Starting phenix.real_space_refine on Tue Jun 17 06:41:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8udg_42149/06_2025/8udg_42149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8udg_42149/06_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_42149/06_2025/8udg_42149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8udg_42149/06_2025/8udg_42149.map" model { file = "/net/cci-nas-00/data/ceres_data/8udg_42149/06_2025/8udg_42149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8udg_42149/06_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-5710/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: 9.16, per 1000 atoms: 0.47 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: 5.14 Conformation dependent library (CDL) restraints added in 1.5 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: 6.81 Time building geometry restraints manager: 6.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9620 1.03 - 1.23: 18 1.23 - 1.42: 4161 1.42 - 1.62: 5854 1.62 - 1.82: 57 Bond restraints: 19710 Sorted by residual: bond pdb=" C SER L 157 " pdb=" N PRO L 158 " ideal model delta sigma weight residual 1.333 1.355 -0.021 1.01e-02 9.80e+03 4.53e+00 bond pdb=" C SER N 157 " pdb=" N PRO N 158 " ideal model delta sigma weight residual 1.333 1.354 -0.021 1.01e-02 9.80e+03 4.22e+00 bond pdb=" N ALA M 120 " pdb=" CA ALA M 120 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.20e-02 6.94e+03 3.28e+00 bond pdb=" C SER M 119 " pdb=" N ALA M 120 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.27e-02 6.20e+03 1.20e+00 bond pdb=" CA VAL H 190 " pdb=" C VAL H 190 " ideal model delta sigma weight residual 1.516 1.526 -0.011 1.11e-02 8.12e+03 9.25e-01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 32544 1.07 - 2.14: 2738 2.14 - 3.20: 217 3.20 - 4.27: 71 4.27 - 5.34: 29 Bond angle restraints: 35599 Sorted by residual: angle pdb=" N VAL H 190 " pdb=" CA VAL H 190 " pdb=" C VAL H 190 " ideal model delta sigma weight residual 109.19 106.11 3.08 8.20e-01 1.49e+00 1.42e+01 angle pdb=" CA VAL H 190 " pdb=" C VAL H 190 " pdb=" N PRO H 191 " ideal model delta sigma weight residual 116.57 120.18 -3.61 9.80e-01 1.04e+00 1.35e+01 angle pdb=" C VAL H 190 " pdb=" CA VAL H 190 " pdb=" CB VAL H 190 " ideal model delta sigma weight residual 109.33 112.38 -3.05 9.80e-01 1.04e+00 9.67e+00 angle pdb=" N GLY H 145 " pdb=" CA GLY H 145 " pdb=" C GLY H 145 " ideal model delta sigma weight residual 111.27 116.40 -5.13 1.67e+00 3.59e-01 9.44e+00 angle pdb=" O SER M 119 " pdb=" C SER M 119 " pdb=" N ALA M 120 " ideal model delta sigma weight residual 122.68 119.07 3.61 1.27e+00 6.20e-01 8.10e+00 ... (remaining 35594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 8574 16.98 - 33.96: 563 33.96 - 50.94: 167 50.94 - 67.92: 74 67.92 - 84.91: 20 Dihedral angle restraints: 9398 sinusoidal: 5099 harmonic: 4299 Sorted by residual: dihedral pdb=" CA SER M 119 " pdb=" C SER M 119 " pdb=" N ALA M 120 " pdb=" CA ALA M 120 " ideal model delta harmonic sigma weight residual 180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 90 " pdb=" CB CYS N 90 " ideal model delta sinusoidal sigma weight residual 93.00 57.52 35.48 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA CYS M 99 " pdb=" C CYS M 99 " pdb=" N VAL M 100 " pdb=" CA VAL M 100 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1071 0.034 - 0.068: 362 0.068 - 0.101: 96 0.101 - 0.135: 45 0.135 - 0.169: 11 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA VAL M 148 " pdb=" N VAL M 148 " pdb=" C VAL M 148 " pdb=" CB VAL M 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA VAL H 190 " pdb=" N VAL H 190 " pdb=" C VAL H 190 " pdb=" CB VAL H 190 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA VAL H 148 " pdb=" N VAL H 148 " pdb=" C VAL H 148 " pdb=" CB VAL H 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1582 not shown) Planarity restraints: 3015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 119 " 0.024 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C SER M 119 " -0.079 2.00e-02 2.50e+03 pdb=" O SER M 119 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA M 120 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 33 " -0.013 2.00e-02 2.50e+03 8.89e-03 2.37e+00 pdb=" CG TYR M 33 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR M 33 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR M 33 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR M 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR M 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR M 33 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR M 33 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR M 33 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR M 33 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR M 33 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR M 33 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 79 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C GLU A 79 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU A 79 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 80 " -0.009 2.00e-02 2.50e+03 ... (remaining 3012 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2170 2.25 - 2.84: 44806 2.84 - 3.42: 50208 3.42 - 4.01: 69800 4.01 - 4.60: 107200 Nonbonded interactions: 274184 Sorted by model distance: nonbonded pdb=" H SER H 162 " pdb=" OD1 ASN H 203 " model vdw 1.662 2.450 nonbonded pdb=" H GLN L 171 " pdb=" O LYS L 175 " model vdw 1.664 2.450 nonbonded pdb=" O ASP B 37 " pdb=" HG1 THR B 41 " model vdw 1.674 2.450 nonbonded pdb=" OE1 GLN A 42 " pdb=" H ILE C 172 " model vdw 1.680 2.450 nonbonded pdb=" H GLY M 15 " pdb=" O LEU M 86 " model vdw 1.685 2.450 ... (remaining 274179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 23 through 135 or (resid 136 and (name N or name CA or nam \ e C or name O or name HA2 or name HA3)) or resid 137 through 181)) selection = (chain 'C' and (resid 23 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name H \ B2 or name HB3 or name HD21 or name HD22)) or (resid 136 and (name N or name CA \ or name C or name O or name HA2 or name HA3)) or resid 137 through 181)) } ncs_group { reference = chain 'H' selection = (chain 'M' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2)) or resid 34 through 219)) } ncs_group { reference = chain 'L' selection = (chain 'N' and (resid 1 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 98 through 213)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.360 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 41.650 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10094 Z= 0.182 Angle : 0.650 5.339 13721 Z= 0.377 Chirality : 0.041 0.169 1585 Planarity : 0.005 0.046 1772 Dihedral : 11.434 84.819 3614 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1293 helix: 0.94 (0.25), residues: 340 sheet: -0.41 (0.23), residues: 456 loop : -0.40 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 50 HIS 0.005 0.001 HIS A 74 PHE 0.009 0.002 PHE A 157 TYR 0.025 0.002 TYR H 33 ARG 0.004 0.001 ARG N 193 Details of bonding type rmsd hydrogen bonds : bond 0.18237 ( 521) hydrogen bonds : angle 7.54637 ( 1458) SS BOND : bond 0.00216 ( 11) SS BOND : angle 1.06216 ( 22) covalent geometry : bond 0.00352 (10083) covalent geometry : angle 0.64945 (13699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.653 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: 0.5894 time to fit residues: 208.6768 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 : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS H 39 GLN L 192 HIS ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.050596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.035155 restraints weight = 205832.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.037559 restraints weight = 116126.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.039424 restraints weight = 75772.333| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 10094 Z= 0.159 Angle : 0.556 19.585 13721 Z= 0.306 Chirality : 0.039 0.148 1585 Planarity : 0.004 0.058 1772 Dihedral : 4.328 17.345 1375 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.17 % Favored : 96.67 % Rotamer: Outliers : 0.09 % Allowed : 1.26 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1293 helix: 2.71 (0.25), residues: 352 sheet: -0.35 (0.23), residues: 458 loop : -0.35 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.006 0.001 HIS B 30 PHE 0.014 0.001 PHE H 101 TYR 0.010 0.001 TYR M 33 ARG 0.003 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 521) hydrogen bonds : angle 5.27247 ( 1458) SS BOND : bond 0.00314 ( 11) SS BOND : angle 4.47176 ( 22) covalent geometry : bond 0.00377 (10083) covalent geometry : angle 0.52635 (13699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9111 (mt) cc_final: 0.8786 (tt) REVERT: B 119 GLU cc_start: 0.9406 (mt-10) cc_final: 0.8946 (mm-30) REVERT: C 64 GLN cc_start: 0.9638 (mt0) cc_final: 0.9325 (mm110) REVERT: C 158 ASN cc_start: 0.9364 (t0) cc_final: 0.8987 (m110) REVERT: H 37 MET cc_start: 0.9163 (mmp) cc_final: 0.8889 (tmm) REVERT: H 106 PHE cc_start: 0.9460 (m-80) cc_final: 0.9153 (m-10) REVERT: L 75 LEU cc_start: 0.9391 (tp) cc_final: 0.9112 (tp) REVERT: L 138 CYS cc_start: 0.7457 (t) cc_final: 0.6793 (t) REVERT: M 45 LEU cc_start: 0.9323 (mt) cc_final: 0.9119 (mp) REVERT: N 164 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8158 (mp0) REVERT: N 181 TYR cc_start: 0.9076 (m-10) cc_final: 0.8771 (m-80) REVERT: N 197 CYS cc_start: 0.8148 (t) cc_final: 0.7574 (t) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.6297 time to fit residues: 165.7425 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 : 1.647 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 107 optimal weight: 0.0000 chunk 76 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS H 39 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.050784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035517 restraints weight = 207908.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037925 restraints weight = 117732.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039810 restraints weight = 76645.640| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 10094 Z= 0.115 Angle : 0.497 9.931 13721 Z= 0.268 Chirality : 0.039 0.140 1585 Planarity : 0.003 0.042 1772 Dihedral : 4.202 29.547 1375 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.25 % Favored : 96.60 % Rotamer: Outliers : 0.18 % Allowed : 0.63 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1293 helix: 2.93 (0.25), residues: 355 sheet: -0.28 (0.24), residues: 458 loop : -0.38 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 47 HIS 0.005 0.001 HIS A 27 PHE 0.005 0.001 PHE A 157 TYR 0.007 0.001 TYR N 38 ARG 0.019 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 521) hydrogen bonds : angle 4.82070 ( 1458) SS BOND : bond 0.00257 ( 11) SS BOND : angle 2.22725 ( 22) covalent geometry : bond 0.00256 (10083) covalent geometry : angle 0.48926 (13699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 1.821 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: A 72 GLU cc_start: 0.9781 (mm-30) cc_final: 0.9400 (tm-30) REVERT: B 97 GLU cc_start: 0.9396 (pt0) cc_final: 0.9128 (pt0) REVERT: B 119 GLU cc_start: 0.9415 (mt-10) cc_final: 0.8867 (mm-30) REVERT: C 64 GLN cc_start: 0.9661 (mt0) cc_final: 0.9349 (mm110) REVERT: H 106 PHE cc_start: 0.9406 (m-80) cc_final: 0.9004 (m-10) REVERT: L 75 LEU cc_start: 0.9390 (tp) cc_final: 0.9104 (tp) REVERT: L 138 CYS cc_start: 0.7498 (t) cc_final: 0.7011 (t) REVERT: L 198 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8915 (mp10) REVERT: M 48 MET cc_start: 0.9222 (mtp) cc_final: 0.8861 (mtp) REVERT: M 83 LEU cc_start: 0.9575 (tp) cc_final: 0.9358 (tp) REVERT: N 164 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8140 (mp0) REVERT: N 181 TYR cc_start: 0.9048 (m-10) cc_final: 0.8798 (m-80) REVERT: N 197 CYS cc_start: 0.8028 (t) cc_final: 0.7232 (p) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.6213 time to fit residues: 150.5799 Evaluate side-chains 157 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN H 39 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.049317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.034300 restraints weight = 214520.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036604 restraints weight = 122475.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.038414 restraints weight = 80313.903| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10094 Z= 0.152 Angle : 0.498 8.122 13721 Z= 0.274 Chirality : 0.038 0.150 1585 Planarity : 0.003 0.037 1772 Dihedral : 4.206 31.362 1375 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.59 % 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: 0.74 (0.24), residues: 1293 helix: 2.70 (0.25), residues: 358 sheet: -0.23 (0.24), residues: 454 loop : -0.39 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.005 0.001 HIS H 59 PHE 0.008 0.001 PHE A 167 TYR 0.008 0.001 TYR H 151 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 521) hydrogen bonds : angle 4.84176 ( 1458) SS BOND : bond 0.00296 ( 11) SS BOND : angle 1.81206 ( 22) covalent geometry : bond 0.00305 (10083) covalent geometry : angle 0.49278 (13699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 1.522 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: B 96 ILE cc_start: 0.9812 (tp) cc_final: 0.9600 (pt) REVERT: B 97 GLU cc_start: 0.9445 (pt0) cc_final: 0.9203 (pt0) REVERT: B 119 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8932 (mm-30) REVERT: C 158 ASN cc_start: 0.9339 (t0) cc_final: 0.9011 (m110) REVERT: H 106 PHE cc_start: 0.9397 (m-80) cc_final: 0.8991 (m-10) REVERT: L 75 LEU cc_start: 0.9418 (tp) cc_final: 0.9092 (tp) REVERT: L 77 ILE cc_start: 0.9646 (mt) cc_final: 0.9381 (tt) REVERT: L 138 CYS cc_start: 0.7563 (t) cc_final: 0.7167 (t) REVERT: M 48 MET cc_start: 0.9296 (mtp) cc_final: 0.8965 (mtp) REVERT: N 64 PHE cc_start: 0.9271 (m-80) cc_final: 0.9021 (m-80) REVERT: N 138 CYS cc_start: 0.7352 (t) cc_final: 0.7022 (t) REVERT: N 197 CYS cc_start: 0.8030 (t) cc_final: 0.7510 (t) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.6096 time to fit residues: 138.1644 Evaluate side-chains 154 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN M 177 GLN N 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.046615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.032529 restraints weight = 231429.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.034659 restraints weight = 133520.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.036319 restraints weight = 88255.311| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10094 Z= 0.250 Angle : 0.614 5.303 13721 Z= 0.350 Chirality : 0.039 0.187 1585 Planarity : 0.004 0.037 1772 Dihedral : 4.851 29.596 1375 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1293 helix: 1.54 (0.25), residues: 358 sheet: -0.50 (0.24), residues: 448 loop : -0.80 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 109 HIS 0.007 0.002 HIS H 170 PHE 0.012 0.002 PHE A 167 TYR 0.013 0.002 TYR M 33 ARG 0.003 0.001 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 521) hydrogen bonds : angle 5.50206 ( 1458) SS BOND : bond 0.00689 ( 11) SS BOND : angle 1.08939 ( 22) covalent geometry : bond 0.00466 (10083) covalent geometry : angle 0.61279 (13699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.593 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 66 LEU cc_start: 0.9678 (mt) cc_final: 0.9428 (mt) REVERT: B 119 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8997 (mm-30) REVERT: H 106 PHE cc_start: 0.9461 (m-80) cc_final: 0.9165 (m-10) REVERT: L 197 CYS cc_start: 0.8876 (t) cc_final: 0.8670 (t) REVERT: N 64 PHE cc_start: 0.9126 (m-80) cc_final: 0.8903 (m-80) REVERT: N 138 CYS cc_start: 0.7261 (t) cc_final: 0.6807 (t) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.6391 time to fit residues: 131.3476 Evaluate side-chains 124 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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: 0.0070 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN H 3 GLN M 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.033467 restraints weight = 219361.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035727 restraints weight = 124970.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.037487 restraints weight = 81910.666| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10094 Z= 0.113 Angle : 0.487 5.386 13721 Z= 0.267 Chirality : 0.039 0.153 1585 Planarity : 0.003 0.034 1772 Dihedral : 4.375 17.279 1375 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.71 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1293 helix: 2.16 (0.25), residues: 370 sheet: -0.37 (0.24), residues: 448 loop : -0.74 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 160 HIS 0.004 0.001 HIS H 59 PHE 0.013 0.001 PHE A 167 TYR 0.040 0.001 TYR M 33 ARG 0.002 0.000 ARG L 193 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 521) hydrogen bonds : angle 4.82565 ( 1458) SS BOND : bond 0.00505 ( 11) SS BOND : angle 1.07469 ( 22) covalent geometry : bond 0.00235 (10083) covalent geometry : angle 0.48566 (13699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.821 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: B 119 GLU cc_start: 0.9444 (mt-10) cc_final: 0.8910 (mm-30) REVERT: H 45 LEU cc_start: 0.9009 (mm) cc_final: 0.8762 (mm) REVERT: L 138 CYS cc_start: 0.7555 (t) cc_final: 0.6542 (t) REVERT: L 197 CYS cc_start: 0.9055 (t) cc_final: 0.8752 (t) REVERT: M 48 MET cc_start: 0.9205 (mtp) cc_final: 0.8849 (mtp) REVERT: N 64 PHE cc_start: 0.9160 (m-80) cc_final: 0.8939 (m-80) REVERT: N 75 LEU cc_start: 0.9204 (tp) cc_final: 0.9000 (tp) REVERT: N 138 CYS cc_start: 0.7416 (t) cc_final: 0.7152 (t) REVERT: N 197 CYS cc_start: 0.7410 (t) cc_final: 0.6979 (t) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.6378 time to fit residues: 134.3541 Evaluate side-chains 144 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 64 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: A 95 GLN C 62 ASN C 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.033489 restraints weight = 221739.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.035745 restraints weight = 127018.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.037494 restraints weight = 83567.386| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10094 Z= 0.134 Angle : 0.490 6.484 13721 Z= 0.271 Chirality : 0.038 0.143 1585 Planarity : 0.003 0.037 1772 Dihedral : 4.308 17.118 1375 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % 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: 0.57 (0.24), residues: 1293 helix: 2.52 (0.25), residues: 358 sheet: -0.31 (0.24), residues: 444 loop : -0.49 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.006 0.001 HIS H 170 PHE 0.012 0.001 PHE A 167 TYR 0.033 0.002 TYR H 33 ARG 0.002 0.000 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 521) hydrogen bonds : angle 4.82080 ( 1458) SS BOND : bond 0.00317 ( 11) SS BOND : angle 0.68444 ( 22) covalent geometry : bond 0.00267 (10083) covalent geometry : angle 0.48961 (13699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.9437 (mt-10) cc_final: 0.8986 (mm-30) REVERT: B 140 THR cc_start: 0.7269 (p) cc_final: 0.7024 (t) REVERT: C 92 ILE cc_start: 0.9347 (mm) cc_final: 0.9029 (mt) REVERT: M 48 MET cc_start: 0.9233 (mtp) cc_final: 0.8878 (mtp) REVERT: M 160 TRP cc_start: 0.8800 (m100) cc_final: 0.8558 (m100) REVERT: N 64 PHE cc_start: 0.9152 (m-80) cc_final: 0.8935 (m-80) REVERT: N 75 LEU cc_start: 0.9228 (tp) cc_final: 0.9015 (tp) REVERT: N 138 CYS cc_start: 0.7382 (t) cc_final: 0.6950 (t) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.6499 time to fit residues: 130.6109 Evaluate side-chains 134 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 4.9990 chunk 122 optimal weight: 0.0870 chunk 115 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN H 177 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.045572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.031714 restraints weight = 238011.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.033793 restraints weight = 137935.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.035422 restraints weight = 91589.888| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 10094 Z= 0.284 Angle : 0.636 5.346 13721 Z= 0.364 Chirality : 0.039 0.137 1585 Planarity : 0.004 0.040 1772 Dihedral : 4.889 18.701 1375 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.96 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1293 helix: 1.29 (0.25), residues: 358 sheet: -0.64 (0.24), residues: 442 loop : -1.02 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 152 HIS 0.008 0.002 HIS H 170 PHE 0.015 0.002 PHE A 167 TYR 0.029 0.002 TYR H 33 ARG 0.006 0.001 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 521) hydrogen bonds : angle 5.57966 ( 1458) SS BOND : bond 0.00411 ( 11) SS BOND : angle 0.82816 ( 22) covalent geometry : bond 0.00533 (10083) covalent geometry : angle 0.63566 (13699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.9693 (mt) cc_final: 0.9454 (mt) REVERT: B 119 GLU cc_start: 0.9604 (mt-10) cc_final: 0.9104 (mm-30) REVERT: C 123 LYS cc_start: 0.9479 (mttt) cc_final: 0.9077 (mmmm) REVERT: H 106 PHE cc_start: 0.9504 (m-10) cc_final: 0.9149 (m-10) REVERT: M 34 ILE cc_start: 0.9882 (mm) cc_final: 0.9668 (tp) REVERT: M 160 TRP cc_start: 0.8850 (m100) cc_final: 0.8222 (m100) REVERT: N 138 CYS cc_start: 0.7142 (t) cc_final: 0.6676 (t) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.6543 time to fit residues: 118.2195 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 : 1.384 ------------------------------------------------------------------------------- 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: 3.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 107 optimal weight: 0.0170 chunk 114 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS C 95 GLN L 39 GLN M 39 GLN M 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.047461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.032994 restraints weight = 219599.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.035234 restraints weight = 126388.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.036979 restraints weight = 83450.225| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10094 Z= 0.109 Angle : 0.486 4.062 13721 Z= 0.265 Chirality : 0.039 0.148 1585 Planarity : 0.003 0.033 1772 Dihedral : 4.425 17.361 1375 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1293 helix: 2.31 (0.25), residues: 355 sheet: -0.57 (0.24), residues: 454 loop : -0.61 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 189 HIS 0.005 0.001 HIS H 59 PHE 0.013 0.001 PHE A 167 TYR 0.029 0.001 TYR H 33 ARG 0.008 0.001 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 521) hydrogen bonds : angle 4.83897 ( 1458) SS BOND : bond 0.00218 ( 11) SS BOND : angle 0.75645 ( 22) covalent geometry : bond 0.00233 (10083) covalent geometry : angle 0.48591 (13699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.9537 (mt-10) cc_final: 0.9027 (mm-30) REVERT: C 92 ILE cc_start: 0.9444 (mm) cc_final: 0.9123 (mt) REVERT: C 122 LEU cc_start: 0.9571 (mt) cc_final: 0.9355 (mt) REVERT: C 123 LYS cc_start: 0.9337 (mttt) cc_final: 0.8948 (mmmm) REVERT: M 34 ILE cc_start: 0.9888 (mm) cc_final: 0.9678 (tp) REVERT: M 48 MET cc_start: 0.9209 (mtp) cc_final: 0.8791 (mtp) REVERT: M 106 PHE cc_start: 0.9560 (m-80) cc_final: 0.9356 (m-10) REVERT: N 64 PHE cc_start: 0.9233 (m-80) cc_final: 0.9026 (m-80) REVERT: N 75 LEU cc_start: 0.9221 (tp) cc_final: 0.8980 (tp) REVERT: N 138 CYS cc_start: 0.7481 (t) cc_final: 0.7062 (t) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.6381 time to fit residues: 125.8672 Evaluate side-chains 131 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 0.0370 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN C 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.048116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.033681 restraints weight = 222309.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.035999 restraints weight = 126160.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037796 restraints weight = 82465.274| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10094 Z= 0.098 Angle : 0.469 4.524 13721 Z= 0.254 Chirality : 0.039 0.141 1585 Planarity : 0.003 0.035 1772 Dihedral : 4.195 19.016 1375 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.33 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1293 helix: 2.73 (0.26), residues: 355 sheet: -0.41 (0.24), residues: 454 loop : -0.45 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 160 HIS 0.011 0.001 HIS C 142 PHE 0.020 0.001 PHE A 167 TYR 0.023 0.001 TYR H 33 ARG 0.007 0.000 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 521) hydrogen bonds : angle 4.52552 ( 1458) SS BOND : bond 0.00256 ( 11) SS BOND : angle 0.98374 ( 22) covalent geometry : bond 0.00216 (10083) covalent geometry : angle 0.46767 (13699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.9688 (mt) cc_final: 0.9479 (mt) REVERT: B 97 GLU cc_start: 0.9421 (pt0) cc_final: 0.9173 (pt0) REVERT: B 119 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9092 (mm-30) REVERT: B 140 THR cc_start: 0.7603 (p) cc_final: 0.7293 (t) REVERT: C 81 ASP cc_start: 0.9630 (t0) cc_final: 0.9320 (t0) REVERT: C 92 ILE cc_start: 0.9372 (mm) cc_final: 0.8987 (mt) REVERT: C 123 LYS cc_start: 0.9308 (mttt) cc_final: 0.8933 (mmmm) REVERT: M 34 ILE cc_start: 0.9892 (mm) cc_final: 0.9661 (tp) REVERT: M 160 TRP cc_start: 0.8732 (m100) cc_final: 0.8092 (m100) REVERT: N 64 PHE cc_start: 0.9240 (m-80) cc_final: 0.9021 (m-80) REVERT: N 75 LEU cc_start: 0.9200 (tp) cc_final: 0.8946 (tp) REVERT: N 138 CYS cc_start: 0.7476 (t) cc_final: 0.7070 (t) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.6461 time to fit residues: 130.0752 Evaluate side-chains 138 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 0.0770 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.032384 restraints weight = 231586.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.034542 restraints weight = 133844.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.036214 restraints weight = 88527.229| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10094 Z= 0.198 Angle : 0.538 4.610 13721 Z= 0.303 Chirality : 0.038 0.138 1585 Planarity : 0.004 0.036 1772 Dihedral : 4.434 17.619 1375 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.03 (0.23), residues: 1293 helix: 1.94 (0.25), residues: 358 sheet: -0.54 (0.24), residues: 452 loop : -0.77 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.005 0.001 HIS H 59 PHE 0.021 0.002 PHE A 167 TYR 0.022 0.002 TYR H 33 ARG 0.007 0.001 ARG M 72 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 521) hydrogen bonds : angle 5.00213 ( 1458) SS BOND : bond 0.00319 ( 11) SS BOND : angle 0.93977 ( 22) covalent geometry : bond 0.00377 (10083) covalent geometry : angle 0.53692 (13699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6406.21 seconds wall clock time: 110 minutes 27.00 seconds (6627.00 seconds total)