Starting phenix.real_space_refine on Tue Jul 29 06:14:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xke_33249/07_2025/7xke_33249.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xke_33249/07_2025/7xke_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_2025/7xke_33249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2025/7xke_33249.map" model { file = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2025/7xke_33249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xke_33249/07_2025/7xke_33249.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 2, '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, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR: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: 5.39, per 1000 atoms: 0.68 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.89 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: 2.29 Time building geometry restraints manager: 2.50 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (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 TRP 0.009 0.001 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.001 PHE B 234 TYR 0.016 0.001 TYR A 358 ARG 0.006 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.13784 ( 392) hydrogen bonds : angle 5.88325 ( 1107) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.63784 ( 6) covalent geometry : bond 0.00638 ( 8089) covalent geometry : angle 0.56452 (10970) *********************** 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 : 0.893 Fit side-chains REVERT: A 45 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 278 ASN cc_start: 0.8593 (m-40) cc_final: 0.8274 (m110) REVERT: B 20 ASP cc_start: 0.8456 (m-30) cc_final: 0.8175 (m-30) REVERT: G 32 LYS cc_start: 0.8294 (tmtt) cc_final: 0.7926 (tmtt) REVERT: G 36 ASP cc_start: 0.7910 (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: 1.5310 time to fit residues: 257.8993 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 : 0.821 ------------------------------------------------------------------------------- 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 82 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.094530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075654 restraints weight = 14744.611| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.65 r_work: 0.2942 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1380 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= 0.144 Angle : 0.544 7.003 10976 Z= 0.290 Chirality : 0.041 0.145 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.301 47.097 1155 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.31 % Allowed : 12.62 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 991 helix: 1.94 (0.28), residues: 365 sheet: -0.25 (0.35), residues: 223 loop : -0.85 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.001 PHE R 856 TYR 0.014 0.001 TYR A 358 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 392) hydrogen bonds : angle 4.50338 ( 1107) SS BOND : bond 0.00187 ( 3) SS BOND : angle 0.59945 ( 6) covalent geometry : bond 0.00326 ( 8089) covalent geometry : angle 0.54375 (10970) *********************** 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 142 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.189 Fit side-chains REVERT: A 45 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 299 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8793 (mm-30) REVERT: B 20 ASP cc_start: 0.8611 (m-30) cc_final: 0.8336 (m-30) REVERT: B 197 ARG cc_start: 0.8723 (mtp-110) cc_final: 0.8359 (mtp-110) REVERT: B 340 ASN cc_start: 0.8541 (t0) cc_final: 0.8234 (t0) REVERT: G 32 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8217 (tmtt) REVERT: G 42 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8020 (tm-30) REVERT: N 65 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8598 (mmmm) REVERT: R 650 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8195 (mmp80) REVERT: R 676 TRP cc_start: 0.7933 (OUTLIER) cc_final: 0.7555 (t-100) REVERT: R 809 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8453 (mttt) REVERT: R 822 GLN cc_start: 0.7195 (tm-30) cc_final: 0.6642 (tm-30) REVERT: R 853 MET cc_start: 0.7984 (tmm) cc_final: 0.7765 (tmm) outliers start: 11 outliers final: 4 residues processed: 138 average time/residue: 1.4177 time to fit residues: 205.8767 Evaluate side-chains 131 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 299 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 3 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 = 0.3425 r_free = 0.3425 target = 0.094679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.076312 restraints weight = 14965.894| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.66 r_work: 0.2953 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1654 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= 0.124 Angle : 0.508 6.901 10976 Z= 0.270 Chirality : 0.040 0.143 1249 Planarity : 0.003 0.042 1383 Dihedral : 4.097 44.647 1153 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.90 % Allowed : 15.95 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 991 helix: 1.94 (0.27), residues: 365 sheet: -0.26 (0.35), residues: 223 loop : -0.83 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE R 856 TYR 0.016 0.001 TYR A 358 ARG 0.007 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 392) hydrogen bonds : angle 4.19381 ( 1107) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.52421 ( 6) covalent geometry : bond 0.00277 ( 8089) covalent geometry : angle 0.50819 (10970) *********************** 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: 16 poor density : 134 time to evaluate : 0.855 Fit side-chains REVERT: A 45 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 392 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8797 (mt-10) REVERT: B 20 ASP cc_start: 0.8653 (m-30) cc_final: 0.8389 (m-30) REVERT: B 32 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8858 (pm20) REVERT: B 43 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8806 (mp) REVERT: B 197 ARG cc_start: 0.8642 (mtp-110) cc_final: 0.8253 (mtp-110) REVERT: B 340 ASN cc_start: 0.8455 (t0) cc_final: 0.8074 (m-40) REVERT: G 42 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8150 (tm-30) REVERT: R 659 GLN cc_start: 0.8680 (mp10) cc_final: 0.8361 (mm-40) REVERT: R 676 TRP cc_start: 0.7916 (OUTLIER) cc_final: 0.7562 (t-100) REVERT: R 791 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8496 (tt) REVERT: R 809 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8325 (mttt) REVERT: R 822 GLN cc_start: 0.7317 (tm-30) cc_final: 0.6709 (tm-30) outliers start: 16 outliers final: 5 residues processed: 141 average time/residue: 1.3753 time to fit residues: 203.9784 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 : 1.000 ------------------------------------------------------------------------------- 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 36 ASP 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 3 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.094676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076429 restraints weight = 14882.812| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.62 r_work: 0.2955 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1827 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= 0.128 Angle : 0.514 7.224 10976 Z= 0.274 Chirality : 0.040 0.146 1249 Planarity : 0.003 0.043 1383 Dihedral : 4.124 43.402 1153 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.26 % Allowed : 18.21 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 991 helix: 1.73 (0.27), residues: 371 sheet: -0.32 (0.35), residues: 220 loop : -0.80 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE R 856 TYR 0.014 0.001 TYR N 80 ARG 0.006 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 392) hydrogen bonds : angle 4.17229 ( 1107) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.45431 ( 6) covalent geometry : bond 0.00288 ( 8089) covalent geometry : angle 0.51355 (10970) *********************** 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 152 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.822 Fit side-chains REVERT: A 45 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 392 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8808 (mt-10) REVERT: B 20 ASP cc_start: 0.8650 (m-30) cc_final: 0.8386 (m-30) REVERT: B 43 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8834 (mp) REVERT: B 340 ASN cc_start: 0.8499 (t0) cc_final: 0.8087 (m-40) REVERT: G 36 ASP cc_start: 0.8942 (m-30) cc_final: 0.8365 (t0) REVERT: G 42 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8145 (tm-30) REVERT: N 76 LYS cc_start: 0.9322 (mmtm) cc_final: 0.9110 (mmmm) REVERT: N 105 ARG cc_start: 0.8307 (mtp85) cc_final: 0.8021 (mtp-110) REVERT: R 659 GLN cc_start: 0.8658 (mp10) cc_final: 0.8357 (mm-40) REVERT: R 676 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.7543 (t-100) REVERT: R 791 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8490 (tt) REVERT: R 809 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8325 (mttt) outliers start: 19 outliers final: 5 residues processed: 143 average time/residue: 1.3355 time to fit residues: 201.3035 Evaluate side-chains 135 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 791 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.091676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.073234 restraints weight = 14896.450| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.60 r_work: 0.2918 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8092 Z= 0.194 Angle : 0.556 7.202 10976 Z= 0.295 Chirality : 0.042 0.167 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.269 42.114 1153 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.50 % Allowed : 18.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 991 helix: 1.76 (0.27), residues: 365 sheet: -0.38 (0.35), residues: 223 loop : -0.84 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.002 PHE B 180 TYR 0.015 0.001 TYR A 339 ARG 0.006 0.001 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 392) hydrogen bonds : angle 4.27661 ( 1107) SS BOND : bond 0.00252 ( 3) SS BOND : angle 0.74171 ( 6) covalent geometry : bond 0.00447 ( 8089) covalent geometry : angle 0.55548 (10970) *********************** 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 151 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.914 Fit side-chains REVERT: A 45 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8448 (tm-30) REVERT: B 20 ASP cc_start: 0.8663 (m-30) cc_final: 0.8397 (m-30) REVERT: B 43 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8893 (mp) REVERT: B 197 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8370 (mtp-110) REVERT: B 340 ASN cc_start: 0.8486 (t0) cc_final: 0.8124 (t0) REVERT: G 26 ASP cc_start: 0.8829 (t70) cc_final: 0.8615 (t0) REVERT: G 36 ASP cc_start: 0.8902 (m-30) cc_final: 0.8693 (m-30) REVERT: G 42 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8285 (tm-30) REVERT: N 3 GLN cc_start: 0.8764 (pt0) cc_final: 0.8278 (pp30) REVERT: N 65 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8705 (mmmm) REVERT: N 76 LYS cc_start: 0.9280 (mmtm) cc_final: 0.9064 (mmmm) REVERT: N 105 ARG cc_start: 0.8342 (mtp85) cc_final: 0.8062 (mtp-110) REVERT: R 659 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8394 (mm-40) REVERT: R 676 TRP cc_start: 0.7874 (OUTLIER) cc_final: 0.7533 (t-100) REVERT: R 768 ASP cc_start: 0.7562 (p0) cc_final: 0.7268 (p0) REVERT: R 809 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8329 (mttt) outliers start: 21 outliers final: 6 residues processed: 141 average time/residue: 1.3879 time to fit residues: 206.1277 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 : 0.961 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.092475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.074219 restraints weight = 14870.403| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.59 r_work: 0.2939 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2091 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= 0.156 Angle : 0.550 7.731 10976 Z= 0.289 Chirality : 0.041 0.148 1249 Planarity : 0.003 0.041 1383 Dihedral : 4.206 40.599 1153 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.26 % Allowed : 19.88 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 991 helix: 1.78 (0.27), residues: 365 sheet: -0.45 (0.35), residues: 218 loop : -0.85 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.012 0.001 TYR A 339 ARG 0.007 0.001 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 392) hydrogen bonds : angle 4.18395 ( 1107) SS BOND : bond 0.00364 ( 3) SS BOND : angle 0.69589 ( 6) covalent geometry : bond 0.00360 ( 8089) covalent geometry : angle 0.54982 (10970) *********************** 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 148 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.948 Fit side-chains REVERT: A 45 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8437 (tm-30) REVERT: B 20 ASP cc_start: 0.8620 (m-30) cc_final: 0.8357 (m-30) REVERT: B 43 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 340 ASN cc_start: 0.8541 (t0) cc_final: 0.8176 (t0) REVERT: G 26 ASP cc_start: 0.8824 (t70) cc_final: 0.8608 (t0) REVERT: G 42 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8263 (tm-30) REVERT: N 3 GLN cc_start: 0.8781 (pt0) cc_final: 0.8290 (pp30) REVERT: N 65 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8720 (mmmm) REVERT: N 105 ARG cc_start: 0.8369 (mtp85) cc_final: 0.8102 (mtp-110) REVERT: R 659 GLN cc_start: 0.8691 (mp10) cc_final: 0.8380 (mm-40) REVERT: R 676 TRP cc_start: 0.7865 (OUTLIER) cc_final: 0.7501 (t-100) REVERT: R 768 ASP cc_start: 0.7555 (p0) cc_final: 0.7240 (p0) REVERT: R 809 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8317 (mttt) outliers start: 19 outliers final: 8 residues processed: 141 average time/residue: 1.3731 time to fit residues: 203.8966 Evaluate side-chains 134 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 72 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3397 r_free = 0.3397 target = 0.093102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074966 restraints weight = 15016.009| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.61 r_work: 0.2953 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2174 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= 0.140 Angle : 0.563 8.956 10976 Z= 0.291 Chirality : 0.041 0.148 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.139 39.719 1153 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.02 % Allowed : 20.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 991 helix: 1.80 (0.27), residues: 366 sheet: -0.44 (0.35), residues: 223 loop : -0.79 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.013 0.001 TYR B 264 ARG 0.008 0.001 ARG R 825 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 392) hydrogen bonds : angle 4.12454 ( 1107) SS BOND : bond 0.00336 ( 3) SS BOND : angle 0.64650 ( 6) covalent geometry : bond 0.00323 ( 8089) covalent geometry : angle 0.56335 (10970) *********************** 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 149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.844 Fit side-chains REVERT: A 45 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8432 (tm-30) REVERT: B 20 ASP cc_start: 0.8622 (m-30) cc_final: 0.8356 (m-30) REVERT: B 43 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8854 (mp) REVERT: B 197 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8043 (mtp-110) REVERT: B 340 ASN cc_start: 0.8466 (t0) cc_final: 0.8168 (t0) REVERT: G 26 ASP cc_start: 0.8809 (t70) cc_final: 0.8582 (t0) REVERT: G 42 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8247 (tm-30) REVERT: N 3 GLN cc_start: 0.8773 (pt0) cc_final: 0.8286 (pp30) REVERT: N 105 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8074 (mtp-110) REVERT: R 659 GLN cc_start: 0.8670 (mp10) cc_final: 0.8365 (mm-40) REVERT: R 676 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7471 (t-100) REVERT: R 768 ASP cc_start: 0.7588 (p0) cc_final: 0.7266 (p0) REVERT: R 809 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8305 (mttt) outliers start: 17 outliers final: 10 residues processed: 142 average time/residue: 1.3753 time to fit residues: 205.6975 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 : 0.928 ------------------------------------------------------------------------------- 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 54 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0270 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN G 18 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 = 0.093991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075863 restraints weight = 15023.430| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.60 r_work: 0.2944 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2234 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= 0.127 Angle : 0.567 11.543 10976 Z= 0.290 Chirality : 0.041 0.148 1249 Planarity : 0.003 0.042 1383 Dihedral : 4.051 38.675 1153 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.79 % Allowed : 21.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 991 helix: 1.85 (0.27), residues: 366 sheet: -0.41 (0.35), residues: 218 loop : -0.78 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 856 TYR 0.013 0.001 TYR A 358 ARG 0.008 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 392) hydrogen bonds : angle 4.03934 ( 1107) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.56590 ( 6) covalent geometry : bond 0.00292 ( 8089) covalent geometry : angle 0.56694 (10970) *********************** 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 147 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.799 Fit side-chains REVERT: A 45 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8440 (tm-30) REVERT: B 20 ASP cc_start: 0.8626 (m-30) cc_final: 0.8358 (m-30) REVERT: B 32 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8787 (pm20) REVERT: B 43 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8742 (mp) REVERT: B 59 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8515 (t80) REVERT: B 197 ARG cc_start: 0.8562 (mtp-110) cc_final: 0.8054 (mtp-110) REVERT: B 340 ASN cc_start: 0.8446 (t0) cc_final: 0.8128 (t0) REVERT: G 26 ASP cc_start: 0.8822 (t70) cc_final: 0.8607 (t0) REVERT: N 3 GLN cc_start: 0.8743 (pt0) cc_final: 0.8296 (pp30) REVERT: N 32 TYR cc_start: 0.8839 (m-80) cc_final: 0.8566 (m-80) REVERT: N 105 ARG cc_start: 0.8329 (mtp85) cc_final: 0.8093 (mtp-110) REVERT: R 659 GLN cc_start: 0.8648 (mp10) cc_final: 0.8358 (mm-40) REVERT: R 676 TRP cc_start: 0.7893 (OUTLIER) cc_final: 0.7561 (t-100) REVERT: R 726 TYR cc_start: 0.8188 (t80) cc_final: 0.7436 (t80) REVERT: R 768 ASP cc_start: 0.7563 (p0) cc_final: 0.7219 (p0) REVERT: R 809 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8318 (mttt) outliers start: 15 outliers final: 10 residues processed: 139 average time/residue: 1.4677 time to fit residues: 214.4437 Evaluate side-chains 149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 751 ASP 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 93 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 0.0010 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 0.0030 chunk 12 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.095102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076999 restraints weight = 15117.388| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.62 r_work: 0.2968 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2276 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= 0.116 Angle : 0.560 8.480 10976 Z= 0.290 Chirality : 0.040 0.144 1249 Planarity : 0.004 0.041 1383 Dihedral : 3.968 38.255 1153 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 991 helix: 1.80 (0.27), residues: 372 sheet: -0.41 (0.35), residues: 223 loop : -0.70 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 856 TYR 0.013 0.001 TYR A 358 ARG 0.009 0.001 ARG R 825 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 392) hydrogen bonds : angle 3.98719 ( 1107) SS BOND : bond 0.00304 ( 3) SS BOND : angle 0.44824 ( 6) covalent geometry : bond 0.00264 ( 8089) covalent geometry : angle 0.56042 (10970) *********************** 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 149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.859 Fit side-chains REVERT: A 45 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 20 ASP cc_start: 0.8646 (m-30) cc_final: 0.8380 (m-30) REVERT: B 43 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8698 (mp) REVERT: B 59 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8488 (t80) REVERT: B 197 ARG cc_start: 0.8551 (mtp-110) cc_final: 0.8044 (mtp-110) REVERT: B 340 ASN cc_start: 0.8466 (t0) cc_final: 0.8118 (t0) REVERT: G 26 ASP cc_start: 0.8828 (t70) cc_final: 0.8605 (t0) REVERT: N 3 GLN cc_start: 0.8726 (pt0) cc_final: 0.8342 (pp30) REVERT: N 32 TYR cc_start: 0.8836 (m-80) cc_final: 0.8523 (m-80) REVERT: N 105 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8103 (mtp-110) REVERT: R 659 GLN cc_start: 0.8640 (mp10) cc_final: 0.8371 (mm-40) REVERT: R 676 TRP cc_start: 0.7937 (OUTLIER) cc_final: 0.7610 (t-100) REVERT: R 726 TYR cc_start: 0.8169 (t80) cc_final: 0.7479 (t80) REVERT: R 768 ASP cc_start: 0.7512 (p0) cc_final: 0.7154 (p0) REVERT: R 809 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8289 (mttt) outliers start: 13 outliers final: 11 residues processed: 142 average time/residue: 1.4668 time to fit residues: 218.3848 Evaluate side-chains 141 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 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 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 751 ASP 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 86 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.093956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075778 restraints weight = 14855.834| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.59 r_work: 0.2953 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2268 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= 0.144 Angle : 0.604 8.938 10976 Z= 0.312 Chirality : 0.041 0.151 1249 Planarity : 0.004 0.042 1383 Dihedral : 4.005 37.898 1153 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.67 % Allowed : 22.26 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.27), residues: 991 helix: 1.82 (0.27), residues: 371 sheet: -0.41 (0.35), residues: 223 loop : -0.70 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 856 TYR 0.014 0.001 TYR A 358 ARG 0.009 0.001 ARG R 825 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 392) hydrogen bonds : angle 4.01664 ( 1107) SS BOND : bond 0.00321 ( 3) SS BOND : angle 0.52066 ( 6) covalent geometry : bond 0.00336 ( 8089) covalent geometry : angle 0.60387 (10970) ********************** 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 142 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.975 Fit side-chains REVERT: A 45 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8418 (tm-30) REVERT: B 20 ASP cc_start: 0.8644 (m-30) cc_final: 0.8365 (m-30) REVERT: B 43 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8702 (mp) REVERT: B 59 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8506 (t80) REVERT: B 197 ARG cc_start: 0.8552 (mtp-110) cc_final: 0.8041 (mtp-110) REVERT: B 340 ASN cc_start: 0.8482 (t0) cc_final: 0.8118 (t0) REVERT: G 26 ASP cc_start: 0.8824 (t70) cc_final: 0.8614 (t0) REVERT: N 3 GLN cc_start: 0.8727 (pt0) cc_final: 0.8254 (pp30) REVERT: N 32 TYR cc_start: 0.8856 (m-80) cc_final: 0.8635 (m-80) REVERT: N 105 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8038 (mtp-110) REVERT: R 659 GLN cc_start: 0.8646 (mp10) cc_final: 0.8345 (mm-40) REVERT: R 676 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.7600 (t-100) REVERT: R 726 TYR cc_start: 0.8221 (t80) cc_final: 0.7507 (t80) REVERT: R 768 ASP cc_start: 0.7575 (p0) cc_final: 0.7235 (p0) REVERT: R 809 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8295 (mttt) outliers start: 14 outliers final: 11 residues processed: 134 average time/residue: 1.4317 time to fit residues: 201.7759 Evaluate side-chains 140 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 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 751 ASP 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 32 optimal weight: 0.0030 chunk 42 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 88 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 32 GLN G 18 GLN N 120 GLN ** R 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.095555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077435 restraints weight = 14936.977| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.63 r_work: 0.2980 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8092 Z= 0.118 Angle : 0.585 8.586 10976 Z= 0.301 Chirality : 0.040 0.150 1249 Planarity : 0.004 0.041 1383 Dihedral : 3.890 37.335 1153 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.79 % Allowed : 22.86 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 991 helix: 1.85 (0.27), residues: 372 sheet: -0.39 (0.35), residues: 223 loop : -0.66 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 856 TYR 0.012 0.001 TYR A 358 ARG 0.008 0.000 ARG R 825 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 392) hydrogen bonds : angle 3.94734 ( 1107) SS BOND : bond 0.00315 ( 3) SS BOND : angle 0.38103 ( 6) covalent geometry : bond 0.00274 ( 8089) covalent geometry : angle 0.58516 (10970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6756.69 seconds wall clock time: 115 minutes 53.57 seconds (6953.57 seconds total)