Starting phenix.real_space_refine on Mon Jul 28 14:54:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kzx_23092/07_2025/7kzx_23092.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kzx_23092/07_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_23092/07_2025/7kzx_23092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kzx_23092/07_2025/7kzx_23092.map" model { file = "/net/cci-nas-00/data/ceres_data/7kzx_23092/07_2025/7kzx_23092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kzx_23092/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.11, per 1000 atoms: 0.68 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: 3.15 Conformation dependent library (CDL) restraints added in 1.3 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: 1.41 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: 3.20 Time building geometry restraints manager: 3.59 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: 4.200 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.720 Find NCS groups from input model: 0.330 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- 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 10664 Z= 0.299 Angle : 0.807 6.881 14519 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 Details of bonding type rmsd hydrogen bonds : bond 0.15515 ( 534) hydrogen bonds : angle 7.24276 ( 1539) SS BOND : bond 0.00311 ( 4) SS BOND : angle 1.17005 ( 8) covalent geometry : bond 0.00615 (10660) covalent geometry : angle 0.80710 (14511) *********************** 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 : 1.211 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: 0.2762 time to fit residues: 44.3675 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 : 1.251 ------------------------------------------------------------------------------- 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 = 51633.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.059603 restraints weight = 31748.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059852 restraints weight = 23769.597| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- 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 10664 Z= 0.202 Angle : 0.709 10.540 14519 Z= 0.375 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 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 534) hydrogen bonds : angle 5.69874 ( 1539) SS BOND : bond 0.00280 ( 4) SS BOND : angle 2.50401 ( 8) covalent geometry : bond 0.00432 (10660) covalent geometry : angle 0.70693 (14511) *********************** 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 : 1.112 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: 0.8555 (ttt) REVERT: A 93 MET cc_start: 0.8906 (mmm) cc_final: 0.8607 (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: 0.9277 (t) cc_final: 0.8985 (m) REVERT: C 5 MET cc_start: 0.8305 (mmm) cc_final: 0.7718 (mmm) REVERT: D 50 TRP cc_start: 0.8481 (t60) cc_final: 0.8125 (t60) REVERT: D 92 GLU cc_start: 0.8196 (tp30) cc_final: 0.7987 (tp30) REVERT: D 157 CYS cc_start: 0.6293 (p) cc_final: 0.6073 (p) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.2018 time to fit residues: 27.4904 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 : 1.208 ------------------------------------------------------------------------------- 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: 0.9980 chunk 98 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.078005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.058120 restraints weight = 52247.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059757 restraints weight = 29124.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.060821 restraints weight = 20159.380| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10664 Z= 0.183 Angle : 0.661 9.555 14519 Z= 0.348 Chirality : 0.043 0.166 1689 Planarity : 0.005 0.054 1826 Dihedral : 5.580 28.102 1461 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.88 % Favored : 93.04 % Rotamer: Outliers : 2.37 % Allowed : 14.64 % 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: -1.50 (0.22), residues: 1337 helix: 0.66 (0.25), residues: 405 sheet: -0.94 (0.27), residues: 334 loop : -2.21 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 93 HIS 0.006 0.001 HIS B 71 PHE 0.021 0.001 PHE E 120 TYR 0.022 0.002 TYR F 104 ARG 0.007 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 534) hydrogen bonds : angle 5.30673 ( 1539) SS BOND : bond 0.00249 ( 4) SS BOND : angle 2.48054 ( 8) covalent geometry : bond 0.00395 (10660) covalent geometry : angle 0.65866 (14511) *********************** 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 92 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8676 (mmm) cc_final: 0.8408 (tpp) REVERT: A 99 LEU cc_start: 0.9569 (mt) cc_final: 0.9339 (mt) REVERT: B 93 MET cc_start: 0.9040 (mmm) cc_final: 0.8802 (mmm) REVERT: B 190 CYS cc_start: 0.9303 (t) cc_final: 0.8960 (m) REVERT: D 50 TRP cc_start: 0.8532 (t60) cc_final: 0.8126 (t60) REVERT: D 92 GLU cc_start: 0.8521 (tp30) cc_final: 0.8177 (tp30) REVERT: D 115 TYR cc_start: 0.8834 (m-80) cc_final: 0.8629 (m-10) REVERT: D 157 CYS cc_start: 0.6560 (p) cc_final: 0.6286 (p) REVERT: E 102 GLN cc_start: 0.7835 (mm110) cc_final: 0.7563 (tp40) outliers start: 27 outliers final: 13 residues processed: 87 average time/residue: 0.1872 time to fit residues: 25.0605 Evaluate side-chains 66 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 6.9990 chunk 80 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** C 200 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 = 0.3833 r_free = 0.3833 target = 0.079148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.060843 restraints weight = 52067.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061233 restraints weight = 30835.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.062256 restraints weight = 22611.328| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10664 Z= 0.138 Angle : 0.629 8.982 14519 Z= 0.327 Chirality : 0.042 0.146 1689 Planarity : 0.004 0.054 1826 Dihedral : 5.321 34.348 1461 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 2.19 % Allowed : 15.34 % Favored : 82.47 % 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: -1.25 (0.23), residues: 1337 helix: 0.88 (0.26), residues: 405 sheet: -0.81 (0.27), residues: 334 loop : -2.08 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 33 HIS 0.005 0.001 HIS B 71 PHE 0.014 0.001 PHE B 101 TYR 0.016 0.001 TYR B 156 ARG 0.007 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 534) hydrogen bonds : angle 4.99830 ( 1539) SS BOND : bond 0.00378 ( 4) SS BOND : angle 2.39138 ( 8) covalent geometry : bond 0.00294 (10660) covalent geometry : angle 0.62671 (14511) *********************** 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 98 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8742 (mmm) cc_final: 0.8443 (tpp) REVERT: A 99 LEU cc_start: 0.9572 (mt) cc_final: 0.9331 (mt) REVERT: B 45 LEU cc_start: 0.9024 (tt) cc_final: 0.8717 (tp) REVERT: B 101 PHE cc_start: 0.7571 (t80) cc_final: 0.6719 (t80) REVERT: B 190 CYS cc_start: 0.9337 (t) cc_final: 0.8982 (m) REVERT: C 167 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7940 (tp30) REVERT: D 50 TRP cc_start: 0.8430 (t60) cc_final: 0.8062 (t60) REVERT: D 92 GLU cc_start: 0.8442 (tp30) cc_final: 0.8234 (tp30) REVERT: D 157 CYS cc_start: 0.6597 (p) cc_final: 0.6332 (p) REVERT: E 97 LEU cc_start: 0.8607 (mt) cc_final: 0.8367 (mp) REVERT: E 102 GLN cc_start: 0.7774 (mm110) cc_final: 0.7497 (tp40) outliers start: 25 outliers final: 15 residues processed: 96 average time/residue: 0.2009 time to fit residues: 28.9940 Evaluate side-chains 72 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** F 16 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 = 0.3794 r_free = 0.3794 target = 0.077301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.057504 restraints weight = 52661.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.059110 restraints weight = 29672.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060146 restraints weight = 20604.530| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10664 Z= 0.230 Angle : 0.663 9.257 14519 Z= 0.348 Chirality : 0.042 0.161 1689 Planarity : 0.005 0.055 1826 Dihedral : 5.345 31.928 1461 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.26 % Favored : 92.67 % Rotamer: Outliers : 3.51 % Allowed : 15.51 % Favored : 80.98 % 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: -1.16 (0.23), residues: 1337 helix: 0.88 (0.26), residues: 400 sheet: -0.78 (0.27), residues: 336 loop : -1.93 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 33 HIS 0.004 0.001 HIS C 200 PHE 0.016 0.002 PHE F 71 TYR 0.019 0.002 TYR D 162 ARG 0.005 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 534) hydrogen bonds : angle 5.00577 ( 1539) SS BOND : bond 0.00289 ( 4) SS BOND : angle 2.37121 ( 8) covalent geometry : bond 0.00499 (10660) covalent geometry : angle 0.66132 (14511) *********************** 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: 40 poor density : 57 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7998 (t60) cc_final: 0.7711 (t60) REVERT: A 93 MET cc_start: 0.8780 (mmm) cc_final: 0.8498 (tpp) REVERT: A 99 LEU cc_start: 0.9586 (mt) cc_final: 0.9358 (mt) REVERT: B 93 MET cc_start: 0.9036 (mmm) cc_final: 0.8730 (mmm) REVERT: B 101 PHE cc_start: 0.7593 (t80) cc_final: 0.6919 (t80) REVERT: D 50 TRP cc_start: 0.8563 (t60) cc_final: 0.8109 (t60) REVERT: D 157 CYS cc_start: 0.6338 (p) cc_final: 0.5764 (p) REVERT: D 171 TRP cc_start: 0.7619 (OUTLIER) cc_final: 0.7189 (m100) REVERT: E 91 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8004 (pp30) REVERT: E 102 GLN cc_start: 0.7913 (mm110) cc_final: 0.7637 (tp40) outliers start: 40 outliers final: 23 residues processed: 93 average time/residue: 0.1917 time to fit residues: 27.3190 Evaluate side-chains 76 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 34 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 99 CYS 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 E residue 91 GLN Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** C 39 GLN ** 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 = 0.3831 r_free = 0.3831 target = 0.078870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.060706 restraints weight = 52517.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.061100 restraints weight = 29061.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.061904 restraints weight = 21827.974| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10664 Z= 0.142 Angle : 0.630 9.286 14519 Z= 0.326 Chirality : 0.042 0.183 1689 Planarity : 0.004 0.053 1826 Dihedral : 5.130 31.344 1461 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.72 % Rotamer: Outliers : 2.80 % Allowed : 16.74 % Favored : 80.46 % 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: -1.06 (0.23), residues: 1337 helix: 1.07 (0.26), residues: 400 sheet: -0.80 (0.28), residues: 334 loop : -1.89 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 33 HIS 0.004 0.001 HIS A 155 PHE 0.014 0.001 PHE E 120 TYR 0.013 0.001 TYR F 104 ARG 0.003 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 534) hydrogen bonds : angle 4.87114 ( 1539) SS BOND : bond 0.00272 ( 4) SS BOND : angle 2.09124 ( 8) covalent geometry : bond 0.00313 (10660) covalent geometry : angle 0.62835 (14511) *********************** 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 96 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8823 (mmm) cc_final: 0.8513 (tpp) REVERT: B 93 MET cc_start: 0.8893 (mmm) cc_final: 0.8674 (mmm) REVERT: B 98 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9160 (mp) REVERT: C 167 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7907 (tp30) REVERT: D 50 TRP cc_start: 0.8463 (t60) cc_final: 0.8101 (t60) REVERT: D 157 CYS cc_start: 0.6255 (p) cc_final: 0.5610 (p) REVERT: D 171 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.7178 (m100) outliers start: 32 outliers final: 22 residues processed: 92 average time/residue: 0.1993 time to fit residues: 27.6256 Evaluate side-chains 79 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 C residue 3 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 34 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 87 ASN Chi-restraints excluded: chain D residue 99 CYS 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: 1.9990 chunk 57 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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** ** 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** ** 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 = 0.3825 r_free = 0.3825 target = 0.078578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.060185 restraints weight = 53275.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.060847 restraints weight = 30825.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061332 restraints weight = 23776.027| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10664 Z= 0.159 Angle : 0.646 13.420 14519 Z= 0.332 Chirality : 0.042 0.190 1689 Planarity : 0.005 0.054 1826 Dihedral : 5.045 29.171 1461 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.34 % Rotamer: Outliers : 2.45 % Allowed : 17.88 % 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: -0.93 (0.23), residues: 1337 helix: 1.17 (0.26), residues: 400 sheet: -0.76 (0.28), residues: 348 loop : -1.80 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 33 HIS 0.005 0.001 HIS A 155 PHE 0.025 0.001 PHE B 49 TYR 0.014 0.001 TYR C 175 ARG 0.003 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 534) hydrogen bonds : angle 4.80159 ( 1539) SS BOND : bond 0.00166 ( 4) SS BOND : angle 2.03859 ( 8) covalent geometry : bond 0.00350 (10660) covalent geometry : angle 0.64453 (14511) *********************** 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 86 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7786 (t60) cc_final: 0.7548 (t60) REVERT: A 93 MET cc_start: 0.8793 (mmm) cc_final: 0.8515 (tpt) REVERT: B 101 PHE cc_start: 0.7422 (t80) cc_final: 0.6931 (t80) REVERT: C 167 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7989 (tp30) REVERT: D 50 TRP cc_start: 0.8462 (t60) cc_final: 0.8095 (t60) REVERT: D 157 CYS cc_start: 0.6187 (p) cc_final: 0.5537 (p) REVERT: D 171 TRP cc_start: 0.7553 (OUTLIER) cc_final: 0.7115 (m100) REVERT: E 5 MET cc_start: 0.8484 (mmt) cc_final: 0.8242 (mmt) REVERT: F 92 GLU cc_start: 0.8222 (pm20) cc_final: 0.7971 (pp20) outliers start: 28 outliers final: 21 residues processed: 82 average time/residue: 0.2082 time to fit residues: 25.7202 Evaluate side-chains 73 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 34 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 F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 168 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.079544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.060137 restraints weight = 53149.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.061839 restraints weight = 29354.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.062909 restraints weight = 19984.375| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10664 Z= 0.131 Angle : 0.634 13.529 14519 Z= 0.324 Chirality : 0.042 0.201 1689 Planarity : 0.004 0.058 1826 Dihedral : 4.884 27.832 1461 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 2.72 % Allowed : 17.79 % Favored : 79.49 % 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: 1.26 (0.26), residues: 400 sheet: -0.57 (0.28), residues: 344 loop : -1.75 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 33 HIS 0.005 0.001 HIS A 155 PHE 0.022 0.001 PHE B 49 TYR 0.010 0.001 TYR F 55 ARG 0.004 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 534) hydrogen bonds : angle 4.67971 ( 1539) SS BOND : bond 0.00301 ( 4) SS BOND : angle 1.99623 ( 8) covalent geometry : bond 0.00287 (10660) covalent geometry : angle 0.63281 (14511) *********************** 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 100 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7795 (t60) cc_final: 0.7394 (t60) REVERT: B 41 MET cc_start: 0.8870 (mmm) cc_final: 0.8600 (mmm) REVERT: B 45 LEU cc_start: 0.8959 (tt) cc_final: 0.8674 (tp) REVERT: B 93 MET cc_start: 0.8873 (mmm) cc_final: 0.8572 (mmm) REVERT: B 101 PHE cc_start: 0.7542 (t80) cc_final: 0.7302 (t80) REVERT: B 225 LYS cc_start: 0.8837 (pttm) cc_final: 0.8175 (tptp) REVERT: C 95 TRP cc_start: 0.7792 (t-100) cc_final: 0.7315 (t-100) REVERT: C 167 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7903 (tp30) REVERT: D 50 TRP cc_start: 0.8376 (t60) cc_final: 0.7935 (t60) REVERT: D 157 CYS cc_start: 0.6338 (p) cc_final: 0.5663 (p) REVERT: D 171 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.7202 (m100) REVERT: E 5 MET cc_start: 0.8506 (mmt) cc_final: 0.8210 (mmt) REVERT: E 82 GLU cc_start: 0.8929 (pm20) cc_final: 0.7752 (pp20) REVERT: F 14 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8135 (pt) outliers start: 31 outliers final: 22 residues processed: 94 average time/residue: 0.2054 time to fit residues: 28.6477 Evaluate side-chains 85 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 34 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 87 ASN Chi-restraints excluded: chain D residue 99 CYS 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 F residue 8 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 106 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** 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 = 0.3831 r_free = 0.3831 target = 0.078855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.059313 restraints weight = 53424.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.060989 restraints weight = 29704.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062068 restraints weight = 20413.704| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10664 Z= 0.164 Angle : 0.659 14.016 14519 Z= 0.337 Chirality : 0.042 0.207 1689 Planarity : 0.004 0.057 1826 Dihedral : 4.888 26.681 1461 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 2.54 % Allowed : 18.84 % Favored : 78.62 % 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: -0.75 (0.23), residues: 1337 helix: 1.29 (0.26), residues: 400 sheet: -0.54 (0.28), residues: 349 loop : -1.74 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 33 HIS 0.005 0.001 HIS A 155 PHE 0.019 0.001 PHE B 49 TYR 0.013 0.001 TYR D 162 ARG 0.003 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 534) hydrogen bonds : angle 4.68884 ( 1539) SS BOND : bond 0.00176 ( 4) SS BOND : angle 1.99018 ( 8) covalent geometry : bond 0.00360 (10660) covalent geometry : angle 0.65778 (14511) *********************** 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: 29 poor density : 63 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7877 (t60) cc_final: 0.7498 (t60) REVERT: B 41 MET cc_start: 0.8881 (mmm) cc_final: 0.8628 (mmm) REVERT: B 45 LEU cc_start: 0.8966 (tt) cc_final: 0.8672 (tp) REVERT: B 93 MET cc_start: 0.8892 (mmm) cc_final: 0.8586 (mmm) REVERT: B 225 LYS cc_start: 0.8865 (pttm) cc_final: 0.8046 (tptp) REVERT: C 95 TRP cc_start: 0.7810 (t-100) cc_final: 0.7337 (t-100) REVERT: C 167 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7927 (tp30) REVERT: D 50 TRP cc_start: 0.8447 (t60) cc_final: 0.7972 (t60) REVERT: D 157 CYS cc_start: 0.6036 (p) cc_final: 0.5487 (p) REVERT: D 171 TRP cc_start: 0.7712 (OUTLIER) cc_final: 0.7245 (m100) REVERT: E 5 MET cc_start: 0.8499 (mmt) cc_final: 0.8274 (mmt) REVERT: E 187 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: F 14 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8130 (pt) outliers start: 29 outliers final: 21 residues processed: 86 average time/residue: 0.2074 time to fit residues: 26.8239 Evaluate side-chains 82 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 34 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 99 CYS Chi-restraints excluded: chain D residue 171 TRP Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.6982 ------------------------------------------------------------------------------- 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** ** 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 = 0.078212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.059744 restraints weight = 52838.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.060440 restraints weight = 29692.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061553 restraints weight = 22384.923| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10664 Z= 0.186 Angle : 0.673 14.099 14519 Z= 0.345 Chirality : 0.043 0.236 1689 Planarity : 0.004 0.056 1826 Dihedral : 4.955 26.115 1461 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.88 % Favored : 93.04 % Rotamer: Outliers : 2.45 % Allowed : 19.02 % Favored : 78.53 % 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 (0.24), residues: 1337 helix: 1.20 (0.26), residues: 403 sheet: -0.48 (0.27), residues: 367 loop : -1.81 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 33 HIS 0.005 0.001 HIS A 155 PHE 0.023 0.002 PHE B 101 TYR 0.017 0.001 TYR D 162 ARG 0.003 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 534) hydrogen bonds : angle 4.75039 ( 1539) SS BOND : bond 0.00208 ( 4) SS BOND : angle 1.88744 ( 8) covalent geometry : bond 0.00406 (10660) covalent geometry : angle 0.67157 (14511) ********************** 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 84 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8809 (mmm) cc_final: 0.8562 (mmm) REVERT: B 93 MET cc_start: 0.8799 (mmm) cc_final: 0.8482 (mmm) REVERT: B 183 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.7979 (mt) REVERT: C 167 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7905 (tp30) REVERT: D 50 TRP cc_start: 0.8479 (t60) cc_final: 0.8046 (t60) REVERT: D 131 ASN cc_start: 0.7406 (m110) cc_final: 0.6664 (m110) REVERT: D 157 CYS cc_start: 0.6452 (p) cc_final: 0.5761 (p) REVERT: D 171 TRP cc_start: 0.7793 (OUTLIER) cc_final: 0.7201 (m100) REVERT: E 82 GLU cc_start: 0.8810 (pm20) cc_final: 0.7560 (pp20) REVERT: E 187 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: F 14 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8218 (pt) outliers start: 28 outliers final: 21 residues processed: 80 average time/residue: 0.1979 time to fit residues: 24.0547 Evaluate side-chains 79 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 34 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 99 CYS 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 E residue 187 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 42 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.079784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063133 restraints weight = 52594.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.063831 restraints weight = 35941.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064004 restraints weight = 25582.813| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10664 Z= 0.131 Angle : 0.651 13.964 14519 Z= 0.331 Chirality : 0.042 0.226 1689 Planarity : 0.004 0.058 1826 Dihedral : 4.793 23.894 1461 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 2.37 % Allowed : 19.02 % Favored : 78.62 % 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: -0.67 (0.24), residues: 1337 helix: 1.25 (0.26), residues: 408 sheet: -0.44 (0.27), residues: 361 loop : -1.71 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 33 HIS 0.005 0.001 HIS A 155 PHE 0.022 0.001 PHE B 101 TYR 0.025 0.001 TYR E 188 ARG 0.003 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 534) hydrogen bonds : angle 4.67663 ( 1539) SS BOND : bond 0.00238 ( 4) SS BOND : angle 1.62220 ( 8) covalent geometry : bond 0.00286 (10660) covalent geometry : angle 0.65025 (14511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3325.09 seconds wall clock time: 58 minutes 46.87 seconds (3526.87 seconds total)