Starting phenix.real_space_refine on Fri Feb 14 17:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kzx_23092/02_2025/7kzx_23092.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kzx_23092/02_2025/7kzx_23092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kzx_23092/02_2025/7kzx_23092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kzx_23092/02_2025/7kzx_23092.map" model { file = "/net/cci-nas-00/data/ceres_data/7kzx_23092/02_2025/7kzx_23092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kzx_23092/02_2025/7kzx_23092.cif" } resolution = 4.0 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= 0.044 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 6658 2.51 5 N 1754 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10432 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2163 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain: "B" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2163 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain: "C" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1460 Classifications: {'peptide': 190} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 179} Chain breaks: 1 Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1468 Classifications: {'peptide': 191} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 180} Chain breaks: 1 Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Time building chain proxies: 6.74, per 1000 atoms: 0.65 Number of scatterers: 10432 At special positions: 0 Unit cell: (75.555, 151.11, 150.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1992 8.00 N 1754 7.00 C 6658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.4 seconds 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 24 sheets defined 32.0% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 13 through 35 removed outlier: 3.579A pdb=" N VAL A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 Processing helix chain 'A' and resid 80 through 107 removed outlier: 3.788A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 138 removed outlier: 3.557A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.826A pdb=" N SER A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 208 removed outlier: 4.183A pdb=" N GLY A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 258 through 277 Processing helix chain 'B' and resid 13 through 35 removed outlier: 3.723A pdb=" N TYR B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 64 removed outlier: 3.846A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.686A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 138 removed outlier: 3.704A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 175 removed outlier: 4.872A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 208 removed outlier: 4.357A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 258 through 277 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.709A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 221 Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 186 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.511A pdb=" N ASP A 235 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL A 245 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 283 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 247 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254 removed outlier: 6.543A pdb=" N LEU A 253 " --> pdb=" O VAL A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 233 removed outlier: 6.201A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 283 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE B 247 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS B 285 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 249 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.409A pdb=" N LEU C 12 " --> pdb=" O GLU C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.270A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.949A pdb=" N ALA C 132 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU C 183 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 134 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 140 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 8 through 9 Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 5.200A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR D 120 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 60 through 63 removed outlier: 5.200A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 106 through 108 removed outlier: 3.518A pdb=" N SER D 108 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 137 through 140 removed outlier: 3.616A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 137 through 140 removed outlier: 3.616A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 213 through 217 Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.538A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.910A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 118 through 120 removed outlier: 5.844A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 7 through 10 Processing sheet with id=AC2, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.898A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 139 removed outlier: 3.512A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 137 through 139 removed outlier: 3.512A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.555A pdb=" N SER F 170 " --> pdb=" O ASN F 214 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN F 214 " --> pdb=" O SER F 170 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1539 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: 3.24 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3322 1.34 - 1.46: 2067 1.46 - 1.57: 5233 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 10660 Sorted by residual: bond pdb=" C LYS E 43 " pdb=" N ALA E 44 " ideal model delta sigma weight residual 1.331 1.287 0.045 1.63e-02 3.76e+03 7.46e+00 bond pdb=" CA ARG C 144 " pdb=" C ARG C 144 " ideal model delta sigma weight residual 1.524 1.471 0.053 2.25e-02 1.98e+03 5.46e+00 bond pdb=" C LYS F 218 " pdb=" N PRO F 219 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.08e-02 8.57e+03 4.16e+00 bond pdb=" C GLN C 39 " pdb=" N LYS C 40 " ideal model delta sigma weight residual 1.330 1.305 0.025 1.47e-02 4.63e+03 2.98e+00 bond pdb=" CB TRP E 93 " pdb=" CG TRP E 93 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.89e+00 ... (remaining 10655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 13391 1.38 - 2.75: 919 2.75 - 4.13: 157 4.13 - 5.50: 28 5.50 - 6.88: 16 Bond angle restraints: 14511 Sorted by residual: angle pdb=" N ILE A 66 " pdb=" CA ILE A 66 " pdb=" C ILE A 66 " ideal model delta sigma weight residual 113.00 107.36 5.64 1.30e+00 5.92e-01 1.88e+01 angle pdb=" C VAL B 149 " pdb=" N GLU B 150 " pdb=" CA GLU B 150 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.45e+00 angle pdb=" C VAL F 51 " pdb=" N ALA F 52 " pdb=" CA ALA F 52 " ideal model delta sigma weight residual 121.63 115.87 5.76 1.92e+00 2.71e-01 9.01e+00 angle pdb=" CA ARG F 111 " pdb=" CB ARG F 111 " pdb=" CG ARG F 111 " ideal model delta sigma weight residual 114.10 119.82 -5.72 2.00e+00 2.50e-01 8.18e+00 angle pdb=" N GLY F 179 " pdb=" CA GLY F 179 " pdb=" C GLY F 179 " ideal model delta sigma weight residual 113.18 106.45 6.73 2.37e+00 1.78e-01 8.06e+00 ... (remaining 14506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 5765 18.18 - 36.35: 412 36.35 - 54.53: 79 54.53 - 72.71: 45 72.71 - 90.88: 20 Dihedral angle restraints: 6321 sinusoidal: 2362 harmonic: 3959 Sorted by residual: dihedral pdb=" CA SER C 94 " pdb=" C SER C 94 " pdb=" N TRP C 95 " pdb=" CA TRP C 95 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS C 196 " pdb=" C CYS C 196 " pdb=" N GLU C 197 " pdb=" CA GLU C 197 " ideal model delta harmonic sigma weight residual 180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PRO B 228 " pdb=" C PRO B 228 " pdb=" N ARG B 229 " pdb=" CA ARG B 229 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 6318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1257 0.047 - 0.094: 341 0.094 - 0.141: 82 0.141 - 0.188: 8 0.188 - 0.235: 1 Chirality restraints: 1689 Sorted by residual: chirality pdb=" CB ILE B 284 " pdb=" CA ILE B 284 " pdb=" CG1 ILE B 284 " pdb=" CG2 ILE B 284 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ARG D 111 " pdb=" N ARG D 111 " pdb=" C ARG D 111 " pdb=" CB ARG D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CB VAL A 230 " pdb=" CA VAL A 230 " pdb=" CG1 VAL A 230 " pdb=" CG2 VAL A 230 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 1686 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO F 166 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 76 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ASP D 76 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP D 76 " 0.014 2.00e-02 2.50e+03 pdb=" N THR D 77 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 195 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C GLN B 195 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN B 195 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA B 196 " -0.012 2.00e-02 2.50e+03 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 141 2.61 - 3.18: 10116 3.18 - 3.75: 16628 3.75 - 4.33: 22413 4.33 - 4.90: 35955 Nonbonded interactions: 85253 Sorted by model distance: nonbonded pdb=" O SER F 34 " pdb=" OH TYR F 104 " model vdw 2.031 3.040 nonbonded pdb=" OG SER C 94 " pdb=" O LEU C 97 " model vdw 2.113 3.040 nonbonded pdb=" OH TYR F 162 " pdb=" OE1 GLU F 165 " model vdw 2.161 3.040 nonbonded pdb=" O ASP C 83 " pdb=" OH TYR C 87 " model vdw 2.161 3.040 nonbonded pdb=" O LEU B 212 " pdb=" NH1 ARG B 217 " model vdw 2.165 3.120 ... (remaining 85248 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' } ncs_group { reference = (chain 'C' and resid 2 through 202) selection = (chain 'E' and (resid 2 through 149 or resid 162 through 202)) } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 2.210 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10660 Z= 0.406 Angle : 0.807 6.881 14511 Z= 0.457 Chirality : 0.045 0.235 1689 Planarity : 0.006 0.080 1826 Dihedral : 15.745 90.882 3759 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.27 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.29 (0.22), residues: 1337 helix: -0.18 (0.25), residues: 398 sheet: -1.17 (0.27), residues: 338 loop : -2.68 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 179 HIS 0.008 0.002 HIS B 155 PHE 0.015 0.002 PHE C 72 TYR 0.028 0.002 TYR F 104 ARG 0.008 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.219 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: A 41 MET cc_start: 0.8504 (ttm) cc_final: 0.8281 (ttt) REVERT: A 99 LEU cc_start: 0.9405 (mt) cc_final: 0.9166 (mt) REVERT: B 190 CYS cc_start: 0.9491 (t) cc_final: 0.9168 (m) REVERT: D 50 TRP cc_start: 0.8398 (t60) cc_final: 0.7994 (t60) REVERT: D 93 ASP cc_start: 0.7952 (m-30) cc_final: 0.7429 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2774 time to fit residues: 44.3041 Evaluate side-chains 56 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN D 188 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.077845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058823 restraints weight = 51634.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.059589 restraints weight = 31764.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059849 restraints weight = 23790.556| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10660 Z= 0.288 Angle : 0.707 10.540 14511 Z= 0.374 Chirality : 0.045 0.187 1689 Planarity : 0.005 0.056 1826 Dihedral : 5.917 38.452 1461 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.08 % Favored : 91.77 % Rotamer: Outliers : 1.31 % Allowed : 11.57 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.73 (0.22), residues: 1337 helix: 0.41 (0.26), residues: 401 sheet: -0.83 (0.28), residues: 312 loop : -2.41 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 93 HIS 0.007 0.001 HIS B 71 PHE 0.018 0.002 PHE F 130 TYR 0.027 0.002 TYR F 104 ARG 0.005 0.001 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8824 (ttm) cc_final: 0.8554 (ttt) REVERT: A 93 MET cc_start: 0.8905 (mmm) cc_final: 0.8606 (tpp) REVERT: A 99 LEU cc_start: 0.9511 (mt) cc_final: 0.9247 (mt) REVERT: B 98 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9001 (mp) REVERT: B 190 CYS cc_start: 0.9278 (t) cc_final: 0.8985 (m) REVERT: C 5 MET cc_start: 0.8304 (mmm) cc_final: 0.7717 (mmm) REVERT: D 50 TRP cc_start: 0.8479 (t60) cc_final: 0.8122 (t60) REVERT: D 92 GLU cc_start: 0.8196 (tp30) cc_final: 0.7987 (tp30) REVERT: D 157 CYS cc_start: 0.6285 (p) cc_final: 0.6065 (p) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.2106 time to fit residues: 28.3001 Evaluate side-chains 63 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain F residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.0060 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.077821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.057889 restraints weight = 52269.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.059546 restraints weight = 29273.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.060621 restraints weight = 20228.302| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10660 Z= 0.277 Angle : 0.667 9.445 14511 Z= 0.351 Chirality : 0.043 0.177 1689 Planarity : 0.005 0.055 1826 Dihedral : 5.610 28.538 1461 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.82 % Rotamer: Outliers : 2.28 % Allowed : 14.72 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.51 (0.22), residues: 1337 helix: 0.66 (0.25), residues: 405 sheet: -0.96 (0.27), residues: 334 loop : -2.23 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 93 HIS 0.005 0.001 HIS B 71 PHE 0.020 0.001 PHE E 120 TYR 0.022 0.002 TYR F 104 ARG 0.006 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8730 (mmm) cc_final: 0.8448 (tpp) REVERT: A 99 LEU cc_start: 0.9562 (mt) cc_final: 0.9333 (mt) REVERT: B 93 MET cc_start: 0.9035 (mmm) cc_final: 0.8814 (mmm) REVERT: B 190 CYS cc_start: 0.9297 (t) cc_final: 0.8964 (m) REVERT: D 50 TRP cc_start: 0.8487 (t60) cc_final: 0.8120 (t60) REVERT: D 92 GLU cc_start: 0.8381 (tp30) cc_final: 0.8014 (tp30) REVERT: D 115 TYR cc_start: 0.8839 (m-80) cc_final: 0.8631 (m-10) REVERT: D 157 CYS cc_start: 0.6265 (p) cc_final: 0.6047 (p) REVERT: E 102 GLN cc_start: 0.7749 (mm110) cc_final: 0.7504 (tp40) outliers start: 26 outliers final: 12 residues processed: 82 average time/residue: 0.1992 time to fit residues: 25.0712 Evaluate side-chains 66 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain F residue 8 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.077765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.060625 restraints weight = 52044.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.060989 restraints weight = 35454.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061327 restraints weight = 28096.143| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10660 Z= 0.274 Angle : 0.654 8.932 14511 Z= 0.342 Chirality : 0.043 0.147 1689 Planarity : 0.005 0.055 1826 Dihedral : 5.529 34.872 1461 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 2.10 % Allowed : 16.13 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.37 (0.23), residues: 1337 helix: 0.81 (0.25), residues: 406 sheet: -0.98 (0.27), residues: 340 loop : -2.11 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 33 HIS 0.004 0.001 HIS A 155 PHE 0.010 0.001 PHE C 72 TYR 0.019 0.002 TYR F 104 ARG 0.006 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8752 (mmm) cc_final: 0.8412 (tpp) REVERT: A 99 LEU cc_start: 0.9463 (mt) cc_final: 0.9238 (mt) REVERT: B 101 PHE cc_start: 0.7146 (t80) cc_final: 0.6300 (t80) REVERT: B 190 CYS cc_start: 0.9224 (t) cc_final: 0.9002 (m) REVERT: C 5 MET cc_start: 0.8182 (mmm) cc_final: 0.7702 (mmm) REVERT: D 50 TRP cc_start: 0.8497 (t60) cc_final: 0.8081 (t60) REVERT: D 92 GLU cc_start: 0.8632 (tp30) cc_final: 0.8397 (tp30) REVERT: D 115 TYR cc_start: 0.8786 (m-80) cc_final: 0.8577 (m-10) REVERT: E 102 GLN cc_start: 0.7860 (mm110) cc_final: 0.7606 (tp40) outliers start: 24 outliers final: 15 residues processed: 85 average time/residue: 0.1945 time to fit residues: 25.3400 Evaluate side-chains 67 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.077775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059106 restraints weight = 52352.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059679 restraints weight = 30990.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060555 restraints weight = 22103.555| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10660 Z= 0.274 Angle : 0.647 10.284 14511 Z= 0.338 Chirality : 0.042 0.167 1689 Planarity : 0.005 0.054 1826 Dihedral : 5.368 31.883 1461 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 3.42 % Allowed : 15.95 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.19 (0.23), residues: 1337 helix: 0.87 (0.26), residues: 406 sheet: -0.80 (0.27), residues: 336 loop : -1.97 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 33 HIS 0.005 0.001 HIS B 71 PHE 0.013 0.001 PHE A 97 TYR 0.017 0.001 TYR F 104 ARG 0.004 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 58 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7930 (t60) cc_final: 0.7570 (t60) REVERT: A 93 MET cc_start: 0.8849 (mmm) cc_final: 0.8545 (tpp) REVERT: A 99 LEU cc_start: 0.9565 (mt) cc_final: 0.9333 (mt) REVERT: A 101 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: B 93 MET cc_start: 0.8874 (mmm) cc_final: 0.8673 (mmm) REVERT: B 101 PHE cc_start: 0.7436 (t80) cc_final: 0.6780 (t80) REVERT: C 5 MET cc_start: 0.8016 (mmm) cc_final: 0.7550 (mmm) REVERT: D 50 TRP cc_start: 0.8546 (t60) cc_final: 0.8164 (t60) REVERT: D 171 TRP cc_start: 0.7549 (OUTLIER) cc_final: 0.7101 (m100) REVERT: E 82 GLU cc_start: 0.8903 (pm20) cc_final: 0.8640 (pm20) REVERT: E 102 GLN cc_start: 0.7874 (mm110) cc_final: 0.7592 (tp40) REVERT: F 188 GLN cc_start: 0.6606 (OUTLIER) cc_final: 0.6397 (mp10) outliers start: 39 outliers final: 24 residues processed: 92 average time/residue: 0.1927 time to fit residues: 27.2753 Evaluate side-chains 75 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 188 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.077819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.059173 restraints weight = 52527.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.060173 restraints weight = 28739.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.060980 restraints weight = 21073.581| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10660 Z= 0.259 Angle : 0.642 9.379 14511 Z= 0.334 Chirality : 0.042 0.199 1689 Planarity : 0.005 0.059 1826 Dihedral : 5.290 32.067 1461 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 3.24 % Allowed : 16.83 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.09 (0.23), residues: 1337 helix: 0.97 (0.26), residues: 406 sheet: -0.77 (0.28), residues: 328 loop : -1.90 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 33 HIS 0.004 0.001 HIS B 250 PHE 0.014 0.001 PHE E 120 TYR 0.015 0.001 TYR F 104 ARG 0.010 0.000 ARG F 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 52 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8830 (mmm) cc_final: 0.8505 (tpp) REVERT: A 99 LEU cc_start: 0.9541 (mt) cc_final: 0.9330 (mt) REVERT: A 101 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8976 (m-80) REVERT: B 41 MET cc_start: 0.8736 (mmm) cc_final: 0.8405 (mmm) REVERT: B 93 MET cc_start: 0.8955 (mmm) cc_final: 0.8740 (mmm) REVERT: B 98 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9154 (mp) REVERT: D 50 TRP cc_start: 0.8508 (t60) cc_final: 0.8106 (t60) REVERT: D 171 TRP cc_start: 0.7609 (OUTLIER) cc_final: 0.7112 (m100) REVERT: E 102 GLN cc_start: 0.7755 (mm110) cc_final: 0.7469 (tp40) outliers start: 37 outliers final: 22 residues processed: 85 average time/residue: 0.2069 time to fit residues: 26.8319 Evaluate side-chains 73 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.078236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.059571 restraints weight = 53102.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060562 restraints weight = 29405.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.061456 restraints weight = 21194.872| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10660 Z= 0.234 Angle : 0.638 11.198 14511 Z= 0.330 Chirality : 0.042 0.191 1689 Planarity : 0.004 0.055 1826 Dihedral : 5.161 30.228 1461 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.97 % Rotamer: Outliers : 3.16 % Allowed : 17.35 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.92 (0.23), residues: 1337 helix: 1.14 (0.26), residues: 400 sheet: -0.80 (0.28), residues: 344 loop : -1.72 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 33 HIS 0.004 0.001 HIS A 155 PHE 0.013 0.001 PHE E 120 TYR 0.013 0.001 TYR D 55 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7831 (t60) cc_final: 0.7600 (t60) REVERT: A 93 MET cc_start: 0.8859 (mmm) cc_final: 0.8532 (tpp) REVERT: A 99 LEU cc_start: 0.9543 (mt) cc_final: 0.9342 (mt) REVERT: B 41 MET cc_start: 0.8696 (mmm) cc_final: 0.8488 (mmm) REVERT: B 93 MET cc_start: 0.8935 (mmm) cc_final: 0.8726 (mmm) REVERT: B 101 PHE cc_start: 0.7491 (t80) cc_final: 0.7063 (t80) REVERT: D 50 TRP cc_start: 0.8497 (t60) cc_final: 0.8133 (t60) REVERT: D 171 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.7158 (m100) REVERT: E 82 GLU cc_start: 0.9002 (pm20) cc_final: 0.8141 (pp20) REVERT: F 14 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8126 (pt) REVERT: F 92 GLU cc_start: 0.8215 (pm20) cc_final: 0.7897 (pp20) outliers start: 36 outliers final: 25 residues processed: 88 average time/residue: 0.1840 time to fit residues: 25.4720 Evaluate side-chains 75 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 105 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 79 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.079056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.060886 restraints weight = 52984.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.061305 restraints weight = 30885.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.062080 restraints weight = 22517.496| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10660 Z= 0.196 Angle : 0.633 13.996 14511 Z= 0.323 Chirality : 0.042 0.260 1689 Planarity : 0.004 0.057 1826 Dihedral : 4.955 28.429 1461 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 2.28 % Allowed : 18.05 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1337 helix: 1.27 (0.26), residues: 400 sheet: -0.68 (0.28), residues: 348 loop : -1.74 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 33 HIS 0.004 0.001 HIS A 155 PHE 0.026 0.001 PHE B 49 TYR 0.011 0.001 TYR F 55 ARG 0.004 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8778 (mmm) cc_final: 0.8380 (tpt) REVERT: B 41 MET cc_start: 0.8722 (mmm) cc_final: 0.8321 (mmm) REVERT: B 45 LEU cc_start: 0.8909 (tt) cc_final: 0.8600 (tp) REVERT: B 93 MET cc_start: 0.8892 (mmm) cc_final: 0.8683 (mmm) REVERT: C 95 TRP cc_start: 0.7766 (t-100) cc_final: 0.7295 (t-100) REVERT: C 167 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7971 (tp30) REVERT: D 50 TRP cc_start: 0.8407 (t60) cc_final: 0.8031 (t60) REVERT: D 171 TRP cc_start: 0.7543 (OUTLIER) cc_final: 0.7152 (m100) REVERT: E 5 MET cc_start: 0.8376 (mmt) cc_final: 0.8055 (mmt) REVERT: F 14 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8113 (pt) REVERT: F 92 GLU cc_start: 0.8165 (pm20) cc_final: 0.7958 (pp20) outliers start: 26 outliers final: 23 residues processed: 86 average time/residue: 0.2294 time to fit residues: 29.4001 Evaluate side-chains 80 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 106 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.079003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.060616 restraints weight = 53404.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.061620 restraints weight = 29010.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.063014 restraints weight = 21439.432| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10660 Z= 0.207 Angle : 0.654 13.828 14511 Z= 0.329 Chirality : 0.042 0.238 1689 Planarity : 0.004 0.057 1826 Dihedral : 4.889 26.943 1461 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 2.63 % Allowed : 18.49 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.76 (0.23), residues: 1337 helix: 1.26 (0.26), residues: 399 sheet: -0.61 (0.28), residues: 348 loop : -1.68 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 33 HIS 0.004 0.001 HIS A 155 PHE 0.024 0.001 PHE B 49 TYR 0.011 0.001 TYR F 55 ARG 0.004 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7855 (OUTLIER) cc_final: 0.7226 (t60) REVERT: B 41 MET cc_start: 0.8752 (mmm) cc_final: 0.8376 (mmm) REVERT: B 45 LEU cc_start: 0.8909 (tt) cc_final: 0.8606 (tp) REVERT: B 93 MET cc_start: 0.8913 (mmm) cc_final: 0.8666 (mmm) REVERT: B 101 PHE cc_start: 0.6980 (t80) cc_final: 0.6709 (t80) REVERT: C 95 TRP cc_start: 0.7785 (t-100) cc_final: 0.7284 (t-100) REVERT: C 167 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7954 (tp30) REVERT: D 50 TRP cc_start: 0.8375 (t60) cc_final: 0.7990 (t60) REVERT: D 171 TRP cc_start: 0.7668 (OUTLIER) cc_final: 0.7217 (m100) REVERT: E 5 MET cc_start: 0.8406 (mmt) cc_final: 0.8093 (mmt) REVERT: E 82 GLU cc_start: 0.8911 (pm20) cc_final: 0.7840 (pp20) REVERT: F 14 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8112 (pt) REVERT: F 92 GLU cc_start: 0.8207 (pm20) cc_final: 0.7857 (pp20) outliers start: 30 outliers final: 24 residues processed: 85 average time/residue: 0.1793 time to fit residues: 23.9051 Evaluate side-chains 85 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 0.0000 chunk 106 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.077149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058495 restraints weight = 53009.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.059499 restraints weight = 29698.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.060881 restraints weight = 21348.689| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10660 Z= 0.338 Angle : 0.705 14.246 14511 Z= 0.360 Chirality : 0.044 0.325 1689 Planarity : 0.005 0.055 1826 Dihedral : 5.120 27.471 1461 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.78 % Favored : 92.15 % Rotamer: Outliers : 2.45 % Allowed : 19.28 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.89 (0.23), residues: 1337 helix: 1.18 (0.26), residues: 397 sheet: -0.64 (0.28), residues: 355 loop : -1.81 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 33 HIS 0.005 0.001 HIS D 217 PHE 0.021 0.002 PHE B 49 TYR 0.022 0.002 TYR D 162 ARG 0.005 0.000 ARG F 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.7213 (t60) REVERT: B 41 MET cc_start: 0.8767 (mmm) cc_final: 0.8450 (mmm) REVERT: B 93 MET cc_start: 0.8926 (mmm) cc_final: 0.8704 (mmm) REVERT: B 101 PHE cc_start: 0.7116 (t80) cc_final: 0.6714 (t80) REVERT: C 167 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7912 (tp30) REVERT: D 50 TRP cc_start: 0.8489 (t60) cc_final: 0.8062 (t60) REVERT: D 131 ASN cc_start: 0.7394 (m110) cc_final: 0.6592 (m110) REVERT: D 171 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.7289 (m100) REVERT: E 82 GLU cc_start: 0.8894 (pm20) cc_final: 0.7598 (pp20) REVERT: F 14 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8239 (pt) REVERT: F 92 GLU cc_start: 0.8222 (pm20) cc_final: 0.7894 (pp20) outliers start: 28 outliers final: 24 residues processed: 77 average time/residue: 0.1831 time to fit residues: 22.3150 Evaluate side-chains 80 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 42 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.079251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.062404 restraints weight = 52721.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.063157 restraints weight = 36730.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.063314 restraints weight = 25515.619| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10660 Z= 0.192 Angle : 0.651 14.226 14511 Z= 0.331 Chirality : 0.044 0.332 1689 Planarity : 0.004 0.058 1826 Dihedral : 4.837 24.992 1461 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 2.02 % Allowed : 19.72 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.78 (0.23), residues: 1337 helix: 1.24 (0.26), residues: 402 sheet: -0.57 (0.28), residues: 347 loop : -1.74 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 33 HIS 0.004 0.001 HIS A 155 PHE 0.021 0.001 PHE B 49 TYR 0.011 0.001 TYR C 50 ARG 0.003 0.000 ARG B 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2951.11 seconds wall clock time: 54 minutes 20.62 seconds (3260.62 seconds total)