Starting phenix.real_space_refine on Sun Nov 17 23:23:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2024/8ouy_17205_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2024/8ouy_17205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2024/8ouy_17205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2024/8ouy_17205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2024/8ouy_17205_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2024/8ouy_17205_trim.cif" } resolution = 3.4 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 50 5.16 5 C 4608 2.51 5 N 1268 2.21 5 O 1378 1.98 5 H 7380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14695 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1131 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "B" Number of atoms: 4977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4977 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4722 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 7, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3773 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.43, per 1000 atoms: 0.51 Number of scatterers: 14695 At special positions: 0 Unit cell: (98.28, 104.76, 95.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 3 11.99 O 1378 8.00 N 1268 7.00 C 4608 6.00 H 7380 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 51.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.775A pdb=" N VAL A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 10' Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 26 through 32 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.992A pdb=" N LYS B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.627A pdb=" N ARG B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 97 Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 165 through 188 removed outlier: 3.545A pdb=" N VAL B 169 " --> pdb=" O MET B 165 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.817A pdb=" N GLU B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 215 through 233 Proline residue: B 227 - end of helix removed outlier: 3.763A pdb=" N SER B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.751A pdb=" N SER B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 5.281A pdb=" N MET B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 308 removed outlier: 3.683A pdb=" N GLY B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 removed outlier: 4.297A pdb=" N LEU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 68 through 79 removed outlier: 3.602A pdb=" N GLU C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 112 through 127 Processing helix chain 'C' and resid 142 through 152 Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 174 through 192 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 221 through 242 removed outlier: 3.746A pdb=" N ALA C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.087A pdb=" N PHE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.501A pdb=" N ILE D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 67 Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.611A pdb=" N ILE D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 4.384A pdb=" N TYR D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.639A pdb=" N GLU D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.570A pdb=" N VAL D 160 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 170 through 187 removed outlier: 3.590A pdb=" N LYS D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.635A pdb=" N GLU B 154 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL B 239 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 156 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL B 241 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 158 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 121 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG B 312 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 316 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 337 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS B 335 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 340 through 342 Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 removed outlier: 7.522A pdb=" N LEU D 146 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR D 194 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 148 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE D 43 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N MET D 239 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU D 45 " --> pdb=" O MET D 239 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE D 241 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N HIS D 47 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LYS D 243 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D 254 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 257 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 171 removed outlier: 6.812A pdb=" N LEU C 133 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP C 206 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 135 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 203 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 248 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 103 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASN C 249 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE C 105 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 274 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG C 275 " --> pdb=" O ALA C 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 252 through 253 338 hydrogen bonds defined for protein. 942 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: 5.67 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7352 1.03 - 1.23: 34 1.23 - 1.42: 2983 1.42 - 1.62: 4367 1.62 - 1.81: 72 Bond restraints: 14808 Sorted by residual: bond pdb=" N GLY C 2 " pdb=" CA GLY C 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.40e+00 bond pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.08e+00 bond pdb=" N LYS A 4 " pdb=" CA LYS A 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N GLY D 20 " pdb=" H GLY D 20 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N GLY C 2 " pdb=" H GLY C 2 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 ... (remaining 14803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.72: 26780 11.72 - 23.44: 0 23.44 - 35.16: 0 35.16 - 46.88: 0 46.88 - 58.60: 1 Bond angle restraints: 26781 Sorted by residual: angle pdb=" C MET B 10 " pdb=" N GLN B 11 " pdb=" H GLN B 11 " ideal model delta sigma weight residual 123.68 65.08 58.60 3.00e+00 1.11e-01 3.82e+02 angle pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" O4' ATP C 401 " ideal model delta sigma weight residual 105.22 101.39 3.83 1.30e+00 5.94e-01 8.72e+00 angle pdb=" C2' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O3' ATP C 401 " ideal model delta sigma weight residual 111.83 105.17 6.66 2.67e+00 1.40e-01 6.23e+00 angle pdb=" C3' ATP C 401 " pdb=" C2' ATP C 401 " pdb=" O2' ATP C 401 " ideal model delta sigma weight residual 111.83 105.41 6.42 2.67e+00 1.40e-01 5.78e+00 angle pdb=" C1' ATP D 302 " pdb=" C2' ATP D 302 " pdb=" O2' ATP D 302 " ideal model delta sigma weight residual 110.58 103.86 6.72 2.79e+00 1.28e-01 5.78e+00 ... (remaining 26776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 6589 31.12 - 62.23: 292 62.23 - 93.35: 33 93.35 - 124.46: 1 124.46 - 155.58: 2 Dihedral angle restraints: 6917 sinusoidal: 3881 harmonic: 3036 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 95.58 -155.58 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 88.76 -148.76 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.52 116.52 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 6914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1057 0.060 - 0.120: 102 0.120 - 0.179: 12 0.179 - 0.239: 1 0.239 - 0.299: 5 Chirality restraints: 1177 Sorted by residual: chirality pdb=" C2' ATP D 302 " pdb=" C1' ATP D 302 " pdb=" C3' ATP D 302 " pdb=" O2' ATP D 302 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP C 401 " pdb=" C2' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" O3' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1174 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 10 " 0.092 2.00e-02 2.50e+03 2.32e-01 5.39e+02 pdb=" N GLN B 11 " -0.399 2.00e-02 2.50e+03 pdb=" CA GLN B 11 " 0.135 2.00e-02 2.50e+03 pdb=" H GLN B 11 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 247 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 37 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO D 38 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 38 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 38 " -0.016 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 340 2.13 - 2.75: 26698 2.75 - 3.37: 39756 3.37 - 3.98: 50200 3.98 - 4.60: 79939 Nonbonded interactions: 196933 Sorted by model distance: nonbonded pdb=" OE1 GLU D 164 " pdb=" H GLU D 164 " model vdw 1.513 2.450 nonbonded pdb=" HG1 THR C 209 " pdb=" OD1 ASN C 249 " model vdw 1.625 2.450 nonbonded pdb=" OD1 ASP C 279 " pdb=" H THR C 280 " model vdw 1.631 2.450 nonbonded pdb=" O LEU D 58 " pdb=" HG1 THR D 62 " model vdw 1.636 2.450 nonbonded pdb=" OE1 GLU D 28 " pdb=" H ASN D 30 " model vdw 1.636 2.450 ... (remaining 196928 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.250 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.200 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.002 0.040 7428 Z= 0.163 Angle : 0.523 6.715 10043 Z= 0.264 Chirality : 0.042 0.299 1177 Planarity : 0.003 0.031 1257 Dihedral : 17.648 155.580 2809 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 907 helix: 0.06 (0.27), residues: 407 sheet: -1.02 (0.41), residues: 153 loop : -0.79 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.007 0.001 PHE B 199 TYR 0.010 0.001 TYR C 72 ARG 0.002 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 PHE cc_start: 0.7807 (m-10) cc_final: 0.7538 (m-10) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4408 time to fit residues: 59.5615 Evaluate side-chains 100 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7428 Z= 0.218 Angle : 0.532 6.205 10043 Z= 0.279 Chirality : 0.039 0.137 1177 Planarity : 0.004 0.031 1257 Dihedral : 10.497 166.297 1069 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.00 % Allowed : 13.82 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.28), residues: 907 helix: 0.32 (0.25), residues: 428 sheet: -1.02 (0.40), residues: 152 loop : -0.83 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 268 HIS 0.005 0.001 HIS B 95 PHE 0.011 0.001 PHE B 346 TYR 0.012 0.001 TYR C 72 ARG 0.004 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: B 192 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7744 (m-70) REVERT: C 23 HIS cc_start: 0.4878 (m90) cc_final: 0.4405 (m170) REVERT: D 32 PHE cc_start: 0.7862 (m-80) cc_final: 0.7595 (m-10) outliers start: 8 outliers final: 5 residues processed: 109 average time/residue: 0.3344 time to fit residues: 49.4827 Evaluate side-chains 104 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7428 Z= 0.235 Angle : 0.527 5.972 10043 Z= 0.274 Chirality : 0.039 0.138 1177 Planarity : 0.004 0.032 1257 Dihedral : 9.362 128.126 1069 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.25 % Allowed : 14.20 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.28), residues: 907 helix: 0.41 (0.25), residues: 430 sheet: -1.23 (0.38), residues: 157 loop : -0.89 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 317 HIS 0.005 0.001 HIS D 60 PHE 0.011 0.001 PHE B 346 TYR 0.013 0.001 TYR C 72 ARG 0.002 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.4844 (m90) cc_final: 0.4409 (m90) REVERT: D 32 PHE cc_start: 0.7914 (m-80) cc_final: 0.7660 (m-10) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.4611 time to fit residues: 68.8761 Evaluate side-chains 105 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7428 Z= 0.223 Angle : 0.515 6.090 10043 Z= 0.268 Chirality : 0.039 0.139 1177 Planarity : 0.004 0.032 1257 Dihedral : 8.982 114.863 1069 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.74 % Allowed : 13.70 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.28), residues: 907 helix: 0.57 (0.26), residues: 428 sheet: -1.39 (0.37), residues: 157 loop : -0.99 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS D 60 PHE 0.011 0.001 PHE B 346 TYR 0.012 0.001 TYR C 72 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.250 Fit side-chains REVERT: C 23 HIS cc_start: 0.4829 (m90) cc_final: 0.4432 (m90) REVERT: D 32 PHE cc_start: 0.7970 (m-80) cc_final: 0.7699 (m-10) outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 0.4436 time to fit residues: 67.2640 Evaluate side-chains 108 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7428 Z= 0.190 Angle : 0.493 6.072 10043 Z= 0.255 Chirality : 0.038 0.137 1177 Planarity : 0.003 0.032 1257 Dihedral : 8.679 101.435 1069 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.74 % Allowed : 14.82 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.28), residues: 907 helix: 0.75 (0.26), residues: 430 sheet: -1.45 (0.37), residues: 157 loop : -1.00 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.003 0.001 HIS D 60 PHE 0.011 0.001 PHE B 346 TYR 0.011 0.001 TYR C 72 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.4729 (m90) cc_final: 0.4293 (m90) REVERT: C 184 GLU cc_start: 0.7610 (tt0) cc_final: 0.7241 (mt-10) REVERT: D 32 PHE cc_start: 0.7939 (m-80) cc_final: 0.7681 (m-10) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 0.4352 time to fit residues: 67.9510 Evaluate side-chains 107 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7428 Z= 0.196 Angle : 0.496 6.103 10043 Z= 0.256 Chirality : 0.038 0.137 1177 Planarity : 0.003 0.032 1257 Dihedral : 8.549 88.352 1069 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.62 % Allowed : 15.07 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.28), residues: 907 helix: 0.85 (0.26), residues: 422 sheet: -1.53 (0.37), residues: 157 loop : -0.94 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 317 HIS 0.004 0.001 HIS D 60 PHE 0.011 0.001 PHE B 346 TYR 0.011 0.001 TYR C 72 ARG 0.002 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.4867 (m90) cc_final: 0.4292 (m90) REVERT: C 184 GLU cc_start: 0.7609 (tt0) cc_final: 0.7282 (mt-10) REVERT: D 32 PHE cc_start: 0.7927 (m-80) cc_final: 0.7667 (m-10) outliers start: 13 outliers final: 12 residues processed: 110 average time/residue: 0.4297 time to fit residues: 65.1887 Evaluate side-chains 110 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.0770 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7428 Z= 0.172 Angle : 0.484 6.083 10043 Z= 0.248 Chirality : 0.038 0.136 1177 Planarity : 0.003 0.037 1257 Dihedral : 8.170 75.551 1069 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.74 % Allowed : 15.07 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.29), residues: 907 helix: 0.97 (0.26), residues: 422 sheet: -1.50 (0.38), residues: 157 loop : -0.86 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.010 0.001 PHE B 346 TYR 0.010 0.001 TYR D 59 ARG 0.010 0.000 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.4888 (m90) cc_final: 0.4342 (m170) REVERT: C 184 GLU cc_start: 0.7579 (tt0) cc_final: 0.7238 (mt-10) REVERT: D 32 PHE cc_start: 0.7902 (m-80) cc_final: 0.7665 (m-10) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.3951 time to fit residues: 58.3711 Evaluate side-chains 110 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7428 Z= 0.174 Angle : 0.481 5.940 10043 Z= 0.247 Chirality : 0.038 0.136 1177 Planarity : 0.003 0.038 1257 Dihedral : 7.908 72.370 1069 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.49 % Allowed : 15.57 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.29), residues: 907 helix: 1.02 (0.26), residues: 422 sheet: -1.48 (0.38), residues: 157 loop : -0.88 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.010 0.001 PHE B 346 TYR 0.010 0.001 TYR C 72 ARG 0.007 0.000 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.4774 (m90) cc_final: 0.4265 (m170) REVERT: C 184 GLU cc_start: 0.7578 (tt0) cc_final: 0.7248 (mt-10) REVERT: D 32 PHE cc_start: 0.7886 (m-80) cc_final: 0.7656 (m-10) outliers start: 12 outliers final: 11 residues processed: 109 average time/residue: 0.4090 time to fit residues: 62.0283 Evaluate side-chains 109 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7428 Z= 0.176 Angle : 0.485 6.017 10043 Z= 0.250 Chirality : 0.038 0.136 1177 Planarity : 0.003 0.035 1257 Dihedral : 7.852 70.008 1069 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.49 % Allowed : 15.57 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.29), residues: 907 helix: 1.09 (0.27), residues: 416 sheet: -1.43 (0.38), residues: 156 loop : -0.85 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.010 0.001 PHE B 346 TYR 0.010 0.001 TYR D 59 ARG 0.006 0.000 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.4685 (m90) cc_final: 0.4165 (m170) REVERT: C 184 GLU cc_start: 0.7583 (tt0) cc_final: 0.7247 (mt-10) REVERT: D 32 PHE cc_start: 0.7960 (m-80) cc_final: 0.7730 (m-10) outliers start: 12 outliers final: 12 residues processed: 104 average time/residue: 0.4284 time to fit residues: 61.9672 Evaluate side-chains 108 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7428 Z= 0.249 Angle : 0.523 6.288 10043 Z= 0.273 Chirality : 0.039 0.140 1177 Planarity : 0.004 0.036 1257 Dihedral : 8.233 79.568 1069 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.49 % Allowed : 15.82 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.28), residues: 907 helix: 0.82 (0.26), residues: 417 sheet: -1.22 (0.41), residues: 138 loop : -1.14 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 268 HIS 0.009 0.001 HIS B 250 PHE 0.011 0.001 PHE B 346 TYR 0.013 0.001 TYR C 72 ARG 0.005 0.000 ARG D 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: D 32 PHE cc_start: 0.7873 (m-80) cc_final: 0.7637 (m-10) outliers start: 12 outliers final: 11 residues processed: 107 average time/residue: 0.4313 time to fit residues: 62.5595 Evaluate side-chains 107 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113596 restraints weight = 29196.197| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.85 r_work: 0.3238 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7428 Z= 0.246 Angle : 0.518 6.312 10043 Z= 0.270 Chirality : 0.039 0.140 1177 Planarity : 0.004 0.034 1257 Dihedral : 8.212 77.865 1069 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.62 % Allowed : 15.69 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.28), residues: 907 helix: 0.75 (0.26), residues: 419 sheet: -1.22 (0.41), residues: 138 loop : -1.19 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 317 HIS 0.006 0.001 HIS B 250 PHE 0.011 0.001 PHE B 346 TYR 0.013 0.001 TYR C 72 ARG 0.005 0.000 ARG D 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.21 seconds wall clock time: 73 minutes 10.36 seconds (4390.36 seconds total)