Starting phenix.real_space_refine on Sun Aug 24 11:46:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8udg_42149/08_2025/8udg_42149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8udg_42149/08_2025/8udg_42149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8udg_42149/08_2025/8udg_42149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8udg_42149/08_2025/8udg_42149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8udg_42149/08_2025/8udg_42149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8udg_42149/08_2025/8udg_42149.map" } resolution = 4.98 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= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians S 43 5.16 5 C 6158 2.51 5 N 1683 2.21 5 O 2013 1.98 5 H 9627 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19524 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2383 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2384 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "C" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2385 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "H" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3160 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3025 Classifications: {'peptide': 209} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3161 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3026 Classifications: {'peptide': 209} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.10, per 1000 atoms: 0.21 Number of scatterers: 19524 At special positions: 0 Unit cell: (99, 176.344, 165.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 O 2013 8.00 N 1683 7.00 C 6158 6.00 H 9627 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 146 " - pdb=" SG CYS M 202 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 197 " distance=2.04 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: 1.81 Conformation dependent library (CDL) restraints added in 711.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 25 sheets defined 28.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 26 through 105 removed outlier: 3.700A pdb=" N HIS A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.579A pdb=" N GLY A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 105 removed outlier: 3.543A pdb=" N HIS B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 125 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.699A pdb=" N GLY B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 105 removed outlier: 3.712A pdb=" N HIS C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 125 Processing helix chain 'C' and resid 145 through 155 removed outlier: 3.625A pdb=" N GLY C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.623A pdb=" N LEU H 195 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 186 through 192 removed outlier: 3.582A pdb=" N SER L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS L 192 " --> pdb=" O GLN L 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 191 through 195 removed outlier: 3.618A pdb=" N LEU M 195 " --> pdb=" O SER M 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 125 through 131 Processing helix chain 'N' and resid 186 through 191 removed outlier: 3.665A pdb=" N SER N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 134 removed outlier: 6.633A pdb=" N CYS A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.628A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.020A pdb=" N CYS H 96 " --> pdb=" O TRP H 109 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TRP H 109 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG H 98 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.005A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.005A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 157 through 160 removed outlier: 4.765A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.416A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.416A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'L' and resid 120 through 122 removed outlier: 5.940A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 157 through 158 Processing sheet with id=AB6, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.649A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.948A pdb=" N CYS M 96 " --> pdb=" O TRP M 109 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP M 109 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG M 98 " --> pdb=" O ASP M 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 126 through 130 removed outlier: 4.920A pdb=" N ALA M 143 " --> pdb=" O VAL M 190 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY M 145 " --> pdb=" O VAL M 188 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL M 188 " --> pdb=" O GLY M 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU M 147 " --> pdb=" O SER M 186 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER M 186 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS M 149 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU M 184 " --> pdb=" O LYS M 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 126 through 130 removed outlier: 4.920A pdb=" N ALA M 143 " --> pdb=" O VAL M 190 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY M 145 " --> pdb=" O VAL M 188 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL M 188 " --> pdb=" O GLY M 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU M 147 " --> pdb=" O SER M 186 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER M 186 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS M 149 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU M 184 " --> pdb=" O LYS M 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 157 through 160 removed outlier: 4.530A pdb=" N TYR M 200 " --> pdb=" O VAL M 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.368A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AC5, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AC6, first strand: chain 'N' and resid 120 through 122 removed outlier: 6.020A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 157 through 158 562 hydrogen bonds defined for protein. 1458 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: 4.82 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9620 1.03 - 1.23: 18 1.23 - 1.42: 4161 1.42 - 1.62: 5854 1.62 - 1.82: 57 Bond restraints: 19710 Sorted by residual: bond pdb=" C SER L 157 " pdb=" N PRO L 158 " ideal model delta sigma weight residual 1.333 1.355 -0.021 1.01e-02 9.80e+03 4.53e+00 bond pdb=" C SER N 157 " pdb=" N PRO N 158 " ideal model delta sigma weight residual 1.333 1.354 -0.021 1.01e-02 9.80e+03 4.22e+00 bond pdb=" N ALA M 120 " pdb=" CA ALA M 120 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.20e-02 6.94e+03 3.28e+00 bond pdb=" C SER M 119 " pdb=" N ALA M 120 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.27e-02 6.20e+03 1.20e+00 bond pdb=" CA VAL H 190 " pdb=" C VAL H 190 " ideal model delta sigma weight residual 1.516 1.526 -0.011 1.11e-02 8.12e+03 9.25e-01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 32544 1.07 - 2.14: 2738 2.14 - 3.20: 217 3.20 - 4.27: 71 4.27 - 5.34: 29 Bond angle restraints: 35599 Sorted by residual: angle pdb=" N VAL H 190 " pdb=" CA VAL H 190 " pdb=" C VAL H 190 " ideal model delta sigma weight residual 109.19 106.11 3.08 8.20e-01 1.49e+00 1.42e+01 angle pdb=" CA VAL H 190 " pdb=" C VAL H 190 " pdb=" N PRO H 191 " ideal model delta sigma weight residual 116.57 120.18 -3.61 9.80e-01 1.04e+00 1.35e+01 angle pdb=" C VAL H 190 " pdb=" CA VAL H 190 " pdb=" CB VAL H 190 " ideal model delta sigma weight residual 109.33 112.38 -3.05 9.80e-01 1.04e+00 9.67e+00 angle pdb=" N GLY H 145 " pdb=" CA GLY H 145 " pdb=" C GLY H 145 " ideal model delta sigma weight residual 111.27 116.40 -5.13 1.67e+00 3.59e-01 9.44e+00 angle pdb=" O SER M 119 " pdb=" C SER M 119 " pdb=" N ALA M 120 " ideal model delta sigma weight residual 122.68 119.07 3.61 1.27e+00 6.20e-01 8.10e+00 ... (remaining 35594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 8574 16.98 - 33.96: 563 33.96 - 50.94: 167 50.94 - 67.92: 74 67.92 - 84.91: 20 Dihedral angle restraints: 9398 sinusoidal: 5099 harmonic: 4299 Sorted by residual: dihedral pdb=" CA SER M 119 " pdb=" C SER M 119 " pdb=" N ALA M 120 " pdb=" CA ALA M 120 " ideal model delta harmonic sigma weight residual 180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 90 " pdb=" CB CYS N 90 " ideal model delta sinusoidal sigma weight residual 93.00 57.52 35.48 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA CYS M 99 " pdb=" C CYS M 99 " pdb=" N VAL M 100 " pdb=" CA VAL M 100 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1071 0.034 - 0.068: 362 0.068 - 0.101: 96 0.101 - 0.135: 45 0.135 - 0.169: 11 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA VAL M 148 " pdb=" N VAL M 148 " pdb=" C VAL M 148 " pdb=" CB VAL M 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA VAL H 190 " pdb=" N VAL H 190 " pdb=" C VAL H 190 " pdb=" CB VAL H 190 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA VAL H 148 " pdb=" N VAL H 148 " pdb=" C VAL H 148 " pdb=" CB VAL H 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1582 not shown) Planarity restraints: 3015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 119 " 0.024 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C SER M 119 " -0.079 2.00e-02 2.50e+03 pdb=" O SER M 119 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA M 120 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 33 " -0.013 2.00e-02 2.50e+03 8.89e-03 2.37e+00 pdb=" CG TYR M 33 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR M 33 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR M 33 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR M 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR M 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR M 33 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR M 33 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR M 33 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR M 33 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR M 33 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR M 33 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 79 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C GLU A 79 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU A 79 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 80 " -0.009 2.00e-02 2.50e+03 ... (remaining 3012 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2170 2.25 - 2.84: 44806 2.84 - 3.42: 50208 3.42 - 4.01: 69800 4.01 - 4.60: 107200 Nonbonded interactions: 274184 Sorted by model distance: nonbonded pdb=" H SER H 162 " pdb=" OD1 ASN H 203 " model vdw 1.662 2.450 nonbonded pdb=" H GLN L 171 " pdb=" O LYS L 175 " model vdw 1.664 2.450 nonbonded pdb=" O ASP B 37 " pdb=" HG1 THR B 41 " model vdw 1.674 2.450 nonbonded pdb=" OE1 GLN A 42 " pdb=" H ILE C 172 " model vdw 1.680 2.450 nonbonded pdb=" H GLY M 15 " pdb=" O LEU M 86 " model vdw 1.685 2.450 ... (remaining 274179 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 23 through 135 or (resid 136 and (name N or name CA or nam \ e C or name O or name HA2 or name HA3)) or resid 137 through 181)) selection = (chain 'C' and (resid 23 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name H \ B2 or name HB3 or name HD21 or name HD22)) or (resid 136 and (name N or name CA \ or name C or name O or name HA2 or name HA3)) or resid 137 through 181)) } ncs_group { reference = chain 'H' selection = (chain 'M' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2)) or resid 34 through 219)) } ncs_group { reference = chain 'L' selection = (chain 'N' and (resid 1 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 98 through 213)) } 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 group one per residue 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.040 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.004 0.028 10094 Z= 0.182 Angle : 0.650 5.339 13721 Z= 0.377 Chirality : 0.041 0.169 1585 Planarity : 0.005 0.046 1772 Dihedral : 11.434 84.819 3614 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: -0.18 (0.23), residues: 1293 helix: 0.94 (0.25), residues: 340 sheet: -0.41 (0.23), residues: 456 loop : -0.40 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 193 TYR 0.025 0.002 TYR H 33 PHE 0.009 0.002 PHE A 157 TRP 0.019 0.002 TRP M 50 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00352 (10083) covalent geometry : angle 0.64945 (13699) SS BOND : bond 0.00216 ( 11) SS BOND : angle 1.06216 ( 22) hydrogen bonds : bond 0.18237 ( 521) hydrogen bonds : angle 7.54637 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.9479 (mt) cc_final: 0.9205 (tp) REVERT: A 108 ILE cc_start: 0.9416 (mt) cc_final: 0.9129 (tt) REVERT: B 43 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9009 (mt-10) REVERT: B 66 LEU cc_start: 0.9468 (mt) cc_final: 0.9160 (mt) REVERT: B 119 GLU cc_start: 0.9442 (mt-10) cc_final: 0.8928 (mm-30) REVERT: B 121 LYS cc_start: 0.9484 (tttt) cc_final: 0.9270 (tttp) REVERT: B 140 THR cc_start: 0.5970 (m) cc_final: 0.5748 (m) REVERT: C 122 LEU cc_start: 0.9653 (mt) cc_final: 0.9419 (mt) REVERT: C 158 ASN cc_start: 0.9138 (t0) cc_final: 0.8918 (t0) REVERT: H 106 PHE cc_start: 0.9369 (m-80) cc_final: 0.8986 (m-10) REVERT: L 75 LEU cc_start: 0.9329 (tp) cc_final: 0.9099 (tp) REVERT: M 45 LEU cc_start: 0.9344 (mt) cc_final: 0.9131 (mp) REVERT: M 48 MET cc_start: 0.9524 (mtp) cc_final: 0.9227 (mtp) REVERT: N 195 TYR cc_start: 0.9051 (m-80) cc_final: 0.8747 (m-80) REVERT: N 197 CYS cc_start: 0.7015 (t) cc_final: 0.6261 (p) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3021 time to fit residues: 106.3698 Evaluate side-chains 183 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN H 39 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS L 198 GLN N 188 GLN N 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.050182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.035013 restraints weight = 212792.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.037367 restraints weight = 121248.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039207 restraints weight = 79344.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.040591 restraints weight = 56697.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.041613 restraints weight = 43394.246| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 10094 Z= 0.176 Angle : 0.562 16.489 13721 Z= 0.311 Chirality : 0.038 0.139 1585 Planarity : 0.004 0.056 1772 Dihedral : 4.425 18.491 1375 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.21 % Rotamer: Outliers : 0.18 % Allowed : 1.44 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: 0.54 (0.24), residues: 1293 helix: 2.57 (0.25), residues: 352 sheet: -0.40 (0.23), residues: 458 loop : -0.42 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 54 TYR 0.011 0.001 TYR M 33 PHE 0.014 0.001 PHE H 101 TRP 0.007 0.001 TRP H 47 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00378 (10083) covalent geometry : angle 0.54216 (13699) SS BOND : bond 0.00656 ( 11) SS BOND : angle 3.76945 ( 22) hydrogen bonds : bond 0.04520 ( 521) hydrogen bonds : angle 5.38459 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9139 (mt) cc_final: 0.8823 (tt) REVERT: B 119 GLU cc_start: 0.9406 (mt-10) cc_final: 0.8974 (mm-30) REVERT: B 125 MET cc_start: 0.8374 (mtp) cc_final: 0.8133 (mtp) REVERT: C 64 GLN cc_start: 0.9642 (mt0) cc_final: 0.9330 (mm110) REVERT: C 81 ASP cc_start: 0.9479 (t70) cc_final: 0.9192 (t0) REVERT: C 85 ASP cc_start: 0.9367 (m-30) cc_final: 0.9149 (m-30) REVERT: H 37 MET cc_start: 0.9231 (mmp) cc_final: 0.8910 (tmm) REVERT: H 48 MET cc_start: 0.9327 (mtp) cc_final: 0.8975 (mtp) REVERT: H 106 PHE cc_start: 0.9500 (m-80) cc_final: 0.9238 (m-10) REVERT: L 75 LEU cc_start: 0.9402 (tp) cc_final: 0.9120 (tp) REVERT: L 138 CYS cc_start: 0.7345 (t) cc_final: 0.6605 (t) REVERT: M 45 LEU cc_start: 0.9341 (mt) cc_final: 0.9134 (mp) REVERT: N 64 PHE cc_start: 0.9289 (m-80) cc_final: 0.9061 (m-80) REVERT: N 164 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8124 (mp0) REVERT: N 181 TYR cc_start: 0.9076 (m-10) cc_final: 0.8680 (m-80) REVERT: N 197 CYS cc_start: 0.7814 (t) cc_final: 0.7209 (t) outliers start: 2 outliers final: 0 residues processed: 199 average time/residue: 0.3119 time to fit residues: 80.9833 Evaluate side-chains 157 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 142 HIS C 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.048448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.033753 restraints weight = 220581.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035971 restraints weight = 126986.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.037713 restraints weight = 83807.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.038983 restraints weight = 60614.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.039980 restraints weight = 47066.442| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 10094 Z= 0.202 Angle : 0.565 9.254 13721 Z= 0.314 Chirality : 0.039 0.182 1585 Planarity : 0.004 0.043 1772 Dihedral : 4.590 29.931 1375 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.75 % Rotamer: Outliers : 0.09 % Allowed : 1.44 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: 0.19 (0.23), residues: 1293 helix: 1.94 (0.25), residues: 355 sheet: -0.34 (0.24), residues: 442 loop : -0.68 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.010 0.001 TYR H 151 PHE 0.011 0.001 PHE A 157 TRP 0.012 0.001 TRP H 160 HIS 0.009 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00396 (10083) covalent geometry : angle 0.55903 (13699) SS BOND : bond 0.00360 ( 11) SS BOND : angle 2.15449 ( 22) hydrogen bonds : bond 0.04181 ( 521) hydrogen bonds : angle 5.35042 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 GLU cc_start: 0.9457 (pt0) cc_final: 0.9242 (pt0) REVERT: B 119 GLU cc_start: 0.9407 (mt-10) cc_final: 0.8887 (mm-30) REVERT: C 59 GLU cc_start: 0.9582 (tp30) cc_final: 0.9170 (tp30) REVERT: H 106 PHE cc_start: 0.9480 (m-80) cc_final: 0.9200 (m-10) REVERT: L 75 LEU cc_start: 0.9433 (tp) cc_final: 0.9143 (tp) REVERT: L 138 CYS cc_start: 0.7534 (t) cc_final: 0.7097 (t) REVERT: M 48 MET cc_start: 0.9191 (mtp) cc_final: 0.8760 (mtp) REVERT: N 64 PHE cc_start: 0.9287 (m-80) cc_final: 0.8994 (m-80) REVERT: N 138 CYS cc_start: 0.7131 (t) cc_final: 0.6860 (t) REVERT: N 197 CYS cc_start: 0.7682 (t) cc_final: 0.7178 (t) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.3153 time to fit residues: 70.5833 Evaluate side-chains 142 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 46 optimal weight: 0.0970 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN C 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.049772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.034723 restraints weight = 215185.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.037048 restraints weight = 123289.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.038857 restraints weight = 81202.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040257 restraints weight = 58308.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041291 restraints weight = 44614.524| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10094 Z= 0.107 Angle : 0.482 7.374 13721 Z= 0.261 Chirality : 0.039 0.149 1585 Planarity : 0.003 0.037 1772 Dihedral : 4.288 32.505 1375 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.48 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.71 (0.24), residues: 1293 helix: 2.72 (0.25), residues: 355 sheet: -0.19 (0.24), residues: 444 loop : -0.51 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 193 TYR 0.010 0.001 TYR N 38 PHE 0.010 0.001 PHE A 167 TRP 0.022 0.001 TRP M 160 HIS 0.004 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00233 (10083) covalent geometry : angle 0.47794 (13699) SS BOND : bond 0.00238 ( 11) SS BOND : angle 1.63949 ( 22) hydrogen bonds : bond 0.03662 ( 521) hydrogen bonds : angle 4.73331 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ILE cc_start: 0.9787 (tp) cc_final: 0.9580 (pt) REVERT: B 97 GLU cc_start: 0.9399 (pt0) cc_final: 0.9198 (pt0) REVERT: B 119 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8919 (mm-30) REVERT: H 106 PHE cc_start: 0.9352 (m-80) cc_final: 0.8939 (m-10) REVERT: L 75 LEU cc_start: 0.9368 (tp) cc_final: 0.9122 (tp) REVERT: L 197 CYS cc_start: 0.8601 (t) cc_final: 0.8165 (t) REVERT: M 48 MET cc_start: 0.9249 (mtp) cc_final: 0.8964 (mtp) REVERT: N 64 PHE cc_start: 0.9269 (m-80) cc_final: 0.9000 (m-80) REVERT: N 138 CYS cc_start: 0.7110 (t) cc_final: 0.6873 (t) REVERT: N 197 CYS cc_start: 0.7739 (t) cc_final: 0.7315 (t) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2945 time to fit residues: 66.8937 Evaluate side-chains 146 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.047995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.033556 restraints weight = 224517.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.035762 restraints weight = 128569.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.037467 restraints weight = 84789.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038763 restraints weight = 61260.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.039687 restraints weight = 47358.226| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10094 Z= 0.171 Angle : 0.514 4.463 13721 Z= 0.289 Chirality : 0.038 0.137 1585 Planarity : 0.004 0.037 1772 Dihedral : 4.339 20.054 1375 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: 0.49 (0.23), residues: 1293 helix: 2.38 (0.25), residues: 358 sheet: -0.24 (0.24), residues: 440 loop : -0.60 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 88 TYR 0.009 0.001 TYR M 33 PHE 0.015 0.001 PHE A 167 TRP 0.009 0.001 TRP N 152 HIS 0.005 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00330 (10083) covalent geometry : angle 0.51332 (13699) SS BOND : bond 0.00311 ( 11) SS BOND : angle 0.91964 ( 22) hydrogen bonds : bond 0.03604 ( 521) hydrogen bonds : angle 4.91295 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8935 (mm-30) REVERT: L 75 LEU cc_start: 0.9440 (tp) cc_final: 0.9164 (tp) REVERT: L 138 CYS cc_start: 0.6967 (t) cc_final: 0.6359 (t) REVERT: L 197 CYS cc_start: 0.8667 (t) cc_final: 0.8212 (t) REVERT: M 48 MET cc_start: 0.9228 (mtp) cc_final: 0.8865 (mtp) REVERT: N 64 PHE cc_start: 0.9157 (m-80) cc_final: 0.8927 (m-80) REVERT: N 197 CYS cc_start: 0.7152 (t) cc_final: 0.6673 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3270 time to fit residues: 67.7377 Evaluate side-chains 137 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 57 optimal weight: 0.0970 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.048458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.033763 restraints weight = 215913.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036008 restraints weight = 123217.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.037763 restraints weight = 81109.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039100 restraints weight = 58467.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040080 restraints weight = 44902.032| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10094 Z= 0.113 Angle : 0.470 4.414 13721 Z= 0.258 Chirality : 0.038 0.149 1585 Planarity : 0.003 0.034 1772 Dihedral : 4.220 20.175 1375 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.71 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: 0.67 (0.24), residues: 1293 helix: 2.74 (0.25), residues: 358 sheet: -0.25 (0.24), residues: 444 loop : -0.55 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 72 TYR 0.036 0.001 TYR M 33 PHE 0.011 0.001 PHE B 138 TRP 0.010 0.001 TRP M 160 HIS 0.004 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00235 (10083) covalent geometry : angle 0.46997 (13699) SS BOND : bond 0.00385 ( 11) SS BOND : angle 0.57723 ( 22) hydrogen bonds : bond 0.03315 ( 521) hydrogen bonds : angle 4.68592 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.9552 (mt) cc_final: 0.9328 (mt) REVERT: B 119 GLU cc_start: 0.9429 (mt-10) cc_final: 0.8990 (mm-30) REVERT: C 125 MET cc_start: 0.9022 (mmp) cc_final: 0.8755 (mmm) REVERT: H 45 LEU cc_start: 0.9099 (mm) cc_final: 0.8746 (mm) REVERT: L 75 LEU cc_start: 0.9399 (tp) cc_final: 0.9120 (tp) REVERT: L 138 CYS cc_start: 0.6941 (t) cc_final: 0.6505 (t) REVERT: L 197 CYS cc_start: 0.8613 (t) cc_final: 0.8123 (t) REVERT: M 48 MET cc_start: 0.9196 (mtp) cc_final: 0.8850 (mtp) REVERT: N 64 PHE cc_start: 0.9273 (m-80) cc_final: 0.9054 (m-80) REVERT: N 138 CYS cc_start: 0.7177 (t) cc_final: 0.6898 (t) REVERT: N 197 CYS cc_start: 0.7602 (t) cc_final: 0.7186 (t) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3053 time to fit residues: 66.3461 Evaluate side-chains 139 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.046088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.032212 restraints weight = 234342.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.034299 restraints weight = 135921.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.035923 restraints weight = 90297.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.037146 restraints weight = 65536.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038058 restraints weight = 50810.730| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10094 Z= 0.266 Angle : 0.613 5.705 13721 Z= 0.351 Chirality : 0.039 0.137 1585 Planarity : 0.004 0.037 1772 Dihedral : 4.754 19.088 1375 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.88 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: -0.15 (0.23), residues: 1293 helix: 1.49 (0.25), residues: 358 sheet: -0.45 (0.25), residues: 446 loop : -0.84 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 72 TYR 0.030 0.002 TYR H 33 PHE 0.018 0.002 PHE A 157 TRP 0.016 0.002 TRP H 36 HIS 0.008 0.002 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00496 (10083) covalent geometry : angle 0.61232 (13699) SS BOND : bond 0.00559 ( 11) SS BOND : angle 1.03031 ( 22) hydrogen bonds : bond 0.03877 ( 521) hydrogen bonds : angle 5.48117 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.9524 (mt-10) cc_final: 0.9019 (mm-30) REVERT: C 59 GLU cc_start: 0.9601 (tp30) cc_final: 0.9222 (tp30) REVERT: C 125 MET cc_start: 0.9071 (mmp) cc_final: 0.8730 (mmm) REVERT: L 138 CYS cc_start: 0.7297 (t) cc_final: 0.6704 (t) REVERT: L 197 CYS cc_start: 0.8725 (t) cc_final: 0.8388 (t) REVERT: M 34 ILE cc_start: 0.9877 (mm) cc_final: 0.9606 (tp) REVERT: N 138 CYS cc_start: 0.7219 (t) cc_final: 0.6837 (t) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3185 time to fit residues: 58.7196 Evaluate side-chains 118 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 106 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN H 39 GLN H 177 GLN M 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.047668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.033227 restraints weight = 217096.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035448 restraints weight = 124083.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.037182 restraints weight = 81605.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.038483 restraints weight = 58663.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039478 restraints weight = 45129.028| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10094 Z= 0.114 Angle : 0.496 4.103 13721 Z= 0.270 Chirality : 0.039 0.149 1585 Planarity : 0.003 0.031 1772 Dihedral : 4.428 21.076 1375 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: 0.46 (0.24), residues: 1293 helix: 2.44 (0.25), residues: 358 sheet: -0.36 (0.25), residues: 444 loop : -0.58 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.030 0.001 TYR H 33 PHE 0.012 0.001 PHE A 157 TRP 0.009 0.001 TRP M 160 HIS 0.005 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00246 (10083) covalent geometry : angle 0.49413 (13699) SS BOND : bond 0.00405 ( 11) SS BOND : angle 1.08332 ( 22) hydrogen bonds : bond 0.03278 ( 521) hydrogen bonds : angle 4.80647 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.9510 (mt-10) cc_final: 0.8978 (mm-30) REVERT: C 125 MET cc_start: 0.9088 (mmp) cc_final: 0.8788 (mmm) REVERT: L 138 CYS cc_start: 0.6939 (t) cc_final: 0.6522 (t) REVERT: L 197 CYS cc_start: 0.8818 (t) cc_final: 0.8415 (t) REVERT: M 34 ILE cc_start: 0.9887 (mm) cc_final: 0.9567 (tp) REVERT: M 48 MET cc_start: 0.8444 (mtt) cc_final: 0.7883 (mtt) REVERT: M 93 LEU cc_start: 0.9605 (mm) cc_final: 0.9364 (tp) REVERT: N 64 PHE cc_start: 0.9222 (m-80) cc_final: 0.9007 (m-80) REVERT: N 75 LEU cc_start: 0.9194 (tp) cc_final: 0.8972 (tp) REVERT: N 138 CYS cc_start: 0.7296 (t) cc_final: 0.6841 (t) REVERT: N 164 GLU cc_start: 0.9073 (tp30) cc_final: 0.8850 (tp30) REVERT: N 181 TYR cc_start: 0.9375 (m-80) cc_final: 0.9093 (m-80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3168 time to fit residues: 63.3443 Evaluate side-chains 130 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.047399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.033143 restraints weight = 221915.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.035326 restraints weight = 127821.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037030 restraints weight = 84643.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038334 restraints weight = 60990.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039275 restraints weight = 46900.869| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10094 Z= 0.126 Angle : 0.484 4.311 13721 Z= 0.267 Chirality : 0.038 0.146 1585 Planarity : 0.003 0.033 1772 Dihedral : 4.296 17.340 1375 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: 0.56 (0.24), residues: 1293 helix: 2.56 (0.25), residues: 358 sheet: -0.33 (0.24), residues: 444 loop : -0.52 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 72 TYR 0.026 0.001 TYR H 33 PHE 0.009 0.001 PHE A 157 TRP 0.008 0.001 TRP N 152 HIS 0.004 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00260 (10083) covalent geometry : angle 0.48322 (13699) SS BOND : bond 0.00237 ( 11) SS BOND : angle 0.90538 ( 22) hydrogen bonds : bond 0.03205 ( 521) hydrogen bonds : angle 4.79976 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.9513 (mt-10) cc_final: 0.8983 (mm-30) REVERT: C 125 MET cc_start: 0.8981 (mmp) cc_final: 0.8743 (mmm) REVERT: C 142 HIS cc_start: 0.8465 (p90) cc_final: 0.8197 (p-80) REVERT: L 138 CYS cc_start: 0.6982 (t) cc_final: 0.6576 (t) REVERT: L 197 CYS cc_start: 0.8849 (t) cc_final: 0.8431 (t) REVERT: M 34 ILE cc_start: 0.9899 (mm) cc_final: 0.9577 (tp) REVERT: M 48 MET cc_start: 0.8534 (mtt) cc_final: 0.7961 (mtt) REVERT: N 64 PHE cc_start: 0.9239 (m-80) cc_final: 0.9015 (m-80) REVERT: N 75 LEU cc_start: 0.9188 (tp) cc_final: 0.8949 (tp) REVERT: N 138 CYS cc_start: 0.7208 (t) cc_final: 0.6754 (t) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3066 time to fit residues: 59.9175 Evaluate side-chains 129 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 6.9990 chunk 43 optimal weight: 0.0020 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.047786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.033379 restraints weight = 220137.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.035617 restraints weight = 125838.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.037357 restraints weight = 82819.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.038666 restraints weight = 59433.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.039622 restraints weight = 45618.326| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10094 Z= 0.105 Angle : 0.471 4.265 13721 Z= 0.256 Chirality : 0.038 0.149 1585 Planarity : 0.003 0.032 1772 Dihedral : 4.219 21.318 1375 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: 0.68 (0.24), residues: 1293 helix: 2.83 (0.26), residues: 358 sheet: -0.33 (0.24), residues: 456 loop : -0.51 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 72 TYR 0.024 0.001 TYR H 33 PHE 0.008 0.001 PHE A 157 TRP 0.007 0.001 TRP M 160 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00224 (10083) covalent geometry : angle 0.47038 (13699) SS BOND : bond 0.00186 ( 11) SS BOND : angle 0.80621 ( 22) hydrogen bonds : bond 0.03093 ( 521) hydrogen bonds : angle 4.61956 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9307 (mtp) cc_final: 0.9028 (ttm) REVERT: B 119 GLU cc_start: 0.9440 (mt-10) cc_final: 0.8916 (mm-30) REVERT: C 125 MET cc_start: 0.9072 (mmp) cc_final: 0.8843 (mmm) REVERT: C 142 HIS cc_start: 0.8456 (p90) cc_final: 0.8208 (p-80) REVERT: L 138 CYS cc_start: 0.6927 (t) cc_final: 0.6309 (t) REVERT: L 197 CYS cc_start: 0.8818 (t) cc_final: 0.8361 (t) REVERT: M 48 MET cc_start: 0.8312 (mtt) cc_final: 0.7760 (mtt) REVERT: N 64 PHE cc_start: 0.9225 (m-80) cc_final: 0.9012 (m-80) REVERT: N 75 LEU cc_start: 0.9175 (tp) cc_final: 0.8931 (tp) REVERT: N 138 CYS cc_start: 0.7227 (t) cc_final: 0.6801 (t) REVERT: N 181 TYR cc_start: 0.9409 (m-80) cc_final: 0.9123 (m-80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2992 time to fit residues: 62.4712 Evaluate side-chains 135 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.047929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.033563 restraints weight = 219473.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.035799 restraints weight = 125860.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037550 restraints weight = 82880.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.038869 restraints weight = 59350.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039818 restraints weight = 45454.432| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10094 Z= 0.106 Angle : 0.473 6.171 13721 Z= 0.256 Chirality : 0.038 0.140 1585 Planarity : 0.003 0.032 1772 Dihedral : 4.116 16.674 1375 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.41 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 aren not related in a simple way. whole: 0.78 (0.24), residues: 1293 helix: 2.92 (0.25), residues: 358 sheet: -0.26 (0.24), residues: 456 loop : -0.48 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 72 TYR 0.023 0.001 TYR H 33 PHE 0.018 0.001 PHE H 172 TRP 0.008 0.001 TRP H 36 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00227 (10083) covalent geometry : angle 0.47193 (13699) SS BOND : bond 0.00229 ( 11) SS BOND : angle 0.81399 ( 22) hydrogen bonds : bond 0.03015 ( 521) hydrogen bonds : angle 4.56107 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3516.12 seconds wall clock time: 60 minutes 52.79 seconds (3652.79 seconds total)