Starting phenix.real_space_refine on Wed Aug 5 09:46:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vv6_65376/08_2026/9vv6_65376.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vv6_65376/08_2026/9vv6_65376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vv6_65376/08_2026/9vv6_65376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vv6_65376/08_2026/9vv6_65376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vv6_65376/08_2026/9vv6_65376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vv6_65376/08_2026/9vv6_65376.map" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.018 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 63 5.16 5 C 5752 2.51 5 N 1546 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9047 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2337 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 399 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "D" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "B" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1932 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'ITN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.28, per 1000 atoms: 0.25 Number of scatterers: 9047 At special positions: 0 Unit cell: (86.112, 121.68, 130.104, 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 63 16.00 O 1686 8.00 N 1546 7.00 C 5752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " 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: 0.94 Conformation dependent library (CDL) restraints added in 344.0 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 37.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 28 through 61 removed outlier: 4.217A pdb=" N LEU A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Proline residue: A 37 - end of helix Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 66 through 85 removed outlier: 3.903A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.602A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 137 Processing helix chain 'A' and resid 146 through 172 removed outlier: 3.744A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Proline residue: A 167 - end of helix removed outlier: 3.934A pdb=" N PHE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.717A pdb=" N TRP A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 228 Processing helix chain 'A' and resid 233 through 270 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 273 through 293 Proline residue: A 289 - end of helix removed outlier: 3.771A pdb=" N ALA A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.664A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 22 Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.781A pdb=" N ARG B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.623A pdb=" N GLN B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.581A pdb=" N ALA B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 4.003A pdb=" N SER B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 358 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.801A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 49 through 52 removed outlier: 3.693A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.531A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.030A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 134 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.603A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.799A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.580A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 273 through 278 removed outlier: 6.411A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE D 278 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU D 284 " --> pdb=" O PHE D 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.779A pdb=" N ARG B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE B 222 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 39 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ASP B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 221 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 257 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 223 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN B 259 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 225 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.649A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.627A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 157 through 161 removed outlier: 3.679A pdb=" N SER E 207 " --> pdb=" O THR E 214 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1251 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: 1.59 Time building geometry restraints manager: 1.20 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: 2922 1.34 - 1.46: 2176 1.46 - 1.58: 4051 1.58 - 1.70: 0 1.70 - 1.83: 88 Bond restraints: 9237 Sorted by residual: bond pdb=" CA VAL E 12 " pdb=" C VAL E 12 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.27e-02 6.20e+03 1.91e+01 bond pdb=" CA GLN E 13 " pdb=" C GLN E 13 " ideal model delta sigma weight residual 1.522 1.487 0.035 9.10e-03 1.21e+04 1.48e+01 bond pdb=" CA LYS D 23 " pdb=" C LYS D 23 " ideal model delta sigma weight residual 1.528 1.490 0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" CA SER E 99 " pdb=" CB SER E 99 " ideal model delta sigma weight residual 1.530 1.479 0.051 1.69e-02 3.50e+03 9.10e+00 bond pdb=" N LEU A 36 " pdb=" CA LEU A 36 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.04e-02 9.25e+03 7.36e+00 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 12472 4.08 - 8.16: 46 8.16 - 12.24: 4 12.24 - 16.32: 0 16.32 - 20.40: 1 Bond angle restraints: 12523 Sorted by residual: angle pdb=" N LYS D 23 " pdb=" CA LYS D 23 " pdb=" C LYS D 23 " ideal model delta sigma weight residual 110.65 100.31 10.34 1.26e+00 6.30e-01 6.74e+01 angle pdb=" C2 ITN A1301 " pdb=" C3 ITN A1301 " pdb=" C5 ITN A1301 " ideal model delta sigma weight residual 116.70 96.30 20.40 3.00e+00 1.11e-01 4.62e+01 angle pdb=" N ILE A 90 " pdb=" CA ILE A 90 " pdb=" C ILE A 90 " ideal model delta sigma weight residual 110.42 106.06 4.36 9.60e-01 1.09e+00 2.07e+01 angle pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" C PHE A 296 " ideal model delta sigma weight residual 111.14 106.34 4.80 1.08e+00 8.57e-01 1.97e+01 angle pdb=" N GLU A 27 " pdb=" CA GLU A 27 " pdb=" C GLU A 27 " ideal model delta sigma weight residual 113.20 108.24 4.96 1.21e+00 6.83e-01 1.68e+01 ... (remaining 12518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 4845 14.85 - 29.69: 478 29.69 - 44.54: 126 44.54 - 59.39: 40 59.39 - 74.24: 9 Dihedral angle restraints: 5498 sinusoidal: 2155 harmonic: 3343 Sorted by residual: dihedral pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 133.94 -40.94 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CA CYS A 24 " pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS A 274 " ideal model delta sinusoidal sigma weight residual 79.00 16.22 62.78 1 2.00e+01 2.50e-03 1.30e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1087 0.048 - 0.096: 262 0.096 - 0.144: 73 0.144 - 0.192: 5 0.192 - 0.241: 2 Chirality restraints: 1429 Sorted by residual: chirality pdb=" CA GLU A 27 " pdb=" N GLU A 27 " pdb=" C GLU A 27 " pdb=" CB GLU A 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU D 55 " pdb=" CB LEU D 55 " pdb=" CD1 LEU D 55 " pdb=" CD2 LEU D 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA THR A 175 " pdb=" N THR A 175 " pdb=" C THR A 175 " pdb=" CB THR A 175 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1426 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 11 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.84e+01 pdb=" C LEU E 11 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU E 11 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL E 12 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 292 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 293 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 293 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 293 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 98 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ARG E 98 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG E 98 " 0.015 2.00e-02 2.50e+03 pdb=" N SER E 99 " 0.013 2.00e-02 2.50e+03 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1198 2.75 - 3.29: 8940 3.29 - 3.83: 15790 3.83 - 4.36: 18815 4.36 - 4.90: 32418 Nonbonded interactions: 77161 Sorted by model distance: nonbonded pdb=" O TRP A 99 " pdb=" OG SER A 181 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 185 " pdb=" OG SER A 188 " model vdw 2.216 3.040 nonbonded pdb=" OE2 GLU D 130 " pdb=" NH1 ARG D 134 " model vdw 2.225 3.120 nonbonded pdb=" O ILE D 58 " pdb=" OG SER D 316 " model vdw 2.257 3.040 nonbonded pdb=" NH1 ARG D 46 " pdb=" OG1 THR D 50 " model vdw 2.259 3.120 ... (remaining 77156 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: 3.320 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.250 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9241 Z= 0.247 Angle : 0.695 20.399 12531 Z= 0.388 Chirality : 0.044 0.241 1429 Planarity : 0.004 0.063 1585 Dihedral : 13.635 74.236 3326 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 1.60 % Allowed : 1.50 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1132 helix: 1.21 (0.26), residues: 398 sheet: 0.23 (0.31), residues: 275 loop : -0.70 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 314 TYR 0.016 0.001 TYR D 59 PHE 0.017 0.001 PHE A 127 TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.25 ( 9237) covalent geometry : angle 0.69438 / 0.39 (12523) SS BOND : bond 0.00159 / 0.08 ( 4) SS BOND : angle 1.01018 / 0.54 ( 8) hydrogen bonds : bond 0.16660 / 10.67 ( 439) hydrogen bonds : angle 7.18970 / 5.29 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.364 Fit side-chains REVERT: D 76 ASP cc_start: 0.6784 (p0) cc_final: 0.6550 (p0) REVERT: B 17 LYS cc_start: 0.7314 (ptpp) cc_final: 0.7027 (ptpp) REVERT: B 314 ASP cc_start: 0.6739 (m-30) cc_final: 0.6506 (m-30) outliers start: 16 outliers final: 5 residues processed: 229 average time/residue: 0.6047 time to fit residues: 147.5531 Evaluate side-chains 205 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 273 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 98 ASN A 116 ASN A 278 ASN A 294 ASN D 16 ASN D 17 GLN D 32 GLN D 36 ASN D 44 GLN D 75 GLN D 155 ASN B 234 GLN B 338 ASN E 195 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117750 restraints weight = 12455.153| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.77 r_work: 0.3491 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9241 Z= 0.157 Angle : 0.586 7.061 12531 Z= 0.312 Chirality : 0.044 0.182 1429 Planarity : 0.004 0.058 1585 Dihedral : 6.227 59.118 1267 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 3.00 % Allowed : 10.11 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1132 helix: 1.80 (0.26), residues: 395 sheet: 0.32 (0.31), residues: 272 loop : -0.62 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 134 TYR 0.022 0.002 TYR C 40 PHE 0.022 0.002 PHE A 296 TRP 0.016 0.002 TRP D 211 HIS 0.006 0.001 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 9237) covalent geometry : angle 0.58565 / 0.31 (12523) SS BOND : bond 0.00315 / 0.16 ( 4) SS BOND : angle 1.12804 / 0.61 ( 8) hydrogen bonds : bond 0.04641 / 2.97 ( 439) hydrogen bonds : angle 5.13474 / 3.77 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.7826 (m110) cc_final: 0.7581 (m-40) REVERT: A 294 ASN cc_start: 0.7883 (t0) cc_final: 0.7552 (t0) REVERT: D 76 ASP cc_start: 0.7386 (p0) cc_final: 0.7104 (p0) REVERT: D 150 ARG cc_start: 0.8672 (mpt180) cc_final: 0.8254 (mpt180) REVERT: D 262 MET cc_start: 0.8268 (tpp) cc_final: 0.7936 (tpp) REVERT: B 8 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 17 LYS cc_start: 0.7738 (ptpp) cc_final: 0.7476 (ptpp) REVERT: B 35 ARG cc_start: 0.8252 (mpp-170) cc_final: 0.8029 (mpp-170) REVERT: B 314 ASP cc_start: 0.7539 (m-30) cc_final: 0.7222 (m-30) REVERT: B 337 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6567 (tm-30) outliers start: 30 outliers final: 12 residues processed: 221 average time/residue: 0.6069 time to fit residues: 143.0324 Evaluate side-chains 212 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 278 ASN A 298 ASN D 32 GLN D 36 ASN D 44 GLN D 75 GLN D 155 ASN E 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.132695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117689 restraints weight = 12482.276| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.75 r_work: 0.3473 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9241 Z= 0.169 Angle : 0.569 6.708 12531 Z= 0.303 Chirality : 0.044 0.202 1429 Planarity : 0.004 0.058 1585 Dihedral : 5.602 56.378 1263 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 3.30 % Allowed : 12.41 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1132 helix: 1.94 (0.25), residues: 396 sheet: 0.45 (0.30), residues: 277 loop : -0.64 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 356 TYR 0.021 0.002 TYR C 40 PHE 0.015 0.002 PHE A 113 TRP 0.016 0.002 TRP B 211 HIS 0.006 0.001 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9237) covalent geometry : angle 0.56824 / 0.30 (12523) SS BOND : bond 0.00333 / 0.17 ( 4) SS BOND : angle 1.05489 / 0.59 ( 8) hydrogen bonds : bond 0.04454 / 2.84 ( 439) hydrogen bonds : angle 4.88141 / 3.59 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 74 ASN cc_start: 0.8012 (m110) cc_final: 0.7757 (m-40) REVERT: A 282 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: A 294 ASN cc_start: 0.7851 (t0) cc_final: 0.7559 (t0) REVERT: C 51 LEU cc_start: 0.3568 (OUTLIER) cc_final: 0.3356 (pp) REVERT: D 76 ASP cc_start: 0.7404 (p0) cc_final: 0.7084 (p0) REVERT: D 150 ARG cc_start: 0.8689 (mpt180) cc_final: 0.8378 (mpt180) REVERT: D 262 MET cc_start: 0.8234 (tpp) cc_final: 0.7929 (tpp) REVERT: B 8 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 17 LYS cc_start: 0.7750 (ptpp) cc_final: 0.7488 (ptpp) REVERT: B 314 ASP cc_start: 0.7546 (m-30) cc_final: 0.7219 (m-30) outliers start: 33 outliers final: 16 residues processed: 229 average time/residue: 0.5919 time to fit residues: 144.6622 Evaluate side-chains 227 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 104 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 298 ASN D 32 GLN D 36 ASN D 44 GLN D 75 GLN D 155 ASN E 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116964 restraints weight = 12566.889| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.77 r_work: 0.3484 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9241 Z= 0.138 Angle : 0.542 6.198 12531 Z= 0.288 Chirality : 0.043 0.200 1429 Planarity : 0.004 0.056 1585 Dihedral : 5.403 57.309 1263 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 3.20 % Allowed : 14.31 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1132 helix: 2.12 (0.25), residues: 396 sheet: 0.48 (0.30), residues: 275 loop : -0.62 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 356 TYR 0.019 0.001 TYR C 40 PHE 0.015 0.001 PHE A 296 TRP 0.016 0.002 TRP D 82 HIS 0.010 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9237) covalent geometry : angle 0.54184 / 0.29 (12523) SS BOND : bond 0.00315 / 0.16 ( 4) SS BOND : angle 0.97044 / 0.55 ( 8) hydrogen bonds : bond 0.04112 / 2.60 ( 439) hydrogen bonds : angle 4.72724 / 3.46 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: C 51 LEU cc_start: 0.3524 (OUTLIER) cc_final: 0.3318 (pp) REVERT: D 76 ASP cc_start: 0.7437 (p0) cc_final: 0.7094 (p0) REVERT: D 150 ARG cc_start: 0.8685 (mpt180) cc_final: 0.8399 (mpt180) REVERT: D 262 MET cc_start: 0.8184 (tpp) cc_final: 0.7908 (tpp) REVERT: B 8 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 17 LYS cc_start: 0.7737 (ptpp) cc_final: 0.7477 (ptpp) REVERT: B 314 ASP cc_start: 0.7540 (m-30) cc_final: 0.7218 (m-30) REVERT: B 337 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6543 (tm-30) outliers start: 32 outliers final: 16 residues processed: 233 average time/residue: 0.5755 time to fit residues: 143.3956 Evaluate side-chains 226 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 30 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 98 ASN A 116 ASN A 278 ASN A 294 ASN A 298 ASN D 32 GLN D 44 GLN D 75 GLN D 155 ASN E 77 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.116096 restraints weight = 12430.910| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.76 r_work: 0.3456 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9241 Z= 0.218 Angle : 0.610 7.028 12531 Z= 0.323 Chirality : 0.047 0.362 1429 Planarity : 0.004 0.064 1585 Dihedral : 5.365 56.360 1259 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 4.00 % Allowed : 14.31 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1132 helix: 1.91 (0.25), residues: 402 sheet: 0.30 (0.30), residues: 282 loop : -0.65 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 356 TYR 0.018 0.002 TYR C 40 PHE 0.018 0.002 PHE D 151 TRP 0.016 0.002 TRP B 211 HIS 0.013 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 ( 9237) covalent geometry : angle 0.60899 / 0.32 (12523) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 1.16724 / 0.65 ( 8) hydrogen bonds : bond 0.04688 / 3.00 ( 439) hydrogen bonds : angle 4.84067 / 3.55 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 294 ASN cc_start: 0.7879 (t0) cc_final: 0.7632 (t0) REVERT: D 150 ARG cc_start: 0.8696 (mpt180) cc_final: 0.8358 (mpt180) REVERT: B 8 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 17 LYS cc_start: 0.7756 (ptpp) cc_final: 0.7500 (ptpp) REVERT: B 53 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7278 (ptp) REVERT: B 314 ASP cc_start: 0.7537 (m-30) cc_final: 0.7208 (m-30) REVERT: B 337 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6565 (tm-30) outliers start: 40 outliers final: 22 residues processed: 226 average time/residue: 0.5966 time to fit residues: 144.0332 Evaluate side-chains 233 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 32 GLN D 44 GLN D 75 GLN D 155 ASN E 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.130682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115482 restraints weight = 12462.704| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.77 r_work: 0.3444 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9241 Z= 0.234 Angle : 0.628 11.001 12531 Z= 0.329 Chirality : 0.047 0.304 1429 Planarity : 0.005 0.062 1585 Dihedral : 5.425 54.870 1259 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 4.70 % Allowed : 14.61 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.25), residues: 1132 helix: 1.78 (0.25), residues: 408 sheet: 0.26 (0.30), residues: 280 loop : -0.67 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 134 TYR 0.018 0.002 TYR C 40 PHE 0.018 0.002 PHE A 113 TRP 0.018 0.002 TRP B 211 HIS 0.011 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 ( 9237) covalent geometry : angle 0.62790 / 0.33 (12523) SS BOND : bond 0.00390 / 0.19 ( 4) SS BOND : angle 1.09963 / 0.61 ( 8) hydrogen bonds : bond 0.04747 / 3.04 ( 439) hydrogen bonds : angle 4.87895 / 3.58 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 264 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6362 (ttt90) REVERT: A 282 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: D 150 ARG cc_start: 0.8693 (mpt180) cc_final: 0.8369 (mpt180) REVERT: B 17 LYS cc_start: 0.7777 (ptpp) cc_final: 0.7520 (ptpp) REVERT: B 314 ASP cc_start: 0.7624 (m-30) cc_final: 0.7291 (m-30) REVERT: B 337 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6568 (tm-30) REVERT: E 156 VAL cc_start: 0.8928 (p) cc_final: 0.8719 (t) REVERT: E 247 GLU cc_start: 0.7447 (mp0) cc_final: 0.7220 (mp0) outliers start: 47 outliers final: 28 residues processed: 228 average time/residue: 0.5987 time to fit residues: 145.6944 Evaluate side-chains 239 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN A 294 ASN A 298 ASN D 32 GLN D 44 GLN D 155 ASN E 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.130778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.115649 restraints weight = 12574.035| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.76 r_work: 0.3450 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9241 Z= 0.215 Angle : 0.623 9.804 12531 Z= 0.326 Chirality : 0.047 0.281 1429 Planarity : 0.005 0.060 1585 Dihedral : 5.392 53.592 1259 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.24 % Favored : 95.58 % Rotamer: Outliers : 4.30 % Allowed : 15.32 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1132 helix: 1.82 (0.25), residues: 408 sheet: 0.28 (0.30), residues: 278 loop : -0.71 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 134 TYR 0.016 0.002 TYR C 40 PHE 0.016 0.002 PHE D 151 TRP 0.018 0.002 TRP B 211 HIS 0.010 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 ( 9237) covalent geometry : angle 0.62228 / 0.33 (12523) SS BOND : bond 0.00385 / 0.19 ( 4) SS BOND : angle 1.04967 / 0.59 ( 8) hydrogen bonds : bond 0.04664 / 2.98 ( 439) hydrogen bonds : angle 4.87092 / 3.58 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.7817 (m-40) cc_final: 0.7603 (m-40) REVERT: A 62 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7671 (mtt) REVERT: A 264 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6364 (ttt90) REVERT: A 282 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: D 150 ARG cc_start: 0.8692 (mpt180) cc_final: 0.8416 (mpt180) REVERT: B 17 LYS cc_start: 0.7764 (ptpp) cc_final: 0.7517 (ptpp) REVERT: B 314 ASP cc_start: 0.7602 (m-30) cc_final: 0.7284 (m-30) REVERT: B 337 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6583 (tm-30) REVERT: E 156 VAL cc_start: 0.8928 (p) cc_final: 0.8710 (t) REVERT: E 247 GLU cc_start: 0.7381 (mp0) cc_final: 0.7120 (mp0) outliers start: 43 outliers final: 29 residues processed: 227 average time/residue: 0.5992 time to fit residues: 145.3496 Evaluate side-chains 240 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN A 294 ASN A 298 ASN D 32 GLN D 44 GLN D 155 ASN E 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.130147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114983 restraints weight = 12445.530| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.76 r_work: 0.3437 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9241 Z= 0.262 Angle : 0.656 8.870 12531 Z= 0.345 Chirality : 0.048 0.316 1429 Planarity : 0.005 0.061 1585 Dihedral : 5.483 52.796 1258 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 4.00 % Allowed : 15.82 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1132 helix: 1.72 (0.25), residues: 404 sheet: 0.16 (0.30), residues: 280 loop : -0.71 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 356 TYR 0.018 0.002 TYR A 82 PHE 0.020 0.002 PHE A 113 TRP 0.017 0.002 TRP B 211 HIS 0.010 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 ( 9237) covalent geometry : angle 0.65620 / 0.34 (12523) SS BOND : bond 0.00405 / 0.20 ( 4) SS BOND : angle 0.94175 / 0.53 ( 8) hydrogen bonds : bond 0.04968 / 3.17 ( 439) hydrogen bonds : angle 4.96448 / 3.65 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 264 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6366 (ttt90) REVERT: A 282 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: D 150 ARG cc_start: 0.8705 (mpt180) cc_final: 0.8376 (mpt180) REVERT: B 17 LYS cc_start: 0.7758 (ptpp) cc_final: 0.7511 (ptpp) REVERT: B 314 ASP cc_start: 0.7626 (m-30) cc_final: 0.7317 (m-30) REVERT: B 337 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6608 (tm-30) REVERT: E 156 VAL cc_start: 0.8924 (p) cc_final: 0.8724 (t) REVERT: E 247 GLU cc_start: 0.7392 (mp0) cc_final: 0.7143 (mp0) outliers start: 40 outliers final: 28 residues processed: 226 average time/residue: 0.5873 time to fit residues: 141.8561 Evaluate side-chains 235 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN A 294 ASN A 298 ASN A 308 ASN D 32 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN E 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117206 restraints weight = 12436.889| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.74 r_work: 0.3463 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9241 Z= 0.173 Angle : 0.611 8.628 12531 Z= 0.320 Chirality : 0.045 0.299 1429 Planarity : 0.005 0.057 1585 Dihedral : 5.309 52.224 1258 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.85 % Rotamer: Outliers : 3.50 % Allowed : 16.72 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1132 helix: 1.98 (0.25), residues: 402 sheet: 0.15 (0.30), residues: 277 loop : -0.70 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 356 TYR 0.017 0.002 TYR A 82 PHE 0.014 0.002 PHE D 151 TRP 0.019 0.002 TRP B 211 HIS 0.008 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 9237) covalent geometry : angle 0.61112 / 0.32 (12523) SS BOND : bond 0.00302 / 0.15 ( 4) SS BOND : angle 0.81476 / 0.46 ( 8) hydrogen bonds : bond 0.04447 / 2.81 ( 439) hydrogen bonds : angle 4.83701 / 3.56 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7743 (mtt) REVERT: A 282 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: D 150 ARG cc_start: 0.8680 (mpt180) cc_final: 0.8436 (mpt180) REVERT: D 262 MET cc_start: 0.8199 (tpp) cc_final: 0.7942 (tpp) REVERT: B 17 LYS cc_start: 0.7732 (ptpp) cc_final: 0.7479 (ptpp) REVERT: B 314 ASP cc_start: 0.7591 (m-30) cc_final: 0.7280 (m-30) REVERT: B 337 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6534 (tm-30) REVERT: E 156 VAL cc_start: 0.8913 (p) cc_final: 0.8697 (t) REVERT: E 246 LEU cc_start: 0.8648 (mp) cc_final: 0.8218 (mp) REVERT: E 247 GLU cc_start: 0.7368 (mp0) cc_final: 0.7091 (mp0) outliers start: 35 outliers final: 26 residues processed: 222 average time/residue: 0.5873 time to fit residues: 139.3451 Evaluate side-chains 232 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 278 ASN A 294 ASN A 298 ASN A 308 ASN D 32 GLN D 44 GLN D 155 ASN E 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116456 restraints weight = 12374.229| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.74 r_work: 0.3465 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9241 Z= 0.171 Angle : 0.620 10.735 12531 Z= 0.323 Chirality : 0.045 0.263 1429 Planarity : 0.005 0.057 1585 Dihedral : 5.262 51.604 1258 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.24 % Favored : 95.58 % Rotamer: Outliers : 3.00 % Allowed : 17.52 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1132 helix: 2.01 (0.25), residues: 402 sheet: 0.01 (0.29), residues: 289 loop : -0.60 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 356 TYR 0.018 0.002 TYR A 82 PHE 0.014 0.002 PHE B 199 TRP 0.019 0.002 TRP D 82 HIS 0.008 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 9237) covalent geometry : angle 0.61958 / 0.32 (12523) SS BOND : bond 0.00298 / 0.15 ( 4) SS BOND : angle 0.82427 / 0.46 ( 8) hydrogen bonds : bond 0.04423 / 2.79 ( 439) hydrogen bonds : angle 4.81734 / 3.55 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7744 (mtt) REVERT: A 282 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: D 22 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7940 (mmt90) REVERT: D 150 ARG cc_start: 0.8684 (mpt180) cc_final: 0.8453 (mpt180) REVERT: D 262 MET cc_start: 0.8158 (tpp) cc_final: 0.7909 (tpp) REVERT: B 17 LYS cc_start: 0.7728 (ptpp) cc_final: 0.7485 (ptpp) REVERT: B 314 ASP cc_start: 0.7603 (m-30) cc_final: 0.7297 (m-30) REVERT: B 337 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6536 (tm-30) REVERT: E 156 VAL cc_start: 0.8909 (p) cc_final: 0.8694 (t) REVERT: E 246 LEU cc_start: 0.8644 (mp) cc_final: 0.8224 (mp) REVERT: E 247 GLU cc_start: 0.7356 (mp0) cc_final: 0.7064 (mp0) outliers start: 30 outliers final: 25 residues processed: 217 average time/residue: 0.5840 time to fit residues: 135.4176 Evaluate side-chains 230 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 105 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 70 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 278 ASN A 294 ASN A 298 ASN A 308 ASN D 32 GLN D 44 GLN D 155 ASN E 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116723 restraints weight = 12319.421| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.74 r_work: 0.3479 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9241 Z= 0.149 Angle : 0.607 11.924 12531 Z= 0.316 Chirality : 0.044 0.232 1429 Planarity : 0.005 0.056 1585 Dihedral : 5.159 50.800 1258 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.20 % Rotamer: Outliers : 3.10 % Allowed : 17.92 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1132 helix: 2.08 (0.25), residues: 402 sheet: 0.05 (0.30), residues: 283 loop : -0.59 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 134 TYR 0.018 0.002 TYR A 82 PHE 0.012 0.001 PHE B 199 TRP 0.019 0.002 TRP D 82 HIS 0.007 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 9237) covalent geometry : angle 0.60678 / 0.32 (12523) SS BOND : bond 0.00283 / 0.14 ( 4) SS BOND : angle 0.76814 / 0.43 ( 8) hydrogen bonds : bond 0.04198 / 2.64 ( 439) hydrogen bonds : angle 4.76486 / 3.52 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.27 seconds wall clock time: 73 minutes 7.75 seconds (4387.75 seconds total)