Starting phenix.real_space_refine on Thu Sep 26 08:31:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/09_2024/7wui_32836.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/09_2024/7wui_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/09_2024/7wui_32836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/09_2024/7wui_32836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/09_2024/7wui_32836.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/09_2024/7wui_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-5461/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: 6.11, per 1000 atoms: 0.63 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: 2.67 Conformation dependent library (CDL) restraints added in 1.2 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: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.943A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.771A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.103A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.002A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.514A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.132A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.863A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.872A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 21 removed outlier: 4.335A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 34 through 43 removed outlier: 3.818A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.508A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 617 through 644 removed outlier: 3.738A pdb=" N ILE R 623 " --> pdb=" O ALA R 619 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR R 624 " --> pdb=" O LEU R 620 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL R 637 " --> pdb=" O ILE R 633 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR R 638 " --> pdb=" O PHE R 634 " (cutoff:3.500A) Processing helix chain 'R' and resid 645 through 650 removed outlier: 3.697A pdb=" N ILE R 648 " --> pdb=" O PHE R 645 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG R 650 " --> pdb=" O LYS R 647 " (cutoff:3.500A) Processing helix chain 'R' and resid 651 through 680 removed outlier: 3.836A pdb=" N ILE R 670 " --> pdb=" O LEU R 666 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA R 678 " --> pdb=" O ASP R 674 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU R 679 " --> pdb=" O SER R 675 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR R 680 " --> pdb=" O TRP R 676 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 716 removed outlier: 3.781A pdb=" N ALA R 688 " --> pdb=" O GLY R 684 " (cutoff:3.500A) Processing helix chain 'R' and resid 725 through 735 removed outlier: 3.887A pdb=" N VAL R 733 " --> pdb=" O LYS R 729 " (cutoff:3.500A) Processing helix chain 'R' and resid 735 through 747 Processing helix chain 'R' and resid 749 through 751 No H-bonds generated for 'chain 'R' and resid 749 through 751' Processing helix chain 'R' and resid 774 through 782 Processing helix chain 'R' and resid 782 through 792 Processing helix chain 'R' and resid 793 through 810 removed outlier: 3.783A pdb=" N ILE R 798 " --> pdb=" O VAL R 794 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL R 799 " --> pdb=" O SER R 795 " (cutoff:3.500A) Processing helix chain 'R' and resid 824 through 834 removed outlier: 4.305A pdb=" N PHE R 832 " --> pdb=" O ALA R 828 " (cutoff:3.500A) Processing helix chain 'R' and resid 836 through 842 removed outlier: 4.123A pdb=" N ALA R 841 " --> pdb=" O TRP R 838 " (cutoff:3.500A) Processing helix chain 'R' and resid 850 through 862 removed outlier: 3.637A pdb=" N TYR R 854 " --> pdb=" O VAL R 850 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU R 862 " --> pdb=" O ILE R 858 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 883 removed outlier: 3.512A pdb=" N ARG R 879 " --> pdb=" O LYS R 875 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.609A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.504A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'L' and resid 600 through 604 removed outlier: 3.622A pdb=" N ILE L 603 " --> pdb=" O SER L 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.824A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.172A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.705A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.678A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.001A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.902A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.590A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.606A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.615A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 4.087A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 18 through 19 Processing sheet with id=AB3, first strand: chain 'R' and resid 753 through 754 removed outlier: 3.691A pdb=" N GLY R 754 " --> pdb=" O TRP R 771 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP R 771 " --> pdb=" O GLY R 754 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.499A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.499A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 68 through 73 Processing sheet with id=AB8, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB9, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.953A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR S 190 " --> pdb=" O ASN S 194 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 3.05 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: 0.720 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.150 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: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- 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 : 0.007 0.143 9868 Z= 0.437 Angle : 1.115 12.420 13349 Z= 0.638 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 1.072 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: 0.2191 time to fit residues: 64.2367 Evaluate side-chains 167 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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: 0.7980 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: 6.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 267 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 31 ASN R 860 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9868 Z= 0.260 Angle : 0.655 8.297 13349 Z= 0.349 Chirality : 0.045 0.205 1494 Planarity : 0.005 0.048 1685 Dihedral : 5.876 38.752 1339 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.72 % Allowed : 9.20 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.78 (0.24), residues: 1190 helix: -0.53 (0.27), residues: 348 sheet: -1.63 (0.30), residues: 281 loop : -1.23 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.007 0.002 HIS B 266 PHE 0.016 0.002 PHE R 786 TYR 0.016 0.002 TYR B 264 ARG 0.006 0.001 ARG N 38 *********************** 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 218 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: B 31 SER cc_start: 0.8226 (m) cc_final: 0.7940 (m) REVERT: B 264 TYR cc_start: 0.7319 (m-10) cc_final: 0.7114 (m-80) REVERT: B 297 TRP cc_start: 0.8255 (m100) cc_final: 0.8038 (m100) REVERT: R 652 TYR cc_start: 0.7698 (m-10) cc_final: 0.7344 (m-10) REVERT: R 731 CYS cc_start: 0.5664 (t) cc_final: 0.5287 (t) REVERT: R 853 MET cc_start: 0.6750 (mmt) cc_final: 0.6328 (mmp) REVERT: S 214 LEU cc_start: 0.5790 (tp) cc_final: 0.5459 (tp) outliers start: 18 outliers final: 13 residues processed: 207 average time/residue: 0.2126 time to fit residues: 61.7504 Evaluate side-chains 186 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 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 384 GLN B 125 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9868 Z= 0.235 Angle : 0.602 10.720 13349 Z= 0.321 Chirality : 0.044 0.190 1494 Planarity : 0.005 0.057 1685 Dihedral : 5.439 36.172 1335 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.97 % Allowed : 11.59 % Favored : 85.44 % 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: -1.47 (0.24), residues: 1190 helix: -0.12 (0.27), residues: 346 sheet: -1.54 (0.30), residues: 273 loop : -1.11 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.007 0.002 HIS B 183 PHE 0.039 0.002 PHE R 778 TYR 0.016 0.002 TYR R 625 ARG 0.005 0.001 ARG N 38 *********************** 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 228 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 275 SER cc_start: 0.7742 (m) cc_final: 0.7351 (p) REVERT: B 78 LYS cc_start: 0.7690 (tppt) cc_final: 0.7335 (tptt) REVERT: B 130 GLU cc_start: 0.6153 (mp0) cc_final: 0.5877 (mp0) REVERT: B 134 ARG cc_start: 0.6455 (ptp-170) cc_final: 0.6059 (ptm160) REVERT: B 217 MET cc_start: 0.6362 (ppp) cc_final: 0.5799 (ppp) REVERT: B 297 TRP cc_start: 0.8362 (m100) cc_final: 0.8063 (m100) REVERT: N 80 TYR cc_start: 0.6951 (m-80) cc_final: 0.6367 (m-80) REVERT: R 731 CYS cc_start: 0.5907 (t) cc_final: 0.5643 (t) REVERT: R 853 MET cc_start: 0.6468 (mmt) cc_final: 0.6026 (mmp) REVERT: S 156 SER cc_start: 0.7153 (m) cc_final: 0.6805 (p) REVERT: S 192 MET cc_start: 0.3487 (mpp) cc_final: 0.2988 (mpp) outliers start: 31 outliers final: 22 residues processed: 211 average time/residue: 0.2047 time to fit residues: 61.1558 Evaluate side-chains 208 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain B residue 122 SER 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 G residue 28 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 780 ILE Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 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 107 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 115 optimal weight: 9.9990 chunk 57 optimal weight: 0.0570 chunk 103 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9868 Z= 0.195 Angle : 0.575 11.049 13349 Z= 0.303 Chirality : 0.043 0.206 1494 Planarity : 0.004 0.048 1685 Dihedral : 5.200 38.849 1335 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.87 % Allowed : 13.98 % Favored : 83.14 % 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: -1.25 (0.24), residues: 1190 helix: 0.18 (0.27), residues: 346 sheet: -1.48 (0.30), residues: 282 loop : -1.01 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.011 0.002 HIS B 183 PHE 0.023 0.002 PHE R 778 TYR 0.011 0.002 TYR A 391 ARG 0.006 0.000 ARG N 38 *********************** 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 221 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 386 MET cc_start: 0.6945 (ptt) cc_final: 0.6698 (ptp) REVERT: A 392 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6563 (mt-10) REVERT: B 122 SER cc_start: 0.7861 (p) cc_final: 0.7651 (t) REVERT: B 130 GLU cc_start: 0.6120 (mp0) cc_final: 0.5568 (mp0) REVERT: B 134 ARG cc_start: 0.6580 (ptp-170) cc_final: 0.6156 (ptm160) REVERT: B 217 MET cc_start: 0.6191 (ppp) cc_final: 0.5595 (ppp) REVERT: B 297 TRP cc_start: 0.8259 (m100) cc_final: 0.7958 (m100) REVERT: N 80 TYR cc_start: 0.7072 (m-80) cc_final: 0.6504 (m-80) REVERT: S 156 SER cc_start: 0.7164 (m) cc_final: 0.6837 (p) REVERT: S 178 LEU cc_start: 0.7757 (tp) cc_final: 0.7533 (tt) REVERT: S 192 MET cc_start: 0.3572 (mpp) cc_final: 0.2464 (mtp) outliers start: 30 outliers final: 17 residues processed: 205 average time/residue: 0.2168 time to fit residues: 62.2758 Evaluate side-chains 196 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.0570 chunk 65 optimal weight: 0.0470 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 230 ASN N 31 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9868 Z= 0.219 Angle : 0.575 8.116 13349 Z= 0.305 Chirality : 0.043 0.204 1494 Planarity : 0.004 0.043 1685 Dihedral : 5.146 40.735 1335 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.78 % Allowed : 15.23 % Favored : 81.99 % 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: -1.06 (0.25), residues: 1190 helix: 0.38 (0.28), residues: 345 sheet: -1.42 (0.29), residues: 294 loop : -0.86 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.008 0.002 HIS A 362 PHE 0.018 0.002 PHE R 778 TYR 0.011 0.002 TYR A 391 ARG 0.006 0.000 ARG N 38 *********************** 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 216 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 1.159 Fit side-chains REVERT: A 275 SER cc_start: 0.7828 (m) cc_final: 0.7415 (p) REVERT: A 392 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6626 (mt-10) REVERT: B 122 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7576 (t) REVERT: B 134 ARG cc_start: 0.6750 (ptp-170) cc_final: 0.6442 (ptm160) REVERT: B 217 MET cc_start: 0.6194 (ppp) cc_final: 0.5716 (ppp) REVERT: B 230 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.7198 (m-40) REVERT: B 297 TRP cc_start: 0.8262 (m100) cc_final: 0.8047 (m100) REVERT: N 38 ARG cc_start: 0.7772 (ptt-90) cc_final: 0.7553 (ptt90) REVERT: N 65 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7683 (tptm) REVERT: N 80 TYR cc_start: 0.7135 (m-80) cc_final: 0.6594 (m-80) REVERT: N 95 TYR cc_start: 0.7852 (m-80) cc_final: 0.7291 (m-80) REVERT: S 156 SER cc_start: 0.7114 (m) cc_final: 0.6764 (p) REVERT: S 178 LEU cc_start: 0.7873 (tp) cc_final: 0.7666 (tt) REVERT: S 192 MET cc_start: 0.3358 (mpp) cc_final: 0.2585 (mtp) REVERT: S 214 LEU cc_start: 0.6002 (tp) cc_final: 0.5056 (tp) outliers start: 29 outliers final: 21 residues processed: 201 average time/residue: 0.2048 time to fit residues: 59.1585 Evaluate side-chains 199 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 339 TRP 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 654 SER 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 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 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** A 384 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9868 Z= 0.247 Angle : 0.594 9.227 13349 Z= 0.313 Chirality : 0.044 0.206 1494 Planarity : 0.004 0.050 1685 Dihedral : 5.181 41.346 1335 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.68 % Allowed : 16.09 % Favored : 81.23 % 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: -1.08 (0.25), residues: 1190 helix: 0.36 (0.28), residues: 345 sheet: -1.46 (0.29), residues: 291 loop : -0.86 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 281 HIS 0.007 0.002 HIS A 362 PHE 0.016 0.002 PHE A 212 TYR 0.014 0.002 TYR A 391 ARG 0.004 0.000 ARG N 38 *********************** 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 222 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 275 SER cc_start: 0.7740 (m) cc_final: 0.7384 (p) REVERT: A 392 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6650 (mt-10) REVERT: B 78 LYS cc_start: 0.7875 (tppt) cc_final: 0.7519 (tptt) REVERT: B 134 ARG cc_start: 0.6834 (ptp-170) cc_final: 0.6597 (ptm160) REVERT: B 217 MET cc_start: 0.6275 (ppp) cc_final: 0.5771 (ppp) REVERT: B 230 ASN cc_start: 0.7648 (m110) cc_final: 0.7241 (m110) REVERT: B 297 TRP cc_start: 0.8332 (m100) cc_final: 0.8089 (m100) REVERT: N 38 ARG cc_start: 0.7823 (ptt-90) cc_final: 0.7587 (ptt90) REVERT: S 156 SER cc_start: 0.7234 (m) cc_final: 0.6840 (p) REVERT: S 192 MET cc_start: 0.3397 (mpp) cc_final: 0.2624 (mtp) outliers start: 28 outliers final: 24 residues processed: 207 average time/residue: 0.1895 time to fit residues: 56.6518 Evaluate side-chains 208 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 250 SER 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 295 ASN 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 174 LEU Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.0040 chunk 97 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9868 Z= 0.219 Angle : 0.586 9.692 13349 Z= 0.309 Chirality : 0.043 0.199 1494 Planarity : 0.004 0.042 1685 Dihedral : 5.133 41.623 1335 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.07 % Allowed : 16.28 % Favored : 80.65 % 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: -0.99 (0.25), residues: 1190 helix: 0.42 (0.28), residues: 347 sheet: -1.45 (0.29), residues: 298 loop : -0.76 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 281 HIS 0.007 0.002 HIS A 362 PHE 0.016 0.002 PHE A 212 TYR 0.013 0.002 TYR A 391 ARG 0.004 0.000 ARG N 38 *********************** 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 222 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6699 (mt-10) REVERT: B 159 THR cc_start: 0.8006 (p) cc_final: 0.7733 (p) REVERT: B 230 ASN cc_start: 0.7395 (m-40) cc_final: 0.7182 (m-40) REVERT: B 284 LEU cc_start: 0.7262 (tt) cc_final: 0.6958 (tt) REVERT: B 297 TRP cc_start: 0.8339 (m100) cc_final: 0.8050 (m100) REVERT: N 38 ARG cc_start: 0.7775 (ptt-90) cc_final: 0.7372 (ptt90) REVERT: N 65 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7649 (tptm) REVERT: N 80 TYR cc_start: 0.7366 (m-80) cc_final: 0.6854 (m-80) REVERT: N 95 TYR cc_start: 0.7966 (m-80) cc_final: 0.7351 (m-80) REVERT: R 723 ILE cc_start: 0.7162 (mp) cc_final: 0.6869 (mm) REVERT: S 100 ILE cc_start: 0.8122 (tt) cc_final: 0.7642 (tt) REVERT: S 156 SER cc_start: 0.7296 (m) cc_final: 0.6931 (p) REVERT: S 192 MET cc_start: 0.3441 (mpp) cc_final: 0.2705 (mtp) outliers start: 32 outliers final: 27 residues processed: 206 average time/residue: 0.2165 time to fit residues: 64.3412 Evaluate side-chains 207 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 339 TRP 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 657 LEU Chi-restraints excluded: chain R residue 682 THR 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 174 LEU Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.0470 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.0000 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 105 optimal weight: 0.0870 overall best weight: 0.2860 ------------------------------------------------------------------------------- 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 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 16 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9868 Z= 0.185 Angle : 0.585 9.761 13349 Z= 0.305 Chirality : 0.043 0.177 1494 Planarity : 0.004 0.042 1685 Dihedral : 5.036 41.583 1335 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.39 % Allowed : 17.72 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.25), residues: 1190 helix: 0.56 (0.28), residues: 347 sheet: -1.43 (0.29), residues: 296 loop : -0.74 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 281 HIS 0.007 0.002 HIS A 362 PHE 0.037 0.002 PHE R 769 TYR 0.012 0.001 TYR A 391 ARG 0.005 0.000 ARG N 38 *********************** 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 212 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6635 (mt-10) REVERT: B 159 THR cc_start: 0.7833 (p) cc_final: 0.7531 (p) REVERT: B 217 MET cc_start: 0.6042 (ppp) cc_final: 0.5514 (pmm) REVERT: B 230 ASN cc_start: 0.7337 (m-40) cc_final: 0.7027 (m110) REVERT: B 284 LEU cc_start: 0.7235 (tt) cc_final: 0.7021 (tt) REVERT: B 297 TRP cc_start: 0.8232 (m100) cc_final: 0.8019 (m100) REVERT: N 38 ARG cc_start: 0.7707 (ptt-90) cc_final: 0.7364 (ptt90) REVERT: N 65 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7600 (tptm) REVERT: N 80 TYR cc_start: 0.7312 (m-80) cc_final: 0.6808 (m-80) REVERT: N 95 TYR cc_start: 0.7947 (m-80) cc_final: 0.7284 (m-80) REVERT: S 100 ILE cc_start: 0.8008 (tt) cc_final: 0.7533 (tt) REVERT: S 156 SER cc_start: 0.7277 (m) cc_final: 0.6868 (p) REVERT: S 192 MET cc_start: 0.3426 (mpp) cc_final: 0.2692 (mtp) outliers start: 25 outliers final: 19 residues processed: 200 average time/residue: 0.2138 time to fit residues: 60.9059 Evaluate side-chains 196 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 657 LEU 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 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 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9868 Z= 0.252 Angle : 0.631 10.012 13349 Z= 0.328 Chirality : 0.045 0.202 1494 Planarity : 0.004 0.048 1685 Dihedral : 5.201 43.336 1335 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.59 % Allowed : 18.10 % Favored : 79.31 % 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: -0.91 (0.25), residues: 1190 helix: 0.40 (0.28), residues: 350 sheet: -1.32 (0.29), residues: 297 loop : -0.71 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.007 0.002 HIS A 41 PHE 0.036 0.002 PHE R 769 TYR 0.015 0.002 TYR S 94 ARG 0.011 0.001 ARG S 180 *********************** 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 212 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6650 (mt-10) REVERT: B 159 THR cc_start: 0.7938 (p) cc_final: 0.7637 (p) REVERT: B 217 MET cc_start: 0.6146 (ppp) cc_final: 0.5542 (ppp) REVERT: B 230 ASN cc_start: 0.7352 (m-40) cc_final: 0.7036 (m110) REVERT: B 284 LEU cc_start: 0.7337 (tt) cc_final: 0.7108 (tt) REVERT: B 297 TRP cc_start: 0.8425 (m100) cc_final: 0.8177 (m100) REVERT: N 38 ARG cc_start: 0.7714 (ptt-90) cc_final: 0.7352 (ptt90) REVERT: N 65 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7664 (tptm) REVERT: N 80 TYR cc_start: 0.7400 (m-80) cc_final: 0.6918 (m-80) REVERT: N 106 ASP cc_start: 0.6743 (p0) cc_final: 0.6356 (p0) REVERT: S 100 ILE cc_start: 0.8138 (tt) cc_final: 0.7676 (tt) REVERT: S 156 SER cc_start: 0.7370 (m) cc_final: 0.6964 (p) REVERT: S 192 MET cc_start: 0.3432 (mpp) cc_final: 0.2370 (mtp) outliers start: 27 outliers final: 23 residues processed: 197 average time/residue: 0.2019 time to fit residues: 56.9245 Evaluate side-chains 205 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 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 B residue 339 TRP 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 682 THR Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 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 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9868 Z= 0.261 Angle : 0.641 10.739 13349 Z= 0.334 Chirality : 0.045 0.200 1494 Planarity : 0.004 0.046 1685 Dihedral : 5.305 43.744 1335 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.59 % Allowed : 17.91 % Favored : 79.50 % 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: -1.01 (0.25), residues: 1190 helix: 0.33 (0.27), residues: 350 sheet: -1.44 (0.29), residues: 295 loop : -0.74 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 281 HIS 0.006 0.002 HIS A 41 PHE 0.035 0.002 PHE R 769 TYR 0.017 0.002 TYR S 94 ARG 0.010 0.001 ARG S 180 ********************** 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 215 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6647 (mt-10) REVERT: B 217 MET cc_start: 0.6167 (ppp) cc_final: 0.5562 (ppp) REVERT: B 230 ASN cc_start: 0.7339 (m-40) cc_final: 0.7059 (m110) REVERT: B 284 LEU cc_start: 0.7336 (tt) cc_final: 0.7126 (tt) REVERT: N 38 ARG cc_start: 0.7793 (ptt-90) cc_final: 0.7400 (ptt90) REVERT: R 866 PHE cc_start: 0.7614 (m-80) cc_final: 0.7389 (m-80) REVERT: S 100 ILE cc_start: 0.8092 (tt) cc_final: 0.7624 (tt) REVERT: S 156 SER cc_start: 0.7321 (m) cc_final: 0.6903 (p) REVERT: S 192 MET cc_start: 0.3441 (mpp) cc_final: 0.2348 (mtp) outliers start: 27 outliers final: 22 residues processed: 201 average time/residue: 0.2027 time to fit residues: 58.6820 Evaluate side-chains 203 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 250 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain 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 657 LEU Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 718 VAL Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** 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 = 0.4164 r_free = 0.4164 target = 0.195138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166972 restraints weight = 10008.512| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.70 r_work: 0.3693 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9868 Z= 0.289 Angle : 0.662 10.346 13349 Z= 0.343 Chirality : 0.046 0.284 1494 Planarity : 0.005 0.049 1685 Dihedral : 5.395 45.062 1335 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.39 % Allowed : 18.68 % 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: -1.07 (0.25), residues: 1190 helix: 0.31 (0.27), residues: 350 sheet: -1.48 (0.29), residues: 296 loop : -0.80 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 281 HIS 0.007 0.002 HIS A 41 PHE 0.036 0.002 PHE R 769 TYR 0.014 0.002 TYR S 94 ARG 0.008 0.001 ARG S 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.29 seconds wall clock time: 46 minutes 1.01 seconds (2761.01 seconds total)