Starting phenix.real_space_refine on Tue May 20 06:36:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8udg_42149/05_2025/8udg_42149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8udg_42149/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8udg_42149/05_2025/8udg_42149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8udg_42149/05_2025/8udg_42149.map" model { file = "/net/cci-nas-00/data/ceres_data/8udg_42149/05_2025/8udg_42149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8udg_42149/05_2025/8udg_42149.cif" } resolution = 4.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.49, per 1000 atoms: 0.49 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: 4.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.87 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: 6.79 Time building geometry restraints manager: 5.91 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: 0.840 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: 0.330 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.980 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.019 0.002 TRP M 50 HIS 0.005 0.001 HIS A 74 PHE 0.009 0.002 PHE A 157 TYR 0.025 0.002 TYR H 33 ARG 0.004 0.001 ARG N 193 Details of bonding type rmsd hydrogen bonds : bond 0.18237 ( 521) hydrogen bonds : angle 7.54637 ( 1458) SS BOND : bond 0.00216 ( 11) SS BOND : angle 1.06216 ( 22) covalent geometry : bond 0.00352 (10083) covalent geometry : angle 0.64945 (13699) *********************** 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 : 1.499 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: A 96 ILE cc_start: 0.9479 (mt) cc_final: 0.9205 (tp) REVERT: A 108 ILE cc_start: 0.9416 (mt) cc_final: 0.9128 (tt) REVERT: B 43 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9014 (mt-10) REVERT: B 50 LYS cc_start: 0.9830 (tttt) cc_final: 0.9609 (ttpp) REVERT: B 66 LEU cc_start: 0.9468 (mt) cc_final: 0.9159 (mt) REVERT: B 119 GLU cc_start: 0.9442 (mt-10) cc_final: 0.8924 (mm-30) REVERT: B 140 THR cc_start: 0.5970 (m) cc_final: 0.5757 (m) REVERT: C 122 LEU cc_start: 0.9653 (mt) cc_final: 0.9420 (mt) REVERT: C 158 ASN cc_start: 0.9138 (t0) cc_final: 0.8919 (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: 0.9130 (mp) REVERT: M 48 MET cc_start: 0.9524 (mtp) cc_final: 0.9226 (mtp) REVERT: M 150 ASP cc_start: 0.9418 (m-30) cc_final: 0.8910 (p0) REVERT: N 195 TYR cc_start: 0.9051 (m-80) cc_final: 0.8746 (m-80) REVERT: N 197 CYS cc_start: 0.7015 (t) cc_final: 0.6274 (p) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.5731 time to fit residues: 201.4599 Evaluate side-chains 182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS H 39 GLN L 192 HIS ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.050595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.035155 restraints weight = 205813.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.037558 restraints weight = 116097.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.039423 restraints weight = 75759.374| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 10094 Z= 0.159 Angle : 0.555 19.543 13721 Z= 0.306 Chirality : 0.039 0.150 1585 Planarity : 0.004 0.058 1772 Dihedral : 4.329 17.347 1375 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.17 % Favored : 96.67 % Rotamer: Outliers : 0.09 % Allowed : 1.26 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1293 helix: 2.71 (0.25), residues: 352 sheet: -0.35 (0.23), residues: 458 loop : -0.35 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.006 0.001 HIS B 30 PHE 0.014 0.001 PHE H 101 TYR 0.010 0.001 TYR M 33 ARG 0.003 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 521) hydrogen bonds : angle 5.27238 ( 1458) SS BOND : bond 0.00314 ( 11) SS BOND : angle 4.46906 ( 22) covalent geometry : bond 0.00378 (10083) covalent geometry : angle 0.52626 (13699) *********************** 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: 1 poor density : 199 time to evaluate : 1.418 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: A 108 ILE cc_start: 0.9111 (mt) cc_final: 0.8787 (tt) REVERT: B 119 GLU cc_start: 0.9406 (mt-10) cc_final: 0.8946 (mm-30) REVERT: C 64 GLN cc_start: 0.9638 (mt0) cc_final: 0.9325 (mm110) REVERT: C 158 ASN cc_start: 0.9364 (t0) cc_final: 0.8988 (m110) REVERT: H 37 MET cc_start: 0.9163 (mmp) cc_final: 0.8889 (tmm) REVERT: H 106 PHE cc_start: 0.9460 (m-80) cc_final: 0.9153 (m-10) REVERT: L 75 LEU cc_start: 0.9391 (tp) cc_final: 0.9112 (tp) REVERT: L 138 CYS cc_start: 0.7461 (t) cc_final: 0.6797 (t) REVERT: M 45 LEU cc_start: 0.9322 (mt) cc_final: 0.9119 (mp) REVERT: N 164 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8159 (mp0) REVERT: N 181 TYR cc_start: 0.9079 (m-10) cc_final: 0.8774 (m-80) REVERT: N 197 CYS cc_start: 0.8150 (t) cc_final: 0.7579 (t) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.5929 time to fit residues: 154.4725 Evaluate side-chains 163 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 0.0060 chunk 76 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS H 39 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.050799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.035517 restraints weight = 207886.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037926 restraints weight = 117896.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039811 restraints weight = 76727.893| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10094 Z= 0.117 Angle : 0.496 9.410 13721 Z= 0.268 Chirality : 0.039 0.144 1585 Planarity : 0.003 0.042 1772 Dihedral : 4.202 29.698 1375 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.25 % Favored : 96.60 % Rotamer: Outliers : 0.18 % Allowed : 0.63 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1293 helix: 2.96 (0.25), residues: 355 sheet: -0.28 (0.24), residues: 458 loop : -0.38 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.005 0.001 HIS A 27 PHE 0.006 0.001 PHE A 157 TYR 0.007 0.001 TYR N 38 ARG 0.017 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 521) hydrogen bonds : angle 4.82687 ( 1458) SS BOND : bond 0.00250 ( 11) SS BOND : angle 2.19878 ( 22) covalent geometry : bond 0.00263 (10083) covalent geometry : angle 0.48834 (13699) *********************** 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 183 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 1.418 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: A 72 GLU cc_start: 0.9782 (mm-30) cc_final: 0.9400 (tm-30) REVERT: B 97 GLU cc_start: 0.9395 (pt0) cc_final: 0.9126 (pt0) REVERT: B 119 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8868 (mm-30) REVERT: C 64 GLN cc_start: 0.9661 (mt0) cc_final: 0.9349 (mm110) REVERT: H 106 PHE cc_start: 0.9407 (m-80) cc_final: 0.9009 (m-10) REVERT: L 75 LEU cc_start: 0.9391 (tp) cc_final: 0.9105 (tp) REVERT: L 138 CYS cc_start: 0.7479 (t) cc_final: 0.6998 (t) REVERT: L 198 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8917 (mp10) REVERT: M 48 MET cc_start: 0.9218 (mtp) cc_final: 0.8856 (mtp) REVERT: M 83 LEU cc_start: 0.9575 (tp) cc_final: 0.9359 (tp) REVERT: N 164 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8140 (mp0) REVERT: N 181 TYR cc_start: 0.9050 (m-10) cc_final: 0.8800 (m-80) REVERT: N 197 CYS cc_start: 0.8028 (t) cc_final: 0.7227 (p) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.6165 time to fit residues: 147.6716 Evaluate side-chains 157 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 117 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN H 39 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN N 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.047805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.033369 restraints weight = 224200.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.035558 restraints weight = 129124.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.037256 restraints weight = 85170.020| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10094 Z= 0.208 Angle : 0.577 7.838 13721 Z= 0.321 Chirality : 0.039 0.150 1585 Planarity : 0.004 0.037 1772 Dihedral : 4.540 31.668 1375 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1293 helix: 1.96 (0.25), residues: 358 sheet: -0.37 (0.24), residues: 452 loop : -0.61 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.006 0.002 HIS H 59 PHE 0.012 0.002 PHE H 152 TYR 0.010 0.002 TYR M 33 ARG 0.003 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 521) hydrogen bonds : angle 5.18847 ( 1458) SS BOND : bond 0.00461 ( 11) SS BOND : angle 1.80017 ( 22) covalent geometry : bond 0.00410 (10083) covalent geometry : angle 0.57294 (13699) *********************** 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 168 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.573 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: A 70 MET cc_start: 0.9478 (mtp) cc_final: 0.9087 (mtp) REVERT: B 66 LEU cc_start: 0.9674 (mt) cc_final: 0.9373 (mt) REVERT: B 119 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8946 (mm-30) REVERT: C 158 ASN cc_start: 0.9365 (t0) cc_final: 0.9039 (m110) REVERT: H 106 PHE cc_start: 0.9453 (m-80) cc_final: 0.9129 (m-10) REVERT: M 48 MET cc_start: 0.9256 (mtp) cc_final: 0.8883 (mtp) REVERT: N 64 PHE cc_start: 0.9150 (m-80) cc_final: 0.8921 (m-80) REVERT: N 138 CYS cc_start: 0.7408 (t) cc_final: 0.7159 (t) REVERT: N 197 CYS cc_start: 0.7421 (t) cc_final: 0.7012 (t) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.6189 time to fit residues: 135.5264 Evaluate side-chains 138 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 177 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.031908 restraints weight = 238338.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.033978 restraints weight = 136792.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.035564 restraints weight = 90583.129| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 10094 Z= 0.291 Angle : 0.666 6.348 13721 Z= 0.380 Chirality : 0.040 0.157 1585 Planarity : 0.004 0.040 1772 Dihedral : 5.020 19.296 1375 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.03 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1293 helix: 0.80 (0.24), residues: 358 sheet: -0.68 (0.24), residues: 444 loop : -1.04 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 160 HIS 0.009 0.002 HIS H 170 PHE 0.015 0.002 PHE C 157 TYR 0.014 0.002 TYR M 33 ARG 0.003 0.001 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 521) hydrogen bonds : angle 5.86276 ( 1458) SS BOND : bond 0.00505 ( 11) SS BOND : angle 1.30667 ( 22) covalent geometry : bond 0.00543 (10083) covalent geometry : angle 0.66424 (13699) *********************** 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 145 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.482 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: B 119 GLU cc_start: 0.9600 (mt-10) cc_final: 0.9106 (mm-30) REVERT: C 92 ILE cc_start: 0.9488 (mm) cc_final: 0.8840 (tt) REVERT: C 158 ASN cc_start: 0.9392 (t0) cc_final: 0.9093 (m110) REVERT: L 75 LEU cc_start: 0.9484 (tp) cc_final: 0.9230 (tp) REVERT: L 138 CYS cc_start: 0.8055 (t) cc_final: 0.7290 (t) REVERT: L 197 CYS cc_start: 0.8947 (t) cc_final: 0.8725 (t) REVERT: N 138 CYS cc_start: 0.7215 (t) cc_final: 0.6694 (t) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.6136 time to fit residues: 116.5313 Evaluate side-chains 122 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN H 3 GLN M 39 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 = 0.3318 r_free = 0.3318 target = 0.047251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.032811 restraints weight = 225790.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.035015 restraints weight = 129084.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036734 restraints weight = 85061.216| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10094 Z= 0.131 Angle : 0.510 4.376 13721 Z= 0.280 Chirality : 0.039 0.151 1585 Planarity : 0.004 0.036 1772 Dihedral : 4.616 17.892 1375 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.49 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1293 helix: 1.92 (0.25), residues: 358 sheet: -0.61 (0.24), residues: 454 loop : -0.81 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 189 HIS 0.005 0.001 HIS H 59 PHE 0.014 0.001 PHE A 167 TYR 0.042 0.002 TYR H 33 ARG 0.010 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 521) hydrogen bonds : angle 5.12968 ( 1458) SS BOND : bond 0.00394 ( 11) SS BOND : angle 0.59428 ( 22) covalent geometry : bond 0.00266 (10083) covalent geometry : angle 0.51006 (13699) *********************** 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 160 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.698 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: B 119 GLU cc_start: 0.9529 (mt-10) cc_final: 0.8994 (mm-30) REVERT: L 138 CYS cc_start: 0.7608 (t) cc_final: 0.7037 (t) REVERT: L 197 CYS cc_start: 0.9019 (t) cc_final: 0.8748 (t) REVERT: M 160 TRP cc_start: 0.8980 (m100) cc_final: 0.8177 (m100) REVERT: N 64 PHE cc_start: 0.9207 (m-80) cc_final: 0.8983 (m-80) REVERT: N 75 LEU cc_start: 0.9226 (tp) cc_final: 0.9019 (tp) REVERT: N 138 CYS cc_start: 0.7557 (t) cc_final: 0.7144 (t) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.6147 time to fit residues: 130.3324 Evaluate side-chains 134 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3311 r_free = 0.3311 target = 0.046898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.032630 restraints weight = 229242.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.034852 restraints weight = 130639.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.036556 restraints weight = 85622.486| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10094 Z= 0.145 Angle : 0.503 4.282 13721 Z= 0.279 Chirality : 0.038 0.148 1585 Planarity : 0.003 0.034 1772 Dihedral : 4.440 17.431 1375 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1293 helix: 2.17 (0.25), residues: 358 sheet: -0.56 (0.24), residues: 454 loop : -0.74 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 152 HIS 0.005 0.001 HIS H 59 PHE 0.010 0.001 PHE C 157 TYR 0.026 0.002 TYR H 33 ARG 0.003 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 521) hydrogen bonds : angle 5.02755 ( 1458) SS BOND : bond 0.00330 ( 11) SS BOND : angle 0.50393 ( 22) covalent geometry : bond 0.00287 (10083) covalent geometry : angle 0.50291 (13699) *********************** 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 154 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.525 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: B 119 GLU cc_start: 0.9534 (mt-10) cc_final: 0.8997 (mm-30) REVERT: L 138 CYS cc_start: 0.7474 (t) cc_final: 0.7057 (t) REVERT: L 197 CYS cc_start: 0.9043 (t) cc_final: 0.8752 (t) REVERT: M 34 ILE cc_start: 0.9868 (mm) cc_final: 0.9615 (tp) REVERT: M 48 MET cc_start: 0.9097 (mtp) cc_final: 0.8872 (mtp) REVERT: N 64 PHE cc_start: 0.9180 (m-80) cc_final: 0.8945 (m-80) REVERT: N 75 LEU cc_start: 0.9227 (tp) cc_final: 0.8997 (tp) REVERT: N 138 CYS cc_start: 0.7414 (t) cc_final: 0.7014 (t) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.6017 time to fit residues: 121.8034 Evaluate side-chains 127 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS B 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.031883 restraints weight = 231890.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034039 restraints weight = 133459.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035686 restraints weight = 88147.342| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10094 Z= 0.186 Angle : 0.532 4.619 13721 Z= 0.297 Chirality : 0.038 0.140 1585 Planarity : 0.004 0.035 1772 Dihedral : 4.523 17.554 1375 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.03 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1293 helix: 1.84 (0.25), residues: 358 sheet: -0.62 (0.24), residues: 452 loop : -0.89 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 152 HIS 0.006 0.001 HIS H 59 PHE 0.009 0.001 PHE B 138 TYR 0.025 0.002 TYR H 33 ARG 0.003 0.001 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 521) hydrogen bonds : angle 5.19070 ( 1458) SS BOND : bond 0.00329 ( 11) SS BOND : angle 0.63706 ( 22) covalent geometry : bond 0.00356 (10083) covalent geometry : angle 0.53143 (13699) *********************** 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 147 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.676 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: B 66 LEU cc_start: 0.9573 (mt) cc_final: 0.9371 (mt) REVERT: B 119 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9037 (mm-30) REVERT: C 81 ASP cc_start: 0.9604 (t0) cc_final: 0.9330 (t0) REVERT: C 92 ILE cc_start: 0.9475 (mm) cc_final: 0.9166 (mt) REVERT: C 123 LYS cc_start: 0.9351 (mttt) cc_final: 0.8977 (mmmm) REVERT: L 75 LEU cc_start: 0.9414 (tp) cc_final: 0.9157 (tp) REVERT: L 138 CYS cc_start: 0.7629 (t) cc_final: 0.6990 (t) REVERT: L 197 CYS cc_start: 0.9058 (t) cc_final: 0.8836 (t) REVERT: M 34 ILE cc_start: 0.9888 (mm) cc_final: 0.9668 (tp) REVERT: N 138 CYS cc_start: 0.7550 (t) cc_final: 0.7164 (t) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.6059 time to fit residues: 118.3915 Evaluate side-chains 123 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.046212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.031991 restraints weight = 230196.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.034155 restraints weight = 132535.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.035842 restraints weight = 87433.307| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10094 Z= 0.161 Angle : 0.512 5.653 13721 Z= 0.284 Chirality : 0.038 0.140 1585 Planarity : 0.004 0.032 1772 Dihedral : 4.500 17.207 1375 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.49 % Favored : 94.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1293 helix: 1.94 (0.25), residues: 358 sheet: -0.69 (0.24), residues: 452 loop : -0.88 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 189 HIS 0.005 0.001 HIS H 59 PHE 0.013 0.001 PHE H 172 TYR 0.023 0.002 TYR H 33 ARG 0.008 0.000 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 521) hydrogen bonds : angle 5.10633 ( 1458) SS BOND : bond 0.00328 ( 11) SS BOND : angle 0.87673 ( 22) covalent geometry : bond 0.00311 (10083) covalent geometry : angle 0.51084 (13699) *********************** 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 147 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.468 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: 0.9554 (mt-10) cc_final: 0.9109 (mm-30) REVERT: B 168 ASP cc_start: 0.9545 (p0) cc_final: 0.9342 (p0) REVERT: C 81 ASP cc_start: 0.9605 (t0) cc_final: 0.9313 (t0) REVERT: C 92 ILE cc_start: 0.9423 (mm) cc_final: 0.9090 (mt) REVERT: C 123 LYS cc_start: 0.9381 (mttt) cc_final: 0.9056 (mmmm) REVERT: M 34 ILE cc_start: 0.9895 (mm) cc_final: 0.9694 (tp) REVERT: N 75 LEU cc_start: 0.9237 (tp) cc_final: 0.8989 (tp) REVERT: N 138 CYS cc_start: 0.7525 (t) cc_final: 0.7123 (t) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.6000 time to fit residues: 115.4552 Evaluate side-chains 127 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.046973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.032633 restraints weight = 227422.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.034868 restraints weight = 130493.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036608 restraints weight = 85604.712| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10094 Z= 0.121 Angle : 0.485 5.164 13721 Z= 0.265 Chirality : 0.039 0.141 1585 Planarity : 0.003 0.033 1772 Dihedral : 4.369 22.834 1375 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.87 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1293 helix: 2.36 (0.25), residues: 358 sheet: -0.59 (0.24), residues: 452 loop : -0.80 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 189 HIS 0.004 0.001 HIS H 59 PHE 0.012 0.001 PHE N 64 TYR 0.022 0.001 TYR H 33 ARG 0.008 0.001 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 521) hydrogen bonds : angle 4.85203 ( 1458) SS BOND : bond 0.00217 ( 11) SS BOND : angle 0.81758 ( 22) covalent geometry : bond 0.00250 (10083) covalent geometry : angle 0.48430 (13699) ********************** 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 151 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.549 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 66 LEU cc_start: 0.9591 (mt) cc_final: 0.9297 (mt) REVERT: B 119 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9066 (mm-30) REVERT: C 81 ASP cc_start: 0.9624 (t0) cc_final: 0.9332 (t0) REVERT: C 92 ILE cc_start: 0.9445 (mm) cc_final: 0.9116 (mt) REVERT: C 123 LYS cc_start: 0.9362 (mttt) cc_final: 0.9032 (mmmm) REVERT: C 158 ASN cc_start: 0.9341 (t0) cc_final: 0.9124 (m110) REVERT: M 34 ILE cc_start: 0.9909 (mm) cc_final: 0.9692 (tp) REVERT: M 48 MET cc_start: 0.8317 (mtt) cc_final: 0.7761 (mtt) REVERT: N 52 ASP cc_start: 0.9261 (t0) cc_final: 0.8787 (m-30) REVERT: N 75 LEU cc_start: 0.9203 (tp) cc_final: 0.8981 (tp) REVERT: N 138 CYS cc_start: 0.7469 (t) cc_final: 0.7157 (t) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.6179 time to fit residues: 123.1341 Evaluate side-chains 131 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.047036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.032571 restraints weight = 224648.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.034822 restraints weight = 128620.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036561 restraints weight = 84519.617| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10094 Z= 0.114 Angle : 0.487 6.723 13721 Z= 0.264 Chirality : 0.038 0.139 1585 Planarity : 0.003 0.032 1772 Dihedral : 4.242 17.937 1375 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.49 % Favored : 95.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1293 helix: 2.44 (0.25), residues: 358 sheet: -0.46 (0.24), residues: 442 loop : -0.71 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 152 HIS 0.004 0.001 HIS H 59 PHE 0.018 0.001 PHE A 157 TYR 0.021 0.001 TYR H 33 ARG 0.006 0.001 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 521) hydrogen bonds : angle 4.75696 ( 1458) SS BOND : bond 0.00208 ( 11) SS BOND : angle 0.74866 ( 22) covalent geometry : bond 0.00241 (10083) covalent geometry : angle 0.48613 (13699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6015.34 seconds wall clock time: 104 minutes 54.52 seconds (6294.52 seconds total)