Starting phenix.real_space_refine on Thu Jan 23 03:45:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8udg_42149/01_2025/8udg_42149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8udg_42149/01_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_42149/01_2025/8udg_42149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8udg_42149/01_2025/8udg_42149.map" model { file = "/net/cci-nas-00/data/ceres_data/8udg_42149/01_2025/8udg_42149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8udg_42149/01_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-5571/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: 9.57, 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: 5.16 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: 1.82 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: 7.77 Time building geometry restraints manager: 6.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9620 1.03 - 1.23: 18 1.23 - 1.42: 4161 1.42 - 1.62: 5854 1.62 - 1.82: 57 Bond restraints: 19710 Sorted by residual: bond pdb=" C SER L 157 " pdb=" N PRO L 158 " ideal model delta sigma weight residual 1.333 1.355 -0.021 1.01e-02 9.80e+03 4.53e+00 bond pdb=" C SER N 157 " pdb=" N PRO N 158 " ideal model delta sigma weight residual 1.333 1.354 -0.021 1.01e-02 9.80e+03 4.22e+00 bond pdb=" N ALA M 120 " pdb=" CA ALA M 120 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.20e-02 6.94e+03 3.28e+00 bond pdb=" C SER M 119 " pdb=" N ALA M 120 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.27e-02 6.20e+03 1.20e+00 bond pdb=" CA VAL H 190 " pdb=" C VAL H 190 " ideal model delta sigma weight residual 1.516 1.526 -0.011 1.11e-02 8.12e+03 9.25e-01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 32544 1.07 - 2.14: 2738 2.14 - 3.20: 217 3.20 - 4.27: 71 4.27 - 5.34: 29 Bond angle restraints: 35599 Sorted by residual: angle pdb=" N VAL H 190 " pdb=" CA VAL H 190 " pdb=" C VAL H 190 " ideal model delta sigma weight residual 109.19 106.11 3.08 8.20e-01 1.49e+00 1.42e+01 angle pdb=" CA VAL H 190 " pdb=" C VAL H 190 " pdb=" N PRO H 191 " ideal model delta sigma weight residual 116.57 120.18 -3.61 9.80e-01 1.04e+00 1.35e+01 angle pdb=" C VAL H 190 " pdb=" CA VAL H 190 " pdb=" CB VAL H 190 " ideal model delta sigma weight residual 109.33 112.38 -3.05 9.80e-01 1.04e+00 9.67e+00 angle pdb=" N GLY H 145 " pdb=" CA GLY H 145 " pdb=" C GLY H 145 " ideal model delta sigma weight residual 111.27 116.40 -5.13 1.67e+00 3.59e-01 9.44e+00 angle pdb=" O SER M 119 " pdb=" C SER M 119 " pdb=" N ALA M 120 " ideal model delta sigma weight residual 122.68 119.07 3.61 1.27e+00 6.20e-01 8.10e+00 ... (remaining 35594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 8574 16.98 - 33.96: 563 33.96 - 50.94: 167 50.94 - 67.92: 74 67.92 - 84.91: 20 Dihedral angle restraints: 9398 sinusoidal: 5099 harmonic: 4299 Sorted by residual: dihedral pdb=" CA SER M 119 " pdb=" C SER M 119 " pdb=" N ALA M 120 " pdb=" CA ALA M 120 " ideal model delta harmonic sigma weight residual 180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 90 " pdb=" CB CYS N 90 " ideal model delta sinusoidal sigma weight residual 93.00 57.52 35.48 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA CYS M 99 " pdb=" C CYS M 99 " pdb=" N VAL M 100 " pdb=" CA VAL M 100 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1071 0.034 - 0.068: 362 0.068 - 0.101: 96 0.101 - 0.135: 45 0.135 - 0.169: 11 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA VAL M 148 " pdb=" N VAL M 148 " pdb=" C VAL M 148 " pdb=" CB VAL M 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA VAL H 190 " pdb=" N VAL H 190 " pdb=" C VAL H 190 " pdb=" CB VAL H 190 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA VAL H 148 " pdb=" N VAL H 148 " pdb=" C VAL H 148 " pdb=" CB VAL H 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1582 not shown) Planarity restraints: 3015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 119 " 0.024 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C SER M 119 " -0.079 2.00e-02 2.50e+03 pdb=" O SER M 119 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA M 120 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 33 " -0.013 2.00e-02 2.50e+03 8.89e-03 2.37e+00 pdb=" CG TYR M 33 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR M 33 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR M 33 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR M 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR M 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR M 33 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR M 33 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR M 33 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR M 33 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR M 33 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR M 33 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 79 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C GLU A 79 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU A 79 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 80 " -0.009 2.00e-02 2.50e+03 ... (remaining 3012 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2170 2.25 - 2.84: 44806 2.84 - 3.42: 50208 3.42 - 4.01: 69800 4.01 - 4.60: 107200 Nonbonded interactions: 274184 Sorted by model distance: nonbonded pdb=" H SER H 162 " pdb=" OD1 ASN H 203 " model vdw 1.662 2.450 nonbonded pdb=" H GLN L 171 " pdb=" O LYS L 175 " model vdw 1.664 2.450 nonbonded pdb=" O ASP B 37 " pdb=" HG1 THR B 41 " model vdw 1.674 2.450 nonbonded pdb=" OE1 GLN A 42 " pdb=" H ILE C 172 " model vdw 1.680 2.450 nonbonded pdb=" H GLY M 15 " pdb=" O LEU M 86 " model vdw 1.685 2.450 ... (remaining 274179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 23 through 135 or (resid 136 and (name N or name CA or nam \ e C or name O or name HA2 or name HA3)) or resid 137 through 181)) selection = (chain 'C' and (resid 23 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name H \ B2 or name HB3 or name HD21 or name HD22)) or (resid 136 and (name N or name CA \ or name C or name O or name HA2 or name HA3)) or resid 137 through 181)) } ncs_group { reference = chain 'H' selection = (chain 'M' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2)) or resid 34 through 219)) } ncs_group { reference = chain 'L' selection = (chain 'N' and (resid 1 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 98 through 213)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.370 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.240 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.030 ------------------------------------------------------------------------------- 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 10083 Z= 0.226 Angle : 0.649 5.339 13699 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 *********************** 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 : 1.513 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: 0.6207 time to fit residues: 220.6132 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 : 1.480 ------------------------------------------------------------------------------- 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: 0.7980 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.050757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.035241 restraints weight = 206272.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037664 restraints weight = 116144.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039537 restraints weight = 75701.247| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 10083 Z= 0.260 Angle : 0.530 13.283 13699 Z= 0.295 Chirality : 0.039 0.140 1585 Planarity : 0.004 0.058 1772 Dihedral : 4.337 17.644 1375 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.09 % Favored : 96.75 % Rotamer: Outliers : 0.09 % Allowed : 1.17 % Favored : 98.74 % 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: 0.64 (0.24), residues: 1293 helix: 2.66 (0.25), residues: 354 sheet: -0.36 (0.23), residues: 458 loop : -0.38 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.007 0.001 HIS B 114 PHE 0.014 0.001 PHE H 101 TYR 0.009 0.001 TYR M 33 ARG 0.005 0.000 ARG B 151 *********************** 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 201 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.456 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: 0.9104 (mt) cc_final: 0.8779 (tt) REVERT: B 97 GLU cc_start: 0.9129 (tt0) cc_final: 0.8765 (mt-10) REVERT: B 119 GLU cc_start: 0.9404 (mt-10) cc_final: 0.8945 (mm-30) REVERT: C 64 GLN cc_start: 0.9637 (mt0) cc_final: 0.9326 (mm110) REVERT: C 158 ASN cc_start: 0.9365 (t0) cc_final: 0.8982 (m110) REVERT: H 37 MET cc_start: 0.9140 (mmp) cc_final: 0.8928 (tmm) REVERT: H 48 MET cc_start: 0.9353 (mtp) cc_final: 0.9029 (mtp) REVERT: H 106 PHE cc_start: 0.9453 (m-80) cc_final: 0.9147 (m-10) REVERT: L 75 LEU cc_start: 0.9388 (tp) cc_final: 0.9110 (tp) REVERT: L 138 CYS cc_start: 0.7426 (t) cc_final: 0.6762 (t) REVERT: M 45 LEU cc_start: 0.9327 (mt) cc_final: 0.9118 (mp) REVERT: N 64 PHE cc_start: 0.9269 (m-80) cc_final: 0.9054 (m-80) REVERT: N 164 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8153 (mp0) REVERT: N 181 TYR cc_start: 0.9078 (m-10) cc_final: 0.8727 (m-80) REVERT: N 197 CYS cc_start: 0.8136 (t) cc_final: 0.7570 (t) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.6223 time to fit residues: 162.3089 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 : 1.583 ------------------------------------------------------------------------------- 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: 0.8980 chunk 32 optimal weight: 0.1980 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.050894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035443 restraints weight = 209464.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.037853 restraints weight = 119436.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.039734 restraints weight = 78116.296| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 10083 Z= 0.167 Angle : 0.488 4.356 13699 Z= 0.264 Chirality : 0.039 0.142 1585 Planarity : 0.003 0.042 1772 Dihedral : 4.190 29.470 1375 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.25 % Favored : 96.60 % Rotamer: Outliers : 0.18 % Allowed : 0.72 % 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: 0.80 (0.24), residues: 1293 helix: 2.93 (0.25), residues: 355 sheet: -0.29 (0.24), residues: 458 loop : -0.39 (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 0.014 0.001 ARG C 88 *********************** 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 185 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.9777 (mm-30) cc_final: 0.9399 (tm-30) REVERT: B 97 GLU cc_start: 0.9065 (tt0) cc_final: 0.8761 (mt-10) REVERT: B 119 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8904 (mm-30) REVERT: C 64 GLN cc_start: 0.9661 (mt0) cc_final: 0.9349 (mm110) REVERT: H 106 PHE cc_start: 0.9418 (m-80) cc_final: 0.9038 (m-10) REVERT: L 75 LEU cc_start: 0.9392 (tp) cc_final: 0.9111 (tp) REVERT: L 138 CYS cc_start: 0.7497 (t) cc_final: 0.7012 (t) REVERT: L 197 CYS cc_start: 0.8936 (t) cc_final: 0.8515 (t) REVERT: M 48 MET cc_start: 0.9220 (mtp) cc_final: 0.8859 (mtp) REVERT: N 164 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8155 (mp0) REVERT: N 181 TYR cc_start: 0.9125 (m-10) cc_final: 0.8814 (m-80) REVERT: N 197 CYS cc_start: 0.8097 (t) cc_final: 0.7267 (p) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.6228 time to fit residues: 150.1263 Evaluate side-chains 157 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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: 7.9990 chunk 119 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 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: 0.4980 chunk 114 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.049430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.034279 restraints weight = 213040.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.036604 restraints weight = 121529.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.038416 restraints weight = 79697.666| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10083 Z= 0.175 Angle : 0.485 4.334 13699 Z= 0.266 Chirality : 0.038 0.146 1585 Planarity : 0.003 0.036 1772 Dihedral : 4.183 31.901 1375 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.75 % Rotamer: Outliers : 0.09 % Allowed : 1.35 % Favored : 98.56 % 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: 0.77 (0.24), residues: 1293 helix: 2.76 (0.25), residues: 358 sheet: -0.24 (0.24), residues: 458 loop : -0.38 (0.30), residues: 477 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 0.009 0.001 PHE A 167 TYR 0.008 0.001 TYR M 33 ARG 0.002 0.000 ARG L 63 *********************** 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 178 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.331 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: B 119 GLU cc_start: 0.9421 (mt-10) cc_final: 0.8910 (mm-30) REVERT: B 139 GLU cc_start: 0.9424 (tt0) cc_final: 0.9220 (pp20) REVERT: C 158 ASN cc_start: 0.9334 (t0) cc_final: 0.9023 (m110) REVERT: H 106 PHE cc_start: 0.9396 (m-80) cc_final: 0.8983 (m-10) REVERT: L 75 LEU cc_start: 0.9412 (tp) cc_final: 0.9181 (tp) REVERT: L 136 LEU cc_start: 0.9684 (mm) cc_final: 0.9474 (mt) REVERT: L 138 CYS cc_start: 0.7494 (t) cc_final: 0.7072 (t) REVERT: M 48 MET cc_start: 0.9288 (mtp) cc_final: 0.8972 (mtp) REVERT: N 64 PHE cc_start: 0.9261 (m-80) cc_final: 0.9016 (m-80) REVERT: N 138 CYS cc_start: 0.7308 (t) cc_final: 0.6972 (t) REVERT: N 197 CYS cc_start: 0.8022 (t) cc_final: 0.7515 (t) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.6274 time to fit residues: 145.6186 Evaluate side-chains 153 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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: 0.8980 chunk 101 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.048859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.034050 restraints weight = 214336.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.036357 restraints weight = 121240.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038157 restraints weight = 79311.616| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10083 Z= 0.174 Angle : 0.475 4.583 13699 Z= 0.261 Chirality : 0.038 0.144 1585 Planarity : 0.003 0.036 1772 Dihedral : 4.090 21.038 1375 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.24), residues: 1293 helix: 2.78 (0.25), residues: 358 sheet: -0.14 (0.24), residues: 452 loop : -0.44 (0.29), residues: 483 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 A 167 TYR 0.007 0.001 TYR M 33 ARG 0.002 0.000 ARG L 63 *********************** 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 175 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.638 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: A 45 ILE cc_start: 0.9810 (mt) cc_final: 0.9555 (tt) REVERT: B 66 LEU cc_start: 0.9677 (mt) cc_final: 0.9423 (mt) REVERT: B 119 GLU cc_start: 0.9321 (mt-10) cc_final: 0.8976 (mm-30) REVERT: H 106 PHE cc_start: 0.9346 (m-80) cc_final: 0.8910 (m-10) REVERT: L 75 LEU cc_start: 0.9443 (tp) cc_final: 0.9187 (tp) REVERT: L 197 CYS cc_start: 0.8838 (t) cc_final: 0.8117 (t) REVERT: M 48 MET cc_start: 0.9174 (mtp) cc_final: 0.8839 (mtp) REVERT: N 64 PHE cc_start: 0.9269 (m-80) cc_final: 0.9039 (m-80) REVERT: N 138 CYS cc_start: 0.7344 (t) cc_final: 0.7023 (t) REVERT: N 197 CYS cc_start: 0.8054 (t) cc_final: 0.7643 (t) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.6301 time to fit residues: 144.4933 Evaluate side-chains 146 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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: 0.5980 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.048652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.033755 restraints weight = 213353.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036065 restraints weight = 121295.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.037856 restraints weight = 79274.798| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10083 Z= 0.169 Angle : 0.474 4.153 13699 Z= 0.260 Chirality : 0.038 0.138 1585 Planarity : 0.003 0.035 1772 Dihedral : 4.102 19.998 1375 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.59 % 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: 0.77 (0.24), residues: 1293 helix: 2.62 (0.25), residues: 370 sheet: -0.04 (0.25), residues: 442 loop : -0.56 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 160 HIS 0.005 0.001 HIS H 59 PHE 0.029 0.001 PHE A 167 TYR 0.031 0.001 TYR M 33 ARG 0.002 0.000 ARG L 63 *********************** 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 165 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.9417 (mt-10) cc_final: 0.8938 (mm-30) REVERT: H 106 PHE cc_start: 0.9322 (m-80) cc_final: 0.8863 (m-10) REVERT: L 75 LEU cc_start: 0.9439 (tp) cc_final: 0.9181 (tp) REVERT: L 138 CYS cc_start: 0.7462 (t) cc_final: 0.6704 (t) REVERT: L 197 CYS cc_start: 0.8382 (t) cc_final: 0.7730 (t) REVERT: M 48 MET cc_start: 0.9203 (mtp) cc_final: 0.8867 (mtp) REVERT: N 64 PHE cc_start: 0.9281 (m-80) cc_final: 0.9070 (m-80) REVERT: N 138 CYS cc_start: 0.7375 (t) cc_final: 0.7148 (t) REVERT: N 197 CYS cc_start: 0.7553 (t) cc_final: 0.7104 (t) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.6545 time to fit residues: 140.7423 Evaluate side-chains 146 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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: 6.9990 chunk 123 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 M 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.047456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.032968 restraints weight = 225583.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.035198 restraints weight = 129136.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036946 restraints weight = 84490.255| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10083 Z= 0.228 Angle : 0.523 4.366 13699 Z= 0.294 Chirality : 0.038 0.144 1585 Planarity : 0.004 0.037 1772 Dihedral : 4.315 17.581 1375 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % 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: 0.41 (0.23), residues: 1293 helix: 2.31 (0.25), residues: 358 sheet: -0.28 (0.25), residues: 450 loop : -0.64 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 152 HIS 0.006 0.001 HIS M 59 PHE 0.022 0.002 PHE A 167 TYR 0.028 0.002 TYR M 33 ARG 0.003 0.000 ARG H 54 *********************** 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 159 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.524 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 57 GLU cc_start: 0.9616 (tt0) cc_final: 0.9297 (tp30) REVERT: B 97 GLU cc_start: 0.9051 (tt0) cc_final: 0.8728 (mt-10) REVERT: B 119 GLU cc_start: 0.9465 (mt-10) cc_final: 0.8973 (mm-30) REVERT: C 92 ILE cc_start: 0.9359 (mm) cc_final: 0.9046 (mt) REVERT: C 142 HIS cc_start: 0.8176 (p90) cc_final: 0.7950 (p-80) REVERT: L 77 ILE cc_start: 0.9662 (mp) cc_final: 0.9392 (tt) REVERT: L 138 CYS cc_start: 0.7033 (t) cc_final: 0.6701 (t) REVERT: L 197 CYS cc_start: 0.8643 (t) cc_final: 0.8266 (t) REVERT: M 48 MET cc_start: 0.9251 (mtp) cc_final: 0.8900 (mtp) REVERT: N 64 PHE cc_start: 0.9158 (m-80) cc_final: 0.8947 (m-80) REVERT: N 138 CYS cc_start: 0.7365 (t) cc_final: 0.7000 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.6542 time to fit residues: 135.9157 Evaluate side-chains 139 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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: 7.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** C 95 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3282 r_free = 0.3282 target = 0.045766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.031794 restraints weight = 233489.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.033907 restraints weight = 134096.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.035553 restraints weight = 88525.109| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10083 Z= 0.307 Angle : 0.614 6.411 13699 Z= 0.347 Chirality : 0.039 0.157 1585 Planarity : 0.004 0.035 1772 Dihedral : 4.762 18.917 1375 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.32 (0.23), residues: 1293 helix: 1.34 (0.25), residues: 358 sheet: -0.58 (0.24), residues: 454 loop : -0.90 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 152 HIS 0.009 0.002 HIS H 170 PHE 0.021 0.002 PHE A 167 TYR 0.024 0.002 TYR H 33 ARG 0.006 0.001 ARG M 72 *********************** 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 145 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.403 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: 0.9603 (mt-10) cc_final: 0.9014 (mm-30) REVERT: H 106 PHE cc_start: 0.9427 (m-10) cc_final: 0.9113 (m-10) REVERT: L 138 CYS cc_start: 0.7551 (t) cc_final: 0.6834 (t) REVERT: M 34 ILE cc_start: 0.9882 (mm) cc_final: 0.9656 (tp) REVERT: N 138 CYS cc_start: 0.7150 (t) cc_final: 0.6673 (t) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.6984 time to fit residues: 130.0445 Evaluate side-chains 117 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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: 5.9990 chunk 101 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.046584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.032371 restraints weight = 227351.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.034551 restraints weight = 130486.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.036246 restraints weight = 85962.187| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10083 Z= 0.191 Angle : 0.520 6.780 13699 Z= 0.288 Chirality : 0.038 0.145 1585 Planarity : 0.004 0.043 1772 Dihedral : 4.547 17.904 1375 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % 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: -0.02 (0.24), residues: 1293 helix: 1.78 (0.26), residues: 355 sheet: -0.57 (0.24), residues: 454 loop : -0.67 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 152 HIS 0.006 0.001 HIS H 59 PHE 0.018 0.002 PHE A 167 TYR 0.030 0.001 TYR H 33 ARG 0.004 0.001 ARG M 72 *********************** 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 149 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.478 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: B 119 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9005 (mm-30) REVERT: H 106 PHE cc_start: 0.9324 (m-10) cc_final: 0.8976 (m-10) REVERT: L 138 CYS cc_start: 0.6082 (t) cc_final: 0.5680 (t) REVERT: M 34 ILE cc_start: 0.9887 (mm) cc_final: 0.9636 (tp) REVERT: M 48 MET cc_start: 0.9102 (mtp) cc_final: 0.8895 (mtp) REVERT: N 75 LEU cc_start: 0.9259 (tp) cc_final: 0.9034 (tp) REVERT: N 138 CYS cc_start: 0.7463 (t) cc_final: 0.7056 (t) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.6545 time to fit residues: 126.3456 Evaluate side-chains 133 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 45 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS B 95 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.047294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.032921 restraints weight = 226604.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.035171 restraints weight = 129392.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036922 restraints weight = 84571.587| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10083 Z= 0.153 Angle : 0.477 5.180 13699 Z= 0.259 Chirality : 0.039 0.144 1585 Planarity : 0.003 0.035 1772 Dihedral : 4.237 17.107 1375 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.87 % Favored : 94.97 % 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: 0.40 (0.24), residues: 1293 helix: 2.32 (0.26), residues: 355 sheet: -0.41 (0.25), residues: 454 loop : -0.50 (0.30), residues: 484 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 0.015 0.001 PHE A 167 TYR 0.026 0.001 TYR H 33 ARG 0.004 0.000 ARG A 151 ********************** 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 152 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.9493 (mt-10) cc_final: 0.8983 (mm-30) REVERT: C 92 ILE cc_start: 0.9397 (mm) cc_final: 0.9109 (mt) REVERT: H 45 LEU cc_start: 0.9056 (mm) cc_final: 0.8783 (mm) REVERT: M 34 ILE cc_start: 0.9881 (mm) cc_final: 0.9634 (tp) REVERT: N 75 LEU cc_start: 0.9202 (tp) cc_final: 0.8988 (tp) REVERT: N 138 CYS cc_start: 0.7533 (t) cc_final: 0.7114 (t) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.6611 time to fit residues: 130.5396 Evaluate side-chains 132 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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: 6.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 chunk 8 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 122 optimal weight: 0.1980 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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 62 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 = 0.3321 r_free = 0.3321 target = 0.047151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.032934 restraints weight = 226129.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.035165 restraints weight = 129419.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.036902 restraints weight = 84946.808| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10083 Z= 0.160 Angle : 0.482 4.755 13699 Z= 0.264 Chirality : 0.038 0.140 1585 Planarity : 0.003 0.033 1772 Dihedral : 4.176 16.815 1375 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.13 % 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: 0.51 (0.24), residues: 1293 helix: 2.48 (0.26), residues: 355 sheet: -0.37 (0.24), residues: 454 loop : -0.46 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.004 0.001 HIS H 59 PHE 0.015 0.001 PHE A 167 TYR 0.025 0.001 TYR H 33 ARG 0.004 0.001 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6011.39 seconds wall clock time: 107 minutes 30.85 seconds (6450.85 seconds total)