Starting phenix.real_space_refine on Wed Jun 11 08:18:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wui_32836/06_2025/7wui_32836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wui_32836/06_2025/7wui_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_32836/06_2025/7wui_32836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wui_32836/06_2025/7wui_32836.map" model { file = "/net/cci-nas-00/data/ceres_data/7wui_32836/06_2025/7wui_32836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wui_32836/06_2025/7wui_32836.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.63, per 1000 atoms: 0.58 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.13 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: 3.15 Time building geometry restraints manager: 2.77 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.490 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- 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 : 25.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.043 0.004 TRP A 281 HIS 0.023 0.004 HIS B 266 PHE 0.040 0.004 PHE B 241 TYR 0.026 0.003 TYR A 358 ARG 0.017 0.001 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.16802 ( 404) hydrogen bonds : angle 9.24425 ( 1131) SS BOND : bond 0.66642 ( 5) SS BOND : angle 11.54814 ( 10) covalent geometry : bond 0.00674 ( 9868) covalent geometry : angle 1.11457 (13349) *********************** 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 : 1.231 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: 0.6934 (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: 0.2176 time to fit residues: 64.2941 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 : 1.096 ------------------------------------------------------------------------------- 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 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** 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 R 860 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 = 0.4215 r_free = 0.4215 target = 0.199997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.172354 restraints weight = 10164.063| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.66 r_work: 0.3873 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9873 Z= 0.207 Angle : 0.678 8.656 13359 Z= 0.360 Chirality : 0.046 0.213 1494 Planarity : 0.005 0.051 1685 Dihedral : 5.970 40.415 1339 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.20 % Allowed : 8.81 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.24), residues: 1190 helix: -0.56 (0.27), residues: 348 sheet: -1.70 (0.30), residues: 282 loop : -1.18 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.007 0.002 HIS A 41 PHE 0.017 0.002 PHE A 212 TYR 0.017 0.002 TYR B 264 ARG 0.006 0.001 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 404) hydrogen bonds : angle 6.78471 ( 1131) SS BOND : bond 0.00688 ( 5) SS BOND : angle 1.17757 ( 10) covalent geometry : bond 0.00460 ( 9868) covalent geometry : angle 0.67729 (13349) *********************** 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 236 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7958 (ptpt) cc_final: 0.7584 (ptmt) REVERT: B 31 SER cc_start: 0.8241 (m) cc_final: 0.7920 (m) REVERT: B 122 SER cc_start: 0.8012 (p) cc_final: 0.6876 (p) REVERT: B 134 ARG cc_start: 0.6688 (ptp-170) cc_final: 0.6359 (ptm160) REVERT: B 297 TRP cc_start: 0.8586 (m100) cc_final: 0.8202 (m100) REVERT: R 621 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6900 (m) REVERT: R 652 TYR cc_start: 0.8001 (m-10) cc_final: 0.7602 (m-10) REVERT: R 731 CYS cc_start: 0.7038 (t) cc_final: 0.6718 (t) REVERT: R 832 PHE cc_start: 0.6879 (m-80) cc_final: 0.6639 (m-10) REVERT: R 853 MET cc_start: 0.7174 (mmt) cc_final: 0.6620 (mmp) REVERT: S 43 LYS cc_start: 0.7112 (ttmt) cc_final: 0.6565 (tptt) REVERT: S 156 SER cc_start: 0.7127 (m) cc_final: 0.6722 (p) outliers start: 23 outliers final: 16 residues processed: 226 average time/residue: 0.2168 time to fit residues: 68.9170 Evaluate side-chains 196 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER 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 772 ILE Chi-restraints excluded: chain R residue 783 VAL 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 59 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 105 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 752 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 = 0.4205 r_free = 0.4205 target = 0.199772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170527 restraints weight = 10065.312| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.78 r_work: 0.3737 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3241 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= 0.182 Angle : 0.624 11.142 13359 Z= 0.331 Chirality : 0.044 0.203 1494 Planarity : 0.005 0.062 1685 Dihedral : 5.566 40.096 1335 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.78 % Allowed : 12.93 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1190 helix: -0.18 (0.27), residues: 345 sheet: -1.58 (0.30), residues: 278 loop : -1.08 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.014 0.002 HIS B 183 PHE 0.029 0.002 PHE R 778 TYR 0.012 0.002 TYR A 391 ARG 0.006 0.001 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 404) hydrogen bonds : angle 6.35505 ( 1131) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.87194 ( 10) covalent geometry : bond 0.00409 ( 9868) covalent geometry : angle 0.62340 (13349) *********************** 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 241 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8003 (ptpt) cc_final: 0.7621 (ptmt) REVERT: A 275 SER cc_start: 0.8334 (m) cc_final: 0.7960 (p) REVERT: A 280 ARG cc_start: 0.7684 (tpt170) cc_final: 0.7429 (ttt-90) REVERT: A 356 ARG cc_start: 0.7086 (tpp-160) cc_final: 0.6459 (ttp80) REVERT: A 389 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7694 (mtm-85) REVERT: B 78 LYS cc_start: 0.8083 (tppt) cc_final: 0.7873 (tptt) REVERT: B 130 GLU cc_start: 0.6524 (mp0) cc_final: 0.6220 (mp0) REVERT: B 134 ARG cc_start: 0.7091 (ptp-170) cc_final: 0.6772 (ptm160) REVERT: B 217 MET cc_start: 0.7168 (ppp) cc_final: 0.6799 (ppp) REVERT: B 297 TRP cc_start: 0.8681 (m100) cc_final: 0.8272 (m100) REVERT: N 74 ASN cc_start: 0.6887 (m-40) cc_final: 0.6635 (m-40) REVERT: R 731 CYS cc_start: 0.7399 (t) cc_final: 0.7157 (t) REVERT: S 156 SER cc_start: 0.7209 (m) cc_final: 0.6789 (p) REVERT: S 192 MET cc_start: 0.3430 (mpp) cc_final: 0.0994 (ptp) outliers start: 29 outliers final: 18 residues processed: 224 average time/residue: 0.2115 time to fit residues: 66.7691 Evaluate side-chains 210 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 319 THR 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 277 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 125 ASN ** B 230 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.197658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169176 restraints weight = 9937.628| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.71 r_work: 0.3711 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9873 Z= 0.174 Angle : 0.603 8.808 13359 Z= 0.320 Chirality : 0.044 0.207 1494 Planarity : 0.005 0.054 1685 Dihedral : 5.420 40.559 1335 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.87 % Allowed : 14.66 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.24), residues: 1190 helix: -0.02 (0.27), residues: 346 sheet: -1.58 (0.30), residues: 287 loop : -0.96 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.007 0.002 HIS B 183 PHE 0.021 0.002 PHE A 376 TYR 0.016 0.002 TYR A 391 ARG 0.005 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 404) hydrogen bonds : angle 6.22380 ( 1131) SS BOND : bond 0.00270 ( 5) SS BOND : angle 0.80956 ( 10) covalent geometry : bond 0.00395 ( 9868) covalent geometry : angle 0.60303 (13349) *********************** 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 237 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7843 (tp30) REVERT: A 216 LYS cc_start: 0.7983 (ptpt) cc_final: 0.7614 (ptmt) REVERT: A 275 SER cc_start: 0.8352 (m) cc_final: 0.7969 (p) REVERT: A 356 ARG cc_start: 0.7195 (tpp-160) cc_final: 0.6566 (ttm110) REVERT: B 130 GLU cc_start: 0.6659 (mp0) cc_final: 0.6062 (mp0) REVERT: B 134 ARG cc_start: 0.7171 (ptp-170) cc_final: 0.6833 (ptm160) REVERT: B 217 MET cc_start: 0.7002 (ppp) cc_final: 0.6599 (ptm) REVERT: B 284 LEU cc_start: 0.7539 (tt) cc_final: 0.7182 (tt) REVERT: B 297 TRP cc_start: 0.8624 (m100) cc_final: 0.8225 (m100) REVERT: S 156 SER cc_start: 0.7276 (m) cc_final: 0.6824 (p) REVERT: S 192 MET cc_start: 0.3407 (mpp) cc_final: 0.1268 (ptp) REVERT: S 231 GLN cc_start: 0.8234 (pm20) cc_final: 0.7613 (pm20) outliers start: 30 outliers final: 20 residues processed: 219 average time/residue: 0.2237 time to fit residues: 68.6828 Evaluate side-chains 225 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 28 ILE 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 635 LEU Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 718 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 197 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 0.0770 chunk 16 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.4540 ------------------------------------------------------------------------------- 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 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 125 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4226 r_free = 0.4226 target = 0.201795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.173710 restraints weight = 9969.752| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.72 r_work: 0.3767 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3637 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= 0.141 Angle : 0.572 9.894 13359 Z= 0.305 Chirality : 0.043 0.180 1494 Planarity : 0.004 0.043 1685 Dihedral : 5.219 40.446 1335 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.59 % Allowed : 15.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1190 helix: 0.20 (0.27), residues: 346 sheet: -1.44 (0.30), residues: 285 loop : -0.93 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.008 0.002 HIS A 362 PHE 0.020 0.002 PHE R 778 TYR 0.014 0.002 TYR A 391 ARG 0.007 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 404) hydrogen bonds : angle 6.02099 ( 1131) SS BOND : bond 0.00107 ( 5) SS BOND : angle 0.73442 ( 10) covalent geometry : bond 0.00321 ( 9868) covalent geometry : angle 0.57221 (13349) *********************** 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 232 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 1.145 Fit side-chains REVERT: A 209 GLU cc_start: 0.6280 (mp0) cc_final: 0.6028 (mp0) REVERT: A 216 LYS cc_start: 0.7915 (ptpt) cc_final: 0.7550 (ptmt) REVERT: A 280 ARG cc_start: 0.7638 (tpt170) cc_final: 0.7303 (ttt-90) REVERT: A 356 ARG cc_start: 0.7229 (tpp-160) cc_final: 0.6699 (ttm110) REVERT: A 392 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6884 (mt-10) REVERT: B 130 GLU cc_start: 0.6545 (mp0) cc_final: 0.6244 (mp0) REVERT: B 134 ARG cc_start: 0.7133 (ptp-170) cc_final: 0.6784 (ptm160) REVERT: B 217 MET cc_start: 0.7045 (ppp) cc_final: 0.6388 (pmm) REVERT: B 230 ASN cc_start: 0.7738 (m110) cc_final: 0.7367 (m110) REVERT: B 284 LEU cc_start: 0.7519 (tt) cc_final: 0.7146 (tt) REVERT: B 297 TRP cc_start: 0.8454 (m100) cc_final: 0.8181 (m100) REVERT: N 38 ARG cc_start: 0.8207 (ptt-90) cc_final: 0.7945 (ptt90) REVERT: N 65 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7715 (tptm) REVERT: N 95 TYR cc_start: 0.8282 (m-80) cc_final: 0.7446 (m-80) REVERT: R 832 PHE cc_start: 0.7290 (m-80) cc_final: 0.6640 (m-80) REVERT: S 156 SER cc_start: 0.7338 (m) cc_final: 0.6892 (p) REVERT: S 192 MET cc_start: 0.3457 (mpp) cc_final: 0.2387 (mtp) outliers start: 27 outliers final: 19 residues processed: 217 average time/residue: 0.2174 time to fit residues: 67.5554 Evaluate side-chains 212 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 175 GLN 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 635 LEU Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 97 VAL 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 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 0.0170 chunk 116 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.198732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.170810 restraints weight = 10038.820| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.70 r_work: 0.3734 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9873 Z= 0.158 Angle : 0.598 8.089 13359 Z= 0.318 Chirality : 0.044 0.243 1494 Planarity : 0.004 0.044 1685 Dihedral : 5.195 40.890 1335 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.78 % Allowed : 16.28 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1190 helix: 0.30 (0.27), residues: 346 sheet: -1.44 (0.29), residues: 295 loop : -0.88 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 281 HIS 0.007 0.002 HIS A 362 PHE 0.018 0.002 PHE A 212 TYR 0.018 0.002 TYR A 391 ARG 0.005 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 404) hydrogen bonds : angle 6.03737 ( 1131) SS BOND : bond 0.00317 ( 5) SS BOND : angle 1.69398 ( 10) covalent geometry : bond 0.00360 ( 9868) covalent geometry : angle 0.59602 (13349) *********************** 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 224 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.017 Fit side-chains REVERT: A 216 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7630 (ptmt) REVERT: A 275 SER cc_start: 0.8372 (m) cc_final: 0.8091 (p) REVERT: A 280 ARG cc_start: 0.7590 (tpt170) cc_final: 0.7357 (ttt-90) REVERT: A 356 ARG cc_start: 0.7282 (tpp-160) cc_final: 0.6752 (ttm110) REVERT: A 392 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6944 (mt-10) REVERT: B 130 GLU cc_start: 0.6395 (mp0) cc_final: 0.6139 (mp0) REVERT: B 134 ARG cc_start: 0.7162 (ptp-170) cc_final: 0.6832 (ptm160) REVERT: B 217 MET cc_start: 0.7068 (ppp) cc_final: 0.6426 (pmm) REVERT: B 230 ASN cc_start: 0.7734 (m110) cc_final: 0.7396 (m110) REVERT: B 284 LEU cc_start: 0.7576 (tt) cc_final: 0.7219 (tt) REVERT: B 297 TRP cc_start: 0.8504 (m100) cc_final: 0.8225 (m100) REVERT: B 325 MET cc_start: 0.8074 (tpp) cc_final: 0.7718 (mmm) REVERT: N 38 ARG cc_start: 0.8139 (ptt-90) cc_final: 0.7874 (ptt90) REVERT: N 65 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7699 (tptm) REVERT: N 95 TYR cc_start: 0.8378 (m-80) cc_final: 0.7522 (m-80) REVERT: R 733 VAL cc_start: 0.8892 (t) cc_final: 0.8688 (t) REVERT: R 832 PHE cc_start: 0.7424 (m-80) cc_final: 0.6808 (m-10) REVERT: S 156 SER cc_start: 0.7475 (m) cc_final: 0.6988 (p) REVERT: S 192 MET cc_start: 0.3491 (mpp) cc_final: 0.2450 (mtp) outliers start: 29 outliers final: 21 residues processed: 208 average time/residue: 0.2105 time to fit residues: 62.2997 Evaluate side-chains 211 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 175 GLN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** 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 125 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.197766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.169826 restraints weight = 10124.986| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.70 r_work: 0.3813 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3976 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= 0.161 Angle : 0.597 8.761 13359 Z= 0.319 Chirality : 0.044 0.221 1494 Planarity : 0.004 0.045 1685 Dihedral : 5.212 41.571 1335 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.87 % Allowed : 17.53 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1190 helix: 0.35 (0.27), residues: 347 sheet: -1.37 (0.30), residues: 287 loop : -0.86 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 281 HIS 0.007 0.002 HIS A 220 PHE 0.017 0.002 PHE A 212 TYR 0.015 0.002 TYR A 391 ARG 0.007 0.000 ARG S 180 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 404) hydrogen bonds : angle 6.02720 ( 1131) SS BOND : bond 0.00171 ( 5) SS BOND : angle 1.35703 ( 10) covalent geometry : bond 0.00368 ( 9868) covalent geometry : angle 0.59635 (13349) *********************** 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 224 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 1.113 Fit side-chains REVERT: A 275 SER cc_start: 0.8384 (m) cc_final: 0.8094 (p) REVERT: A 280 ARG cc_start: 0.7582 (tpt170) cc_final: 0.7341 (ttt-90) REVERT: A 356 ARG cc_start: 0.7161 (tpp-160) cc_final: 0.6660 (ttm110) REVERT: A 392 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6898 (mt-10) REVERT: B 130 GLU cc_start: 0.6369 (mp0) cc_final: 0.6142 (mp0) REVERT: B 134 ARG cc_start: 0.7268 (ptp-170) cc_final: 0.6957 (ptm160) REVERT: B 217 MET cc_start: 0.7114 (ppp) cc_final: 0.6478 (pmm) REVERT: B 230 ASN cc_start: 0.7715 (m110) cc_final: 0.7394 (m110) REVERT: B 264 TYR cc_start: 0.7998 (m-80) cc_final: 0.7786 (m-80) REVERT: B 284 LEU cc_start: 0.7548 (tt) cc_final: 0.7208 (tt) REVERT: B 297 TRP cc_start: 0.8528 (m100) cc_final: 0.8218 (m100) REVERT: N 38 ARG cc_start: 0.8186 (ptt-90) cc_final: 0.7908 (ptt90) REVERT: N 65 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7730 (tptm) REVERT: N 95 TYR cc_start: 0.8411 (m-80) cc_final: 0.7555 (m-80) REVERT: R 635 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6551 (tt) REVERT: S 100 ILE cc_start: 0.8257 (tt) cc_final: 0.7802 (tt) REVERT: S 156 SER cc_start: 0.7510 (m) cc_final: 0.6996 (p) REVERT: S 192 MET cc_start: 0.3603 (mpp) cc_final: 0.2647 (mtp) REVERT: S 214 LEU cc_start: 0.6261 (tp) cc_final: 0.5355 (tp) outliers start: 30 outliers final: 21 residues processed: 209 average time/residue: 0.2002 time to fit residues: 60.0805 Evaluate side-chains 208 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR 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 635 LEU 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 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 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 220 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 16 ASN B 125 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.191159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162130 restraints weight = 10182.289| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.74 r_work: 0.3645 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9873 Z= 0.197 Angle : 0.625 8.531 13359 Z= 0.333 Chirality : 0.045 0.212 1494 Planarity : 0.005 0.053 1685 Dihedral : 5.379 42.779 1335 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.59 % Allowed : 18.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1190 helix: 0.26 (0.27), residues: 347 sheet: -1.41 (0.31), residues: 269 loop : -0.80 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 281 HIS 0.006 0.002 HIS A 41 PHE 0.018 0.002 PHE A 212 TYR 0.024 0.002 TYR A 358 ARG 0.005 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 404) hydrogen bonds : angle 6.14360 ( 1131) SS BOND : bond 0.00324 ( 5) SS BOND : angle 1.21954 ( 10) covalent geometry : bond 0.00452 ( 9868) covalent geometry : angle 0.62484 (13349) *********************** 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 236 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 1.053 Fit side-chains REVERT: A 209 GLU cc_start: 0.6531 (mp0) cc_final: 0.6316 (mp0) REVERT: A 275 SER cc_start: 0.8536 (m) cc_final: 0.8246 (p) REVERT: A 280 ARG cc_start: 0.7680 (tpt170) cc_final: 0.7439 (ttt-90) REVERT: A 356 ARG cc_start: 0.7358 (tpp-160) cc_final: 0.7143 (tpp80) REVERT: A 392 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7019 (mt-10) REVERT: B 134 ARG cc_start: 0.7176 (ptp-170) cc_final: 0.6953 (ptm160) REVERT: B 217 MET cc_start: 0.7169 (ppp) cc_final: 0.6547 (pmm) REVERT: B 230 ASN cc_start: 0.7718 (m110) cc_final: 0.7421 (m110) REVERT: B 284 LEU cc_start: 0.7625 (tt) cc_final: 0.7330 (tt) REVERT: B 297 TRP cc_start: 0.8715 (m100) cc_final: 0.8480 (m100) REVERT: N 38 ARG cc_start: 0.8209 (ptt-90) cc_final: 0.7921 (ptt90) REVERT: S 156 SER cc_start: 0.7503 (m) cc_final: 0.6921 (p) REVERT: S 192 MET cc_start: 0.3673 (mpp) cc_final: 0.2806 (mtp) REVERT: S 214 LEU cc_start: 0.6290 (tp) cc_final: 0.5391 (tp) outliers start: 27 outliers final: 20 residues processed: 221 average time/residue: 0.2212 time to fit residues: 68.3383 Evaluate side-chains 220 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR 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 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 776 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 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 29 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.191140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162712 restraints weight = 10039.579| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.71 r_work: 0.3676 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9873 Z= 0.201 Angle : 0.647 9.143 13359 Z= 0.341 Chirality : 0.046 0.238 1494 Planarity : 0.005 0.051 1685 Dihedral : 5.455 41.946 1335 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.49 % Allowed : 18.97 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1190 helix: 0.05 (0.27), residues: 353 sheet: -1.54 (0.30), residues: 287 loop : -0.76 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 281 HIS 0.006 0.002 HIS A 41 PHE 0.019 0.002 PHE A 212 TYR 0.015 0.002 TYR S 94 ARG 0.008 0.001 ARG S 180 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 404) hydrogen bonds : angle 6.26221 ( 1131) SS BOND : bond 0.00192 ( 5) SS BOND : angle 1.07449 ( 10) covalent geometry : bond 0.00465 ( 9868) covalent geometry : angle 0.64636 (13349) *********************** 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 233 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 1.193 Fit side-chains REVERT: A 209 GLU cc_start: 0.6605 (mp0) cc_final: 0.6308 (mp0) REVERT: A 275 SER cc_start: 0.8321 (m) cc_final: 0.8092 (p) REVERT: A 280 ARG cc_start: 0.7694 (tpt170) cc_final: 0.7470 (ttt-90) REVERT: A 386 MET cc_start: 0.7755 (ptp) cc_final: 0.7534 (ptt) REVERT: A 392 GLU cc_start: 0.7611 (mm-30) cc_final: 0.6996 (mt-10) REVERT: B 183 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7568 (m170) REVERT: B 217 MET cc_start: 0.7187 (ppp) cc_final: 0.6586 (pmm) REVERT: B 230 ASN cc_start: 0.7694 (m110) cc_final: 0.7402 (m110) REVERT: B 284 LEU cc_start: 0.7511 (tt) cc_final: 0.7276 (tt) REVERT: B 290 ASP cc_start: 0.6987 (m-30) cc_final: 0.6632 (m-30) REVERT: B 297 TRP cc_start: 0.8745 (m100) cc_final: 0.8502 (m100) REVERT: B 325 MET cc_start: 0.8229 (tpp) cc_final: 0.7835 (mmm) REVERT: N 38 ARG cc_start: 0.8216 (ptt-90) cc_final: 0.7930 (ptt90) REVERT: R 672 LEU cc_start: 0.7888 (mm) cc_final: 0.7592 (mp) REVERT: R 793 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.6994 (m-40) REVERT: S 100 ILE cc_start: 0.8292 (tt) cc_final: 0.7839 (tt) REVERT: S 156 SER cc_start: 0.7541 (m) cc_final: 0.6966 (p) REVERT: S 192 MET cc_start: 0.3698 (mpp) cc_final: 0.2891 (mtp) REVERT: S 214 LEU cc_start: 0.6351 (tp) cc_final: 0.5454 (tp) outliers start: 26 outliers final: 20 residues processed: 223 average time/residue: 0.2678 time to fit residues: 85.1441 Evaluate side-chains 221 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 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 178 THR Chi-restraints excluded: chain B residue 183 HIS 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 N residue 35 ASN 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 776 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain R residue 793 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 48 optimal weight: 0.0980 chunk 119 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** ** 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 230 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4164 r_free = 0.4164 target = 0.194933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167264 restraints weight = 10098.019| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.71 r_work: 0.3738 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9873 Z= 0.160 Angle : 0.634 9.859 13359 Z= 0.332 Chirality : 0.045 0.240 1494 Planarity : 0.005 0.046 1685 Dihedral : 5.370 40.584 1335 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.49 % Allowed : 19.35 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1190 helix: 0.11 (0.27), residues: 358 sheet: -1.50 (0.30), residues: 287 loop : -0.77 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 281 HIS 0.009 0.002 HIS A 362 PHE 0.018 0.002 PHE A 212 TYR 0.019 0.002 TYR A 358 ARG 0.010 0.001 ARG S 180 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 404) hydrogen bonds : angle 6.20964 ( 1131) SS BOND : bond 0.00206 ( 5) SS BOND : angle 1.12883 ( 10) covalent geometry : bond 0.00372 ( 9868) covalent geometry : angle 0.63371 (13349) ********************** 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 226 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 1.024 Fit side-chains REVERT: A 392 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7002 (mt-10) REVERT: B 183 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7430 (m170) REVERT: B 217 MET cc_start: 0.7118 (ppp) cc_final: 0.6524 (pmm) REVERT: B 230 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7251 (m110) REVERT: B 290 ASP cc_start: 0.7022 (m-30) cc_final: 0.6719 (m-30) REVERT: B 297 TRP cc_start: 0.8622 (m100) cc_final: 0.8282 (m100) REVERT: B 325 MET cc_start: 0.8109 (tpp) cc_final: 0.7735 (mmm) REVERT: N 38 ARG cc_start: 0.8151 (ptt-90) cc_final: 0.7879 (ptt90) REVERT: N 95 TYR cc_start: 0.8525 (m-80) cc_final: 0.7673 (m-80) REVERT: R 618 MET cc_start: 0.5156 (mtm) cc_final: 0.4261 (pmm) REVERT: R 733 VAL cc_start: 0.9004 (t) cc_final: 0.8795 (t) REVERT: R 793 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7115 (m-40) REVERT: S 100 ILE cc_start: 0.8244 (tt) cc_final: 0.7805 (tt) REVERT: S 156 SER cc_start: 0.7543 (m) cc_final: 0.6947 (p) REVERT: S 192 MET cc_start: 0.3655 (mpp) cc_final: 0.2845 (mtp) REVERT: S 214 LEU cc_start: 0.6278 (tp) cc_final: 0.5346 (tp) outliers start: 26 outliers final: 19 residues processed: 212 average time/residue: 0.2214 time to fit residues: 67.5655 Evaluate side-chains 217 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 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 125 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS 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 315 VAL 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 R residue 793 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 111 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 67 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 125 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.197239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.169709 restraints weight = 10111.264| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.71 r_work: 0.3728 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9873 Z= 0.153 Angle : 0.630 9.760 13359 Z= 0.330 Chirality : 0.045 0.235 1494 Planarity : 0.004 0.046 1685 Dihedral : 5.327 40.664 1335 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.39 % Allowed : 19.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1190 helix: 0.17 (0.27), residues: 358 sheet: -1.47 (0.30), residues: 282 loop : -0.78 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 281 HIS 0.011 0.002 HIS A 362 PHE 0.022 0.002 PHE R 832 TYR 0.029 0.002 TYR A 360 ARG 0.012 0.001 ARG S 180 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 404) hydrogen bonds : angle 6.14700 ( 1131) SS BOND : bond 0.00219 ( 5) SS BOND : angle 1.00949 ( 10) covalent geometry : bond 0.00353 ( 9868) covalent geometry : angle 0.62998 (13349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6474.99 seconds wall clock time: 113 minutes 14.92 seconds (6794.92 seconds total)