Starting phenix.real_space_refine on Fri Jul 3 00:15:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xke_33249/07_2026/7xke_33249.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xke_33249/07_2026/7xke_33249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2026/7xke_33249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2026/7xke_33249.map" model { file = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2026/7xke_33249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2026/7xke_33249.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2026/7xke_33249.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2026/7xke_33249.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 3759 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 50 5.16 5 C 5067 2.51 5 N 1365 2.21 5 O 1440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7922 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1905 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} 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: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2012 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 247} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'AND': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.47, per 1000 atoms: 0.19 Number of scatterers: 7922 At special positions: 0 Unit cell: (93.628, 122.032, 93.628, 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 50 16.00 O 1440 8.00 N 1365 7.00 C 5067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 275.0 milliseconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 41.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 23 through 50 removed outlier: 3.954A pdb=" N GLN A 39 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.592A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.517A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.160A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.538A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.854A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.506A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.530A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.624A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.842A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 619 through 645 Processing helix chain 'R' and resid 646 through 649 removed outlier: 3.904A pdb=" N ARG R 649 " --> pdb=" O GLU R 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 646 through 649' Processing helix chain 'R' and resid 651 through 677 removed outlier: 3.811A pdb=" N GLN R 659 " --> pdb=" O LYS R 655 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 716 removed outlier: 3.994A pdb=" N CYS R 686 " --> pdb=" O THR R 682 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE R 687 " --> pdb=" O ARG R 683 " (cutoff:3.500A) Processing helix chain 'R' and resid 725 through 735 removed outlier: 3.600A pdb=" N VAL R 733 " --> pdb=" O LYS R 729 " (cutoff:3.500A) Processing helix chain 'R' and resid 736 through 749 removed outlier: 3.567A pdb=" N SER R 749 " --> pdb=" O VAL R 745 " (cutoff:3.500A) Processing helix chain 'R' and resid 750 through 754 removed outlier: 4.034A pdb=" N TYR R 753 " --> pdb=" O PRO R 750 " (cutoff:3.500A) Processing helix chain 'R' and resid 776 through 782 removed outlier: 4.252A pdb=" N ILE R 780 " --> pdb=" O VAL R 776 " (cutoff:3.500A) Processing helix chain 'R' and resid 782 through 809 Processing helix chain 'R' and resid 822 through 834 Processing helix chain 'R' and resid 835 through 838 Processing helix chain 'R' and resid 839 through 846 removed outlier: 4.311A pdb=" N PHE R 843 " --> pdb=" O GLY R 839 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY R 846 " --> pdb=" O PHE R 842 " (cutoff:3.500A) Processing helix chain 'R' and resid 849 through 862 removed outlier: 3.801A pdb=" N THR R 861 " --> pdb=" O ALA R 857 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 883 removed outlier: 3.524A pdb=" N ARG R 879 " --> pdb=" O LYS R 875 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG R 883 " --> pdb=" O ARG R 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.732A pdb=" N VAL A 234 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG A 52 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE A 255 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 54 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL A 257 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 56 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASP A 259 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.299A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.325A 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 105 removed outlier: 6.816A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.899A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.729A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.642A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.592A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.034A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1107 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: 0.99 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1267 1.31 - 1.44: 2275 1.44 - 1.56: 4470 1.56 - 1.69: 7 1.69 - 1.81: 70 Bond restraints: 8089 Sorted by residual: bond pdb=" C5 AND R1001 " pdb=" C6 AND R1001 " ideal model delta sigma weight residual 1.332 1.684 -0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" C15 AND R1001 " pdb=" C16 AND R1001 " ideal model delta sigma weight residual 1.535 1.741 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C14 AND R1001 " pdb=" C15 AND R1001 " ideal model delta sigma weight residual 1.529 1.683 -0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C13 AND R1001 " pdb=" C17 AND R1001 " ideal model delta sigma weight residual 1.514 1.661 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C11 AND R1001 " pdb=" C12 AND R1001 " ideal model delta sigma weight residual 1.531 1.642 -0.111 2.00e-02 2.50e+03 3.07e+01 ... (remaining 8084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 10759 1.70 - 3.40: 172 3.40 - 5.10: 32 5.10 - 6.80: 5 6.80 - 8.50: 2 Bond angle restraints: 10970 Sorted by residual: angle pdb=" N TRP R 676 " pdb=" CA TRP R 676 " pdb=" C TRP R 676 " ideal model delta sigma weight residual 111.36 115.96 -4.60 1.09e+00 8.42e-01 1.78e+01 angle pdb=" N HIS R 710 " pdb=" CA HIS R 710 " pdb=" C HIS R 710 " ideal model delta sigma weight residual 111.07 107.12 3.95 1.07e+00 8.73e-01 1.36e+01 angle pdb=" N MET A 35 " pdb=" CA MET A 35 " pdb=" C MET A 35 " ideal model delta sigma weight residual 113.18 108.76 4.42 1.21e+00 6.83e-01 1.33e+01 angle pdb=" N LYS A 42 " pdb=" CA LYS A 42 " pdb=" C LYS A 42 " ideal model delta sigma weight residual 111.69 108.06 3.63 1.23e+00 6.61e-01 8.73e+00 angle pdb=" N GLU A 299 " pdb=" CA GLU A 299 " pdb=" CB GLU A 299 " ideal model delta sigma weight residual 110.16 114.42 -4.26 1.48e+00 4.57e-01 8.30e+00 ... (remaining 10965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4372 17.63 - 35.27: 319 35.27 - 52.90: 57 52.90 - 70.53: 8 70.53 - 88.16: 6 Dihedral angle restraints: 4762 sinusoidal: 1834 harmonic: 2928 Sorted by residual: dihedral pdb=" CB CYS R 686 " pdb=" SG CYS R 686 " pdb=" SG CYS R 770 " pdb=" CB CYS R 770 " ideal model delta sinusoidal sigma weight residual -86.00 -127.60 41.60 1 1.00e+01 1.00e-02 2.42e+01 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 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG B 219 " pdb=" C ARG B 219 " pdb=" N GLN B 220 " pdb=" CA GLN B 220 " ideal model delta harmonic sigma weight residual 180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1142 0.073 - 0.146: 103 0.146 - 0.219: 2 0.219 - 0.292: 0 0.292 - 0.365: 2 Chirality restraints: 1249 Sorted by residual: chirality pdb=" C13 AND R1001 " pdb=" C12 AND R1001 " pdb=" C14 AND R1001 " pdb=" C17 AND R1001 " both_signs ideal model delta sigma weight residual False -2.72 -2.35 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C9 AND R1001 " pdb=" C10 AND R1001 " pdb=" C11 AND R1001 " pdb=" C8 AND R1001 " both_signs ideal model delta sigma weight residual False -2.46 -2.77 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C14 AND R1001 " pdb=" C13 AND R1001 " pdb=" C15 AND R1001 " pdb=" C8 AND R1001 " both_signs ideal model delta sigma weight residual False -2.32 -2.49 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1246 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 34 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C LYS A 34 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 34 " 0.019 2.00e-02 2.50e+03 pdb=" N MET A 35 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO B 236 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 262 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ASP A 262 " 0.026 2.00e-02 2.50e+03 pdb=" O ASP A 262 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 263 " -0.009 2.00e-02 2.50e+03 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 977 2.75 - 3.29: 7953 3.29 - 3.83: 13638 3.83 - 4.36: 15791 4.36 - 4.90: 27783 Nonbonded interactions: 66142 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.213 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.230 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.246 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD2 ASP B 154 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.262 3.040 ... (remaining 66137 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.006 0.352 8092 Z= 0.314 Angle : 0.565 8.499 10976 Z= 0.312 Chirality : 0.044 0.365 1249 Planarity : 0.003 0.045 1383 Dihedral : 12.866 88.163 2861 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.24 % Allowed : 0.71 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.27), residues: 991 helix: 1.43 (0.28), residues: 376 sheet: -0.30 (0.35), residues: 226 loop : -0.88 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.016 0.001 TYR A 358 PHE 0.015 0.001 PHE B 234 TRP 0.009 0.001 TRP B 82 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.31 ( 8089) covalent geometry : angle 0.56452 / 0.31 (10970) SS BOND : bond 0.00291 / 0.14 ( 3) SS BOND : angle 0.63784 / 0.31 ( 6) hydrogen bonds : bond 0.13784 / 9.41 ( 392) hydrogen bonds : angle 5.88325 / 4.02 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.175 Fit side-chains REVERT: A 45 GLN cc_start: 0.8549 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 278 ASN cc_start: 0.8592 (m-40) cc_final: 0.8273 (m110) REVERT: B 20 ASP cc_start: 0.8456 (m-30) cc_final: 0.8131 (m-30) REVERT: G 32 LYS cc_start: 0.8294 (tmtt) cc_final: 0.7926 (tmtt) REVERT: G 36 ASP cc_start: 0.7909 (m-30) cc_final: 0.7478 (m-30) REVERT: G 42 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7443 (tm-30) REVERT: R 822 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7021 (tm-30) outliers start: 2 outliers final: 2 residues processed: 161 average time/residue: 0.5886 time to fit residues: 99.3034 Evaluate side-chains 122 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076987 restraints weight = 14972.122| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.69 r_work: 0.2968 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8092 Z= 0.127 Angle : 0.541 7.190 10976 Z= 0.287 Chirality : 0.040 0.140 1249 Planarity : 0.004 0.041 1383 Dihedral : 4.297 46.977 1107 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.43 % Allowed : 12.86 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.27), residues: 991 helix: 1.97 (0.28), residues: 365 sheet: -0.23 (0.35), residues: 223 loop : -0.85 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.014 0.001 TYR A 358 PHE 0.023 0.001 PHE R 856 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8089) covalent geometry : angle 0.54051 / 0.29 (10970) SS BOND : bond 0.00177 / 0.09 ( 3) SS BOND : angle 0.52577 / 0.26 ( 6) hydrogen bonds : bond 0.03808 / 2.60 ( 392) hydrogen bonds : angle 4.44143 / 3.08 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.245 Fit side-chains REVERT: A 45 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8295 (tm-30) REVERT: B 20 ASP cc_start: 0.8631 (m-30) cc_final: 0.8316 (m-30) REVERT: B 197 ARG cc_start: 0.8548 (mtp-110) cc_final: 0.8135 (mtp-110) REVERT: B 340 ASN cc_start: 0.8539 (t0) cc_final: 0.8162 (m-40) REVERT: G 42 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8118 (tm-30) REVERT: N 65 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8607 (mmmm) REVERT: R 650 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8255 (mmp80) REVERT: R 676 TRP cc_start: 0.7999 (OUTLIER) cc_final: 0.7581 (t-100) REVERT: R 809 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8409 (mttt) REVERT: R 822 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6757 (tm-30) REVERT: R 853 MET cc_start: 0.8042 (tmm) cc_final: 0.7817 (tmm) outliers start: 12 outliers final: 3 residues processed: 140 average time/residue: 0.5202 time to fit residues: 76.5495 Evaluate side-chains 132 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.094844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076644 restraints weight = 14793.166| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.64 r_work: 0.2959 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8092 Z= 0.126 Angle : 0.513 6.722 10976 Z= 0.273 Chirality : 0.040 0.145 1249 Planarity : 0.003 0.042 1383 Dihedral : 4.157 44.772 1105 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.67 % Allowed : 15.95 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 991 helix: 1.96 (0.28), residues: 365 sheet: -0.27 (0.35), residues: 223 loop : -0.83 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.016 0.001 TYR A 358 PHE 0.016 0.001 PHE R 856 TRP 0.010 0.001 TRP A 244 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8089) covalent geometry : angle 0.51341 / 0.27 (10970) SS BOND : bond 0.00158 / 0.08 ( 3) SS BOND : angle 0.47176 / 0.23 ( 6) hydrogen bonds : bond 0.03578 / 2.47 ( 392) hydrogen bonds : angle 4.20810 / 2.93 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.185 Fit side-chains REVERT: A 45 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 392 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8839 (mt-10) REVERT: B 20 ASP cc_start: 0.8656 (m-30) cc_final: 0.8360 (m-30) REVERT: B 32 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8842 (pm20) REVERT: B 43 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 340 ASN cc_start: 0.8486 (t0) cc_final: 0.8099 (m-40) REVERT: G 26 ASP cc_start: 0.8798 (t70) cc_final: 0.8581 (t0) REVERT: G 42 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8136 (tm-30) REVERT: R 659 GLN cc_start: 0.8674 (mp10) cc_final: 0.8363 (mm-40) REVERT: R 676 TRP cc_start: 0.7934 (OUTLIER) cc_final: 0.7575 (t-100) REVERT: R 791 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8499 (tt) REVERT: R 809 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8307 (mttt) REVERT: R 822 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6693 (tm-30) outliers start: 14 outliers final: 5 residues processed: 143 average time/residue: 0.5447 time to fit residues: 81.9258 Evaluate side-chains 138 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 791 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 3 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077035 restraints weight = 15096.751| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.66 r_work: 0.2965 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8092 Z= 0.117 Angle : 0.513 7.246 10976 Z= 0.271 Chirality : 0.040 0.144 1249 Planarity : 0.003 0.042 1383 Dihedral : 4.131 43.438 1105 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.90 % Allowed : 17.50 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 991 helix: 1.88 (0.27), residues: 371 sheet: -0.28 (0.35), residues: 218 loop : -0.78 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 280 TYR 0.014 0.001 TYR A 358 PHE 0.014 0.001 PHE R 856 TRP 0.010 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8089) covalent geometry : angle 0.51275 / 0.27 (10970) SS BOND : bond 0.00133 / 0.06 ( 3) SS BOND : angle 0.42460 / 0.20 ( 6) hydrogen bonds : bond 0.03414 / 2.36 ( 392) hydrogen bonds : angle 4.08363 / 2.85 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.208 Fit side-chains REVERT: A 45 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 20 ASP cc_start: 0.8562 (m-30) cc_final: 0.8270 (m-30) REVERT: B 43 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8774 (mp) REVERT: B 197 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.8121 (mtp-110) REVERT: B 340 ASN cc_start: 0.8286 (t0) cc_final: 0.7868 (m-40) REVERT: G 42 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7936 (tm-30) REVERT: N 3 GLN cc_start: 0.8652 (pt0) cc_final: 0.8166 (pp30) REVERT: N 76 LYS cc_start: 0.9313 (mmtm) cc_final: 0.9097 (mmmm) REVERT: N 105 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7887 (mtp-110) REVERT: R 659 GLN cc_start: 0.8541 (mp10) cc_final: 0.8243 (mm-40) REVERT: R 676 TRP cc_start: 0.7776 (OUTLIER) cc_final: 0.7480 (t-100) REVERT: R 726 TYR cc_start: 0.8130 (t80) cc_final: 0.7471 (t80) REVERT: R 791 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8450 (tt) REVERT: R 809 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8305 (mttt) outliers start: 16 outliers final: 6 residues processed: 139 average time/residue: 0.5404 time to fit residues: 79.1040 Evaluate side-chains 138 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 704 MET Chi-restraints excluded: chain R residue 791 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 120 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073789 restraints weight = 15167.141| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.63 r_work: 0.2905 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8092 Z= 0.178 Angle : 0.544 7.257 10976 Z= 0.289 Chirality : 0.041 0.163 1249 Planarity : 0.004 0.043 1383 Dihedral : 4.277 42.237 1105 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.74 % Allowed : 17.50 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.27), residues: 991 helix: 1.86 (0.27), residues: 365 sheet: -0.34 (0.35), residues: 223 loop : -0.82 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.015 0.001 TYR A 358 PHE 0.014 0.002 PHE B 180 TRP 0.012 0.001 TRP A 244 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8089) covalent geometry : angle 0.54439 / 0.29 (10970) SS BOND : bond 0.00245 / 0.12 ( 3) SS BOND : angle 0.67221 / 0.36 ( 6) hydrogen bonds : bond 0.03740 / 2.59 ( 392) hydrogen bonds : angle 4.20524 / 2.92 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.226 Fit side-chains REVERT: A 45 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 20 ASP cc_start: 0.8647 (m-30) cc_final: 0.8332 (m-30) REVERT: B 43 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8884 (mp) REVERT: B 197 ARG cc_start: 0.8665 (mtp-110) cc_final: 0.8353 (mtp-110) REVERT: B 340 ASN cc_start: 0.8513 (t0) cc_final: 0.8156 (t0) REVERT: G 42 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8256 (tm-30) REVERT: N 65 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8748 (mmmm) REVERT: N 76 LYS cc_start: 0.9285 (mmtm) cc_final: 0.9065 (mmmm) REVERT: N 105 ARG cc_start: 0.8327 (mtp85) cc_final: 0.8040 (mtp-110) REVERT: R 659 GLN cc_start: 0.8680 (mp10) cc_final: 0.8366 (mm-40) REVERT: R 676 TRP cc_start: 0.7841 (OUTLIER) cc_final: 0.7501 (t-100) REVERT: R 809 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8338 (mttt) outliers start: 23 outliers final: 7 residues processed: 143 average time/residue: 0.5610 time to fit residues: 84.5060 Evaluate side-chains 131 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 3 GLN N 120 GLN ** R 881 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 = 0.3384 r_free = 0.3384 target = 0.092204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.073929 restraints weight = 15014.062| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.60 r_work: 0.2932 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8092 Z= 0.171 Angle : 0.556 7.723 10976 Z= 0.291 Chirality : 0.041 0.152 1249 Planarity : 0.003 0.043 1383 Dihedral : 4.279 40.977 1105 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.26 % Allowed : 19.05 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.27), residues: 991 helix: 1.73 (0.27), residues: 371 sheet: -0.41 (0.35), residues: 223 loop : -0.80 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.013 0.001 TYR A 339 PHE 0.013 0.001 PHE R 832 TRP 0.011 0.001 TRP A 244 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 8089) covalent geometry : angle 0.55547 / 0.29 (10970) SS BOND : bond 0.00328 / 0.16 ( 3) SS BOND : angle 0.77070 / 0.39 ( 6) hydrogen bonds : bond 0.03659 / 2.54 ( 392) hydrogen bonds : angle 4.19330 / 2.92 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 20 ASP cc_start: 0.8647 (m-30) cc_final: 0.8328 (m-30) REVERT: B 43 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8872 (mp) REVERT: B 340 ASN cc_start: 0.8459 (t0) cc_final: 0.8094 (t0) REVERT: G 26 ASP cc_start: 0.8823 (t70) cc_final: 0.8559 (t0) REVERT: G 42 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8258 (tm-30) REVERT: N 3 GLN cc_start: 0.8752 (pt0) cc_final: 0.8227 (pp30) REVERT: N 65 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8683 (mmmm) REVERT: N 105 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8070 (mtp-110) REVERT: R 659 GLN cc_start: 0.8690 (mp10) cc_final: 0.8373 (mm-40) REVERT: R 676 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.7488 (t-100) REVERT: R 809 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8327 (mttt) outliers start: 19 outliers final: 7 residues processed: 140 average time/residue: 0.5732 time to fit residues: 84.2513 Evaluate side-chains 133 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 120 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.093765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.075619 restraints weight = 15033.649| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.62 r_work: 0.2942 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8092 Z= 0.126 Angle : 0.558 8.937 10976 Z= 0.287 Chirality : 0.040 0.144 1249 Planarity : 0.003 0.042 1383 Dihedral : 4.166 39.968 1105 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.14 % Allowed : 20.48 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.27), residues: 991 helix: 1.91 (0.27), residues: 365 sheet: -0.49 (0.34), residues: 223 loop : -0.78 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.012 0.001 TYR A 358 PHE 0.011 0.001 PHE R 856 TRP 0.011 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8089) covalent geometry : angle 0.55805 / 0.29 (10970) SS BOND : bond 0.00314 / 0.15 ( 3) SS BOND : angle 0.58477 / 0.28 ( 6) hydrogen bonds : bond 0.03409 / 2.37 ( 392) hydrogen bonds : angle 4.08448 / 2.85 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8416 (tm-30) REVERT: B 20 ASP cc_start: 0.8644 (m-30) cc_final: 0.8334 (m-30) REVERT: B 43 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8806 (mp) REVERT: B 340 ASN cc_start: 0.8506 (t0) cc_final: 0.8155 (t0) REVERT: G 26 ASP cc_start: 0.8815 (t70) cc_final: 0.8608 (t0) REVERT: G 42 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8229 (tm-30) REVERT: N 3 GLN cc_start: 0.8731 (pt0) cc_final: 0.8229 (pp30) REVERT: N 65 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8682 (mmmm) REVERT: N 105 ARG cc_start: 0.8345 (mtp85) cc_final: 0.8122 (mtp-110) REVERT: R 659 GLN cc_start: 0.8640 (mp10) cc_final: 0.8341 (mm-40) REVERT: R 676 TRP cc_start: 0.7821 (OUTLIER) cc_final: 0.7461 (t-100) REVERT: R 791 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8527 (tt) REVERT: R 796 MET cc_start: 0.8557 (tpp) cc_final: 0.8257 (tpp) REVERT: R 809 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8320 (mttt) outliers start: 18 outliers final: 10 residues processed: 138 average time/residue: 0.5654 time to fit residues: 82.0212 Evaluate side-chains 136 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 777 VAL Chi-restraints excluded: chain R residue 791 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN N 120 GLN ** R 881 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 = 0.3409 r_free = 0.3409 target = 0.093732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075541 restraints weight = 15087.626| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.62 r_work: 0.2944 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8092 Z= 0.136 Angle : 0.571 10.829 10976 Z= 0.292 Chirality : 0.041 0.151 1249 Planarity : 0.003 0.042 1383 Dihedral : 4.160 39.402 1105 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.90 % Allowed : 20.95 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.27), residues: 991 helix: 1.80 (0.27), residues: 371 sheet: -0.46 (0.35), residues: 223 loop : -0.75 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 317 TYR 0.019 0.001 TYR N 80 PHE 0.011 0.001 PHE R 856 TRP 0.010 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8089) covalent geometry : angle 0.57066 / 0.29 (10970) SS BOND : bond 0.00298 / 0.14 ( 3) SS BOND : angle 0.48260 / 0.24 ( 6) hydrogen bonds : bond 0.03432 / 2.39 ( 392) hydrogen bonds : angle 4.08090 / 2.86 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8419 (tm-30) REVERT: B 20 ASP cc_start: 0.8636 (m-30) cc_final: 0.8333 (m-30) REVERT: B 32 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8765 (pm20) REVERT: B 43 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8769 (mp) REVERT: B 340 ASN cc_start: 0.8456 (t0) cc_final: 0.8160 (t0) REVERT: G 26 ASP cc_start: 0.8808 (t70) cc_final: 0.8590 (t0) REVERT: G 42 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8242 (tm-30) REVERT: N 3 GLN cc_start: 0.8723 (pt0) cc_final: 0.8234 (pp30) REVERT: N 32 TYR cc_start: 0.8849 (m-80) cc_final: 0.8564 (m-80) REVERT: N 105 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8160 (mtp-110) REVERT: R 659 GLN cc_start: 0.8624 (mp10) cc_final: 0.8337 (mm-40) REVERT: R 676 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.7570 (t-100) REVERT: R 726 TYR cc_start: 0.8227 (t80) cc_final: 0.7466 (t80) REVERT: R 796 MET cc_start: 0.8559 (tpp) cc_final: 0.8237 (tpp) REVERT: R 809 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8322 (mttt) outliers start: 16 outliers final: 10 residues processed: 139 average time/residue: 0.6539 time to fit residues: 95.5503 Evaluate side-chains 147 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.0020 chunk 59 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 120 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076737 restraints weight = 14804.976| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.62 r_work: 0.2961 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8092 Z= 0.119 Angle : 0.568 11.930 10976 Z= 0.291 Chirality : 0.040 0.147 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.105 38.900 1105 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.43 % Allowed : 21.43 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.27), residues: 991 helix: 1.80 (0.27), residues: 371 sheet: -0.47 (0.35), residues: 223 loop : -0.70 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 317 TYR 0.019 0.001 TYR N 80 PHE 0.011 0.001 PHE R 856 TRP 0.010 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8089) covalent geometry : angle 0.56779 / 0.29 (10970) SS BOND : bond 0.00292 / 0.14 ( 3) SS BOND : angle 0.48015 / 0.22 ( 6) hydrogen bonds : bond 0.03320 / 2.31 ( 392) hydrogen bonds : angle 4.02754 / 2.82 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7705 (pp20) REVERT: A 45 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 20 ASP cc_start: 0.8639 (m-30) cc_final: 0.8337 (m-30) REVERT: B 43 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8721 (mp) REVERT: B 340 ASN cc_start: 0.8441 (t0) cc_final: 0.8108 (t0) REVERT: G 42 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8240 (tm-30) REVERT: N 3 GLN cc_start: 0.8710 (pt0) cc_final: 0.8210 (pp30) REVERT: N 32 TYR cc_start: 0.8853 (m-80) cc_final: 0.8598 (m-80) REVERT: N 105 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8130 (mtp-110) REVERT: R 659 GLN cc_start: 0.8641 (mp10) cc_final: 0.8332 (mm-40) REVERT: R 676 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.7564 (t-100) REVERT: R 726 TYR cc_start: 0.8167 (t80) cc_final: 0.7544 (t80) REVERT: R 796 MET cc_start: 0.8558 (tpp) cc_final: 0.8220 (tpp) REVERT: R 809 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8308 (mttt) outliers start: 12 outliers final: 7 residues processed: 144 average time/residue: 0.6557 time to fit residues: 99.1596 Evaluate side-chains 137 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.0370 chunk 87 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 120 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077171 restraints weight = 14933.401| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.64 r_work: 0.2970 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8092 Z= 0.123 Angle : 0.591 8.894 10976 Z= 0.306 Chirality : 0.040 0.151 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.036 38.347 1105 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.19 % Allowed : 22.62 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.27), residues: 991 helix: 1.83 (0.27), residues: 370 sheet: -0.43 (0.35), residues: 223 loop : -0.69 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.019 0.001 TYR N 80 PHE 0.011 0.001 PHE R 856 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 8089) covalent geometry : angle 0.59122 / 0.31 (10970) SS BOND : bond 0.00298 / 0.14 ( 3) SS BOND : angle 0.41851 / 0.19 ( 6) hydrogen bonds : bond 0.03263 / 2.27 ( 392) hydrogen bonds : angle 4.00530 / 2.80 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8290 (tm-30) REVERT: B 20 ASP cc_start: 0.8578 (m-30) cc_final: 0.8267 (m-30) REVERT: B 43 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8660 (mp) REVERT: B 340 ASN cc_start: 0.8278 (t0) cc_final: 0.7895 (t0) REVERT: G 42 GLU cc_start: 0.8222 (tm-30) cc_final: 0.8007 (tm-30) REVERT: N 3 GLN cc_start: 0.8609 (pt0) cc_final: 0.8171 (pp30) REVERT: N 32 TYR cc_start: 0.8767 (m-80) cc_final: 0.8522 (m-80) REVERT: N 105 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7969 (mtp-110) REVERT: N 106 ASP cc_start: 0.8525 (p0) cc_final: 0.8236 (p0) REVERT: R 659 GLN cc_start: 0.8532 (mp10) cc_final: 0.8234 (mm-40) REVERT: R 676 TRP cc_start: 0.7861 (OUTLIER) cc_final: 0.7565 (t-100) REVERT: R 726 TYR cc_start: 0.8119 (t80) cc_final: 0.7563 (t80) REVERT: R 796 MET cc_start: 0.8371 (tpp) cc_final: 0.8020 (tpp) REVERT: R 809 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8288 (mttt) outliers start: 10 outliers final: 7 residues processed: 137 average time/residue: 0.6571 time to fit residues: 94.3676 Evaluate side-chains 137 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN N 120 GLN ** R 881 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 = 0.3458 r_free = 0.3458 target = 0.096608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078580 restraints weight = 14968.116| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.63 r_work: 0.3007 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8092 Z= 0.115 Angle : 0.585 8.703 10976 Z= 0.301 Chirality : 0.040 0.147 1249 Planarity : 0.004 0.042 1383 Dihedral : 3.950 37.791 1105 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.31 % Allowed : 22.98 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.28), residues: 991 helix: 1.84 (0.27), residues: 372 sheet: -0.38 (0.35), residues: 223 loop : -0.65 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 280 TYR 0.018 0.001 TYR N 80 PHE 0.011 0.001 PHE R 856 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 8089) covalent geometry : angle 0.58474 / 0.30 (10970) SS BOND : bond 0.00287 / 0.14 ( 3) SS BOND : angle 0.37539 / 0.15 ( 6) hydrogen bonds : bond 0.03156 / 2.19 ( 392) hydrogen bonds : angle 3.94406 / 2.76 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2792.89 seconds wall clock time: 48 minutes 17.70 seconds (2897.70 seconds total)