34 % Favored : 80.08 % 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: -0.83 (0.25), residues: 1190 helix: 0.53 (0.27), residues: 347 sheet: -1.17 (0.30), residues: 285 loop : -0.80 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.015 0.002 TYR A 391 PHE 0.031 0.002 PHE R 769 TRP 0.020 0.002 TRP A 281 HIS 0.009 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9868) covalent geometry : angle 0.60332 (13349) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.87544 ( 10) hydrogen bonds : bond 0.03890 ( 404) hydrogen bonds : angle 5.80216 ( 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 199 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7963 (ptpt) cc_final: 0.7581 (ptmt) REVERT: A 275 SER cc_start: 0.8312 (m) cc_final: 0.8053 (p) REVERT: A 280 ARG cc_start: 0.7802 (tpt90) cc_final: 0.7426 (ttt-90) REVERT: A 356 ARG cc_start: 0.6962 (tpp-160) cc_final: 0.6639 (ttm110) REVERT: A 392 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6948 (mt-10) REVERT: B 134 ARG cc_start: 0.7403 (ptp-170) cc_final: 0.7178 (ptm160) REVERT: B 217 MET cc_start: 0.6868 (ppp) cc_final: 0.6429 (ppp) REVERT: N 38 ARG cc_start: 0.8190 (ptt-90) cc_final: 0.7646 (ptt90) REVERT: N 65 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7667 (tptm) REVERT: N 80 TYR cc_start: 0.7867 (m-80) cc_final: 0.7216 (m-80) REVERT: R 618 MET cc_start: 0.4987 (mtm) cc_final: 0.4251 (pmm) REVERT: R 672 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7203 (mp) REVERT: R 717 LYS cc_start: 0.7277 (tmtt) cc_final: 0.7026 (tmtt) REVERT: S 83 MET cc_start: 0.4419 (mtp) cc_final: 0.4107 (ttm) REVERT: S 156 SER cc_start: 0.7383 (m) cc_final: 0.6934 (p) REVERT: S 192 MET cc_start: 0.3064 (mpp) cc_final: 0.2145 (mtp) outliers start: 27 outliers final: 21 residues processed: 188 average time/residue: 0.0882 time to fit residues: 23.6041 Evaluate side-chains 192 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 370 GLU 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 295 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 672 LEU Chi-restraints excluded: chain R residue 682 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 0.0010 chunk 29 optimal weight: 0.0670 chunk 101 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 230 ASN ** 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 = 0.4252 r_free = 0.4252 target = 0.204355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.177213 restraints weight = 10128.897| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.70 r_work: 0.3813 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9873 Z= 0.146 Angle : 0.602 10.557 13359 Z= 0.313 Chirality : 0.044 0.219 1494 Planarity : 0.004 0.047 1685 Dihedral : 5.160 41.029 1335 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 17.43 % Favored : 80.08 % 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: -0.81 (0.25), residues: 1190 helix: 0.54 (0.27), residues: 352 sheet: -1.15 (0.30), residues: 285 loop : -0.80 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 180 TYR 0.017 0.002 TYR A 358 PHE 0.029 0.002 PHE R 769 TRP 0.020 0.002 TRP A 281 HIS 0.008 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9868) covalent geometry : angle 0.60167 (13349) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.62007 ( 10) hydrogen bonds : bond 0.03812 ( 404) hydrogen bonds : angle 5.76744 ( 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 201 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7533 (ptmt) REVERT: A 275 SER cc_start: 0.8291 (m) cc_final: 0.8033 (p) REVERT: A 280 ARG cc_start: 0.7694 (tpt90) cc_final: 0.7331 (ttt-90) REVERT: A 356 ARG cc_start: 0.6955 (tpp-160) cc_final: 0.6601 (ttp80) REVERT: A 392 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6949 (mt-10) REVERT: B 134 ARG cc_start: 0.7401 (ptp-170) cc_final: 0.7175 (ptm160) REVERT: B 217 MET cc_start: 0.6806 (ppp) cc_final: 0.6392 (ppp) REVERT: B 230 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.6857 (m110) REVERT: B 284 LEU cc_start: 0.7454 (tt) cc_final: 0.7141 (tt) REVERT: N 38 ARG cc_start: 0.8177 (ptt-90) cc_final: 0.7663 (ptt90) REVERT: N 65 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7707 (tptm) REVERT: N 80 TYR cc_start: 0.7883 (m-80) cc_final: 0.7200 (m-80) REVERT: R 618 MET cc_start: 0.4968 (mtm) cc_final: 0.4242 (pmm) REVERT: R 672 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7194 (mp) REVERT: R 717 LYS cc_start: 0.7281 (tmtt) cc_final: 0.7047 (tmtt) REVERT: S 156 SER cc_start: 0.7504 (m) cc_final: 0.7017 (p) REVERT: S 192 MET cc_start: 0.3057 (mpp) cc_final: 0.2158 (mtp) outliers start: 26 outliers final: 22 residues processed: 190 average time/residue: 0.0924 time to fit residues: 25.0725 Evaluate side-chains 196 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 672 LEU Chi-restraints excluded: chain R residue 682 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 chunk 59 optimal weight: 0.0050 chunk 119 optimal weight: 0.0020 chunk 44 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 overall best weight: 0.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN S 82 GLN ** 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 = 0.4320 r_free = 0.4320 target = 0.211513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.184370 restraints weight = 10140.996| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.74 r_work: 0.3887 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9873 Z= 0.121 Angle : 0.585 10.498 13359 Z= 0.304 Chirality : 0.043 0.218 1494 Planarity : 0.004 0.057 1685 Dihedral : 5.058 40.983 1335 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.20 % Allowed : 17.91 % Favored : 79.89 % 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: -0.69 (0.25), residues: 1190 helix: 0.67 (0.28), residues: 353 sheet: -1.13 (0.30), residues: 294 loop : -0.71 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 180 TYR 0.014 0.001 TYR A 391 PHE 0.026 0.002 PHE R 769 TRP 0.021 0.002 TRP A 281 HIS 0.007 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9868) covalent geometry : angle 0.58501 (13349) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.57627 ( 10) hydrogen bonds : bond 0.03566 ( 404) hydrogen bonds : angle 5.65443 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.61 seconds wall clock time: 48 minutes 24.72 seconds (2904.72 seconds total)