Starting phenix.real_space_refine on Wed Mar 4 05:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xke_33249/03_2026/7xke_33249.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xke_33249/03_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_33249/03_2026/7xke_33249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xke_33249/03_2026/7xke_33249.map" model { file = "/net/cci-nas-00/data/ceres_data/7xke_33249/03_2026/7xke_33249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xke_33249/03_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-5986/lib/python3.9/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: 1.77, per 1000 atoms: 0.22 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: 0.93 Conformation dependent library (CDL) restraints added in 232.5 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: 0.33 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: 1.26 Time building geometry restraints manager: 1.11 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: 4411 17.63 - 35.27: 328 35.27 - 52.90: 57 52.90 - 70.53: 8 70.53 - 88.16: 6 Dihedral angle restraints: 4810 sinusoidal: 1882 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 4807 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 12.845 88.163 2909 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 covalent geometry : bond 0.00638 ( 8089) covalent geometry : angle 0.56452 (10970) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.63784 ( 6) hydrogen bonds : bond 0.13784 ( 392) hydrogen bonds : angle 5.88325 ( 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 : 0.187 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: 0.7621 time to fit residues: 127.7643 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 : 0.248 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.095282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.076964 restraints weight = 14966.243| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.69 r_work: 0.2969 rms_B_bonded: 3.04 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: 0.8343 moved from start: 0.1430 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 : 0.537 7.285 10976 Z= 0.285 Chirality : 0.040 0.136 1249 Planarity : 0.004 0.041 1383 Dihedral : 4.231 46.777 1155 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.43 % Allowed : 12.62 % Favored : 85.95 % 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: -0.23 (0.35), residues: 223 loop : -0.84 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 280 TYR 0.014 0.001 TYR A 358 PHE 0.021 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 covalent geometry : bond 0.00282 ( 8089) covalent geometry : angle 0.53690 (10970) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.55308 ( 6) hydrogen bonds : bond 0.03929 ( 392) hydrogen bonds : angle 4.44635 ( 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 146 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.307 Fit side-chains REVERT: A 45 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8319 (tm-30) REVERT: B 20 ASP cc_start: 0.8626 (m-30) cc_final: 0.8311 (m-30) REVERT: B 197 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8141 (mtp-110) REVERT: B 340 ASN cc_start: 0.8548 (t0) cc_final: 0.8167 (m-40) REVERT: G 32 LYS cc_start: 0.8662 (tmtt) cc_final: 0.8265 (tmtt) REVERT: G 42 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8100 (tm-30) REVERT: N 65 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8621 (mmmm) REVERT: R 650 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8249 (mmp80) REVERT: R 676 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.7592 (t-100) REVERT: R 809 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8403 (mttt) REVERT: R 822 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6756 (tm-30) REVERT: R 853 MET cc_start: 0.8040 (tmm) cc_final: 0.7813 (tmm) outliers start: 12 outliers final: 3 residues processed: 141 average time/residue: 0.6533 time to fit residues: 96.7789 Evaluate side-chains 131 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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: 0.7980 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3418 r_free = 0.3418 target = 0.094261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.076029 restraints weight = 14797.544| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.62 r_work: 0.2948 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1655 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= 0.134 Angle : 0.514 6.712 10976 Z= 0.274 Chirality : 0.040 0.148 1249 Planarity : 0.003 0.042 1383 Dihedral : 4.106 44.619 1153 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.90 % Allowed : 15.71 % 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: 0.44 (0.27), residues: 991 helix: 1.92 (0.27), residues: 365 sheet: -0.33 (0.35), residues: 225 loop : -0.83 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.016 0.001 TYR A 358 PHE 0.015 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 covalent geometry : bond 0.00303 ( 8089) covalent geometry : angle 0.51421 (10970) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.53819 ( 6) hydrogen bonds : bond 0.03619 ( 392) hydrogen bonds : angle 4.20452 ( 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 152 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.303 Fit side-chains REVERT: A 45 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8397 (tm-30) REVERT: A 392 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8841 (mt-10) REVERT: B 20 ASP cc_start: 0.8651 (m-30) cc_final: 0.8348 (m-30) REVERT: B 32 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8797 (pm20) REVERT: B 43 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8809 (mp) REVERT: B 340 ASN cc_start: 0.8457 (t0) cc_final: 0.8086 (m-40) REVERT: G 42 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8152 (tm-30) REVERT: R 650 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8249 (mmp80) REVERT: R 659 GLN cc_start: 0.8673 (mp10) cc_final: 0.8360 (mm-40) REVERT: R 676 TRP cc_start: 0.7948 (OUTLIER) cc_final: 0.7575 (t-100) REVERT: R 809 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8323 (mttt) REVERT: R 822 GLN cc_start: 0.7323 (tm-30) cc_final: 0.6703 (tm-30) outliers start: 16 outliers final: 5 residues processed: 142 average time/residue: 0.6999 time to fit residues: 104.2289 Evaluate side-chains 135 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 N residue 11 LEU Chi-restraints excluded: chain R residue 650 ARG Chi-restraints excluded: chain R residue 676 TRP Chi-restraints excluded: chain R residue 777 VAL 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: 1.9990 chunk 96 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3403 r_free = 0.3403 target = 0.093325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074895 restraints weight = 15172.971| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.63 r_work: 0.2934 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8092 Z= 0.154 Angle : 0.532 7.089 10976 Z= 0.282 Chirality : 0.041 0.150 1249 Planarity : 0.003 0.043 1383 Dihedral : 4.175 43.237 1153 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.38 % Allowed : 17.74 % Favored : 79.88 % 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: 1.78 (0.27), residues: 371 sheet: -0.31 (0.35), residues: 218 loop : -0.81 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.015 0.001 TYR A 358 PHE 0.013 0.001 PHE R 856 TRP 0.011 0.001 TRP A 244 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8089) covalent geometry : angle 0.53224 (10970) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.55636 ( 6) hydrogen bonds : bond 0.03620 ( 392) hydrogen bonds : angle 4.16310 ( 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 146 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.308 Fit side-chains REVERT: A 45 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 20 ASP cc_start: 0.8661 (m-30) cc_final: 0.8352 (m-30) REVERT: B 43 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8858 (mp) REVERT: B 197 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8311 (mtp-110) REVERT: B 340 ASN cc_start: 0.8518 (t0) cc_final: 0.8166 (t0) REVERT: G 42 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8115 (tm-30) REVERT: N 3 GLN cc_start: 0.8769 (pt0) cc_final: 0.8235 (pp30) REVERT: N 105 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7996 (mtp-110) REVERT: R 647 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8381 (ttmp) REVERT: R 659 GLN cc_start: 0.8660 (mp10) cc_final: 0.8356 (mm-40) REVERT: R 676 TRP cc_start: 0.7863 (OUTLIER) cc_final: 0.7534 (t-100) REVERT: R 809 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8342 (mttt) outliers start: 20 outliers final: 6 residues processed: 138 average time/residue: 0.6632 time to fit residues: 96.4129 Evaluate side-chains 128 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3419 r_free = 0.3419 target = 0.094254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075976 restraints weight = 15036.577| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.63 r_work: 0.2953 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1956 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= 0.126 Angle : 0.520 8.040 10976 Z= 0.274 Chirality : 0.040 0.149 1249 Planarity : 0.003 0.043 1383 Dihedral : 4.088 42.182 1153 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.38 % Allowed : 18.45 % Favored : 79.17 % 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: 1.82 (0.27), residues: 371 sheet: -0.34 (0.35), residues: 218 loop : -0.79 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 280 TYR 0.013 0.001 TYR A 358 PHE 0.013 0.001 PHE R 856 TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8089) covalent geometry : angle 0.51967 (10970) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.42493 ( 6) hydrogen bonds : bond 0.03487 ( 392) hydrogen bonds : angle 4.07878 ( 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 149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.304 Fit side-chains REVERT: A 45 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 20 ASP cc_start: 0.8665 (m-30) cc_final: 0.8378 (m-30) REVERT: B 43 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8844 (mp) REVERT: B 197 ARG cc_start: 0.8637 (mtp-110) cc_final: 0.8315 (mtp-110) REVERT: B 340 ASN cc_start: 0.8518 (t0) cc_final: 0.8149 (t0) REVERT: G 26 ASP cc_start: 0.8789 (t70) cc_final: 0.8531 (t0) REVERT: G 42 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8137 (tm-30) REVERT: N 3 GLN cc_start: 0.8732 (pt0) cc_final: 0.8220 (pp30) REVERT: N 105 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8016 (mtp-110) REVERT: R 647 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8459 (mmtm) REVERT: R 659 GLN cc_start: 0.8637 (mp10) cc_final: 0.8339 (mm-40) REVERT: R 676 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.7494 (t-100) REVERT: R 768 ASP cc_start: 0.7507 (p0) cc_final: 0.7227 (p0) REVERT: R 809 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8332 (mttt) outliers start: 20 outliers final: 8 residues processed: 139 average time/residue: 0.6828 time to fit residues: 99.6861 Evaluate side-chains 138 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 146 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3379 r_free = 0.3379 target = 0.091819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073452 restraints weight = 15038.423| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.59 r_work: 0.2922 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8092 Z= 0.188 Angle : 0.569 8.319 10976 Z= 0.298 Chirality : 0.042 0.156 1249 Planarity : 0.004 0.043 1383 Dihedral : 4.251 41.145 1153 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.26 % Allowed : 19.29 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.27), residues: 991 helix: 1.69 (0.27), residues: 371 sheet: -0.41 (0.34), residues: 223 loop : -0.83 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.015 0.001 TYR A 339 PHE 0.013 0.001 PHE R 832 TRP 0.012 0.001 TRP A 244 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8089) covalent geometry : angle 0.56864 (10970) SS BOND : bond 0.00355 ( 3) SS BOND : angle 0.84006 ( 6) hydrogen bonds : bond 0.03742 ( 392) hydrogen bonds : angle 4.20811 ( 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 149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8458 (tm-30) REVERT: B 20 ASP cc_start: 0.8646 (m-30) cc_final: 0.8329 (m-30) REVERT: B 43 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8899 (mp) REVERT: B 340 ASN cc_start: 0.8490 (t0) cc_final: 0.8123 (t0) REVERT: G 26 ASP cc_start: 0.8808 (t70) cc_final: 0.8581 (t0) REVERT: G 42 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8273 (tm-30) REVERT: N 76 LYS cc_start: 0.9316 (mmtm) cc_final: 0.9100 (mmmm) REVERT: N 105 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8074 (mtp-110) REVERT: R 647 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8507 (mmtm) REVERT: R 659 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8379 (mm-40) REVERT: R 676 TRP cc_start: 0.7844 (OUTLIER) cc_final: 0.7502 (t-100) REVERT: R 768 ASP cc_start: 0.7559 (p0) cc_final: 0.7266 (p0) REVERT: R 809 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8333 (mttt) outliers start: 19 outliers final: 7 residues processed: 140 average time/residue: 0.6430 time to fit residues: 94.5259 Evaluate side-chains 128 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 261 LEU 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 659 GLN 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: 2.9990 chunk 76 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3396 r_free = 0.3396 target = 0.092916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.074735 restraints weight = 15106.838| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.61 r_work: 0.2932 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2157 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= 0.142 Angle : 0.560 7.971 10976 Z= 0.291 Chirality : 0.041 0.146 1249 Planarity : 0.003 0.042 1383 Dihedral : 4.188 40.091 1153 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.90 % Allowed : 20.48 % Favored : 77.62 % 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: 0.29 (0.27), residues: 991 helix: 1.73 (0.27), residues: 371 sheet: -0.47 (0.35), residues: 218 loop : -0.84 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 317 TYR 0.012 0.001 TYR A 358 PHE 0.012 0.001 PHE N 29 TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8089) covalent geometry : angle 0.56029 (10970) SS BOND : bond 0.00327 ( 3) SS BOND : angle 0.62586 ( 6) hydrogen bonds : bond 0.03548 ( 392) hydrogen bonds : angle 4.13415 ( 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 147 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8424 (tm-30) REVERT: B 20 ASP cc_start: 0.8623 (m-30) cc_final: 0.8320 (m-30) REVERT: B 43 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 340 ASN cc_start: 0.8529 (t0) cc_final: 0.8178 (t0) REVERT: G 26 ASP cc_start: 0.8787 (t70) cc_final: 0.8554 (t0) REVERT: G 42 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8213 (tm-30) REVERT: N 3 GLN cc_start: 0.8738 (pt0) cc_final: 0.8251 (pp30) REVERT: N 105 ARG cc_start: 0.8362 (mtp85) cc_final: 0.8112 (mtp-110) REVERT: R 647 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8492 (mmtm) REVERT: R 659 GLN cc_start: 0.8638 (mp10) cc_final: 0.8341 (mm-40) REVERT: R 676 TRP cc_start: 0.7784 (OUTLIER) cc_final: 0.7465 (t-100) REVERT: R 768 ASP cc_start: 0.7590 (p0) cc_final: 0.7286 (p0) REVERT: R 809 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8325 (mttt) outliers start: 16 outliers final: 10 residues processed: 140 average time/residue: 0.6815 time to fit residues: 100.0201 Evaluate side-chains 134 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 58 ILE Chi-restraints excluded: chain B residue 146 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3368 r_free = 0.3368 target = 0.091258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072895 restraints weight = 15191.312| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.60 r_work: 0.2891 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8092 Z= 0.192 Angle : 0.599 10.822 10976 Z= 0.308 Chirality : 0.042 0.156 1249 Planarity : 0.004 0.043 1383 Dihedral : 4.300 39.507 1153 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.02 % Allowed : 21.07 % Favored : 76.90 % 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: 0.15 (0.27), residues: 991 helix: 1.63 (0.27), residues: 371 sheet: -0.48 (0.34), residues: 223 loop : -0.99 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 317 TYR 0.014 0.001 TYR A 339 PHE 0.013 0.001 PHE R 832 TRP 0.012 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8089) covalent geometry : angle 0.59875 (10970) SS BOND : bond 0.00385 ( 3) SS BOND : angle 0.81198 ( 6) hydrogen bonds : bond 0.03753 ( 392) hydrogen bonds : angle 4.21418 ( 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 140 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.321 Fit side-chains REVERT: A 45 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8454 (tm-30) REVERT: B 20 ASP cc_start: 0.8636 (m-30) cc_final: 0.8338 (m-30) REVERT: B 43 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8868 (mp) REVERT: B 59 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8642 (t80) REVERT: B 197 ARG cc_start: 0.8666 (mtp-110) cc_final: 0.8364 (ttm-80) REVERT: B 340 ASN cc_start: 0.8486 (t0) cc_final: 0.8186 (t0) REVERT: G 26 ASP cc_start: 0.8779 (t70) cc_final: 0.8556 (t0) REVERT: G 42 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8270 (tm-30) REVERT: N 3 GLN cc_start: 0.8753 (pt0) cc_final: 0.8245 (pp30) REVERT: N 105 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8129 (mtp-110) REVERT: R 647 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8488 (mmtm) REVERT: R 659 GLN cc_start: 0.8686 (mp10) cc_final: 0.8374 (mm-40) REVERT: R 676 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.7514 (t-100) REVERT: R 768 ASP cc_start: 0.7566 (p0) cc_final: 0.7273 (p0) REVERT: R 809 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8335 (mttt) outliers start: 17 outliers final: 8 residues processed: 133 average time/residue: 0.7070 time to fit residues: 98.6157 Evaluate side-chains 130 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 146 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3408 r_free = 0.3408 target = 0.093651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.075517 restraints weight = 14838.552| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.58 r_work: 0.2949 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8092 Z= 0.125 Angle : 0.577 11.820 10976 Z= 0.295 Chirality : 0.041 0.151 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.120 38.432 1153 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.31 % Allowed : 21.67 % Favored : 77.02 % 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: 0.28 (0.27), residues: 991 helix: 1.82 (0.27), residues: 366 sheet: -0.54 (0.34), residues: 223 loop : -0.87 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 825 TYR 0.012 0.001 TYR B 264 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 covalent geometry : bond 0.00284 ( 8089) covalent geometry : angle 0.57728 (10970) SS BOND : bond 0.00298 ( 3) SS BOND : angle 0.48951 ( 6) hydrogen bonds : bond 0.03420 ( 392) hydrogen bonds : angle 4.07293 ( 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 142 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8416 (tm-30) REVERT: B 20 ASP cc_start: 0.8643 (m-30) cc_final: 0.8360 (m-30) REVERT: B 43 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8801 (mp) REVERT: B 340 ASN cc_start: 0.8445 (t0) cc_final: 0.8141 (t0) REVERT: G 26 ASP cc_start: 0.8777 (t70) cc_final: 0.8566 (t0) REVERT: G 42 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8251 (tm-30) REVERT: N 105 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8076 (mtp-110) REVERT: R 647 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8485 (mmtm) REVERT: R 659 GLN cc_start: 0.8656 (mp10) cc_final: 0.8343 (mm-40) REVERT: R 676 TRP cc_start: 0.7937 (OUTLIER) cc_final: 0.7592 (t-100) REVERT: R 768 ASP cc_start: 0.7538 (p0) cc_final: 0.7223 (p0) REVERT: R 796 MET cc_start: 0.8560 (tpp) cc_final: 0.8269 (tpp) REVERT: R 809 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8318 (mttt) outliers start: 11 outliers final: 10 residues processed: 137 average time/residue: 0.6943 time to fit residues: 99.7212 Evaluate side-chains 137 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 58 ILE Chi-restraints excluded: chain B residue 146 LEU 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: 1.9990 chunk 21 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 3 GLN N 120 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075871 restraints weight = 15009.623| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.60 r_work: 0.2954 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2290 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= 0.129 Angle : 0.579 8.915 10976 Z= 0.297 Chirality : 0.041 0.153 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.055 37.833 1153 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.55 % Allowed : 21.90 % Favored : 76.55 % 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: 0.35 (0.27), residues: 991 helix: 1.78 (0.27), residues: 372 sheet: -0.48 (0.34), residues: 223 loop : -0.79 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 825 TYR 0.014 0.001 TYR A 358 PHE 0.012 0.001 PHE R 832 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8089) covalent geometry : angle 0.57892 (10970) SS BOND : bond 0.00304 ( 3) SS BOND : angle 0.45493 ( 6) hydrogen bonds : bond 0.03398 ( 392) hydrogen bonds : angle 4.04351 ( 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: 13 poor density : 130 time to evaluate : 0.334 Fit side-chains REVERT: A 45 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 20 ASP cc_start: 0.8646 (m-30) cc_final: 0.8352 (m-30) REVERT: B 43 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8728 (mp) REVERT: B 197 ARG cc_start: 0.8648 (mtp-110) cc_final: 0.8323 (ttm-80) REVERT: B 340 ASN cc_start: 0.8449 (t0) cc_final: 0.8100 (t0) REVERT: G 26 ASP cc_start: 0.8811 (t70) cc_final: 0.8610 (t0) REVERT: G 42 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8257 (tm-30) REVERT: N 3 GLN cc_start: 0.8713 (pt0) cc_final: 0.8234 (pp30) REVERT: N 32 TYR cc_start: 0.8859 (m-80) cc_final: 0.8618 (m-80) REVERT: N 105 ARG cc_start: 0.8305 (mtp85) cc_final: 0.8068 (mtp-110) REVERT: R 647 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8484 (mmtm) REVERT: R 659 GLN cc_start: 0.8668 (mp10) cc_final: 0.8431 (mm-40) REVERT: R 676 TRP cc_start: 0.7938 (OUTLIER) cc_final: 0.7620 (t-100) REVERT: R 726 TYR cc_start: 0.8190 (t80) cc_final: 0.7448 (t80) REVERT: R 768 ASP cc_start: 0.7605 (p0) cc_final: 0.7260 (p0) REVERT: R 796 MET cc_start: 0.8541 (tpp) cc_final: 0.8239 (tpp) REVERT: R 809 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8298 (mttt) outliers start: 13 outliers final: 10 residues processed: 137 average time/residue: 0.6536 time to fit residues: 94.1895 Evaluate side-chains 142 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 58 ILE Chi-restraints excluded: chain B residue 146 LEU 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: 0.7980 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 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 = 0.3417 r_free = 0.3417 target = 0.094153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075971 restraints weight = 15033.016| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.61 r_work: 0.2955 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2336 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= 0.131 Angle : 0.582 8.873 10976 Z= 0.297 Chirality : 0.041 0.151 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.036 37.452 1153 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.43 % Allowed : 22.38 % 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: 0.39 (0.27), residues: 991 helix: 1.89 (0.27), residues: 367 sheet: -0.45 (0.34), residues: 223 loop : -0.82 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.014 0.001 TYR A 358 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 covalent geometry : bond 0.00302 ( 8089) covalent geometry : angle 0.58214 (10970) SS BOND : bond 0.00309 ( 3) SS BOND : angle 0.44058 ( 6) hydrogen bonds : bond 0.03368 ( 392) hydrogen bonds : angle 4.02185 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3221.23 seconds wall clock time: 55 minutes 29.55 seconds (3329.55 seconds total)