Starting phenix.real_space_refine on Tue Mar 3 18:14:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzr_27806/03_2026/8dzr_27806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzr_27806/03_2026/8dzr_27806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dzr_27806/03_2026/8dzr_27806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzr_27806/03_2026/8dzr_27806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dzr_27806/03_2026/8dzr_27806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzr_27806/03_2026/8dzr_27806.map" } resolution = 2.61 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 2 4.86 5 C 5092 2.51 5 N 1322 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7944 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1934 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1494 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 4 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 8, 'GLU:plan': 5, 'HIS:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2455 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 4, 'ARG:plan': 9, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 251 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'U9I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.89, per 1000 atoms: 0.24 Number of scatterers: 7944 At special positions: 0 Unit cell: (86.24, 121.44, 124.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 58 16.00 O 1470 8.00 N 1322 7.00 C 5092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 302.9 milliseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.1% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 57 through 80 removed outlier: 4.098A pdb=" N ILE A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 110 Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.540A pdb=" N VAL A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 162 removed outlier: 5.024A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.960A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.674A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 298 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 309 through 332 removed outlier: 3.875A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.522A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.718A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 removed outlier: 4.048A pdb=" N THR B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.568A pdb=" N ILE B 285 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS B 286 " --> pdb=" O LEU B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 286' Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.595A pdb=" N ASN B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 352 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.586A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.072A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 200 removed outlier: 3.568A pdb=" N GLY A 198 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 211 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 209 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.342A pdb=" N ILE B 221 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.760A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.538A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.073A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.580A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.113A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.619A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.962A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.962A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 3.812A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 148 427 hydrogen bonds defined for protein. 1203 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: 1.30 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2055 1.33 - 1.45: 1638 1.45 - 1.58: 4322 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 8100 Sorted by residual: bond pdb=" CA SER C 161 " pdb=" CB SER C 161 " ideal model delta sigma weight residual 1.532 1.482 0.050 1.68e-02 3.54e+03 8.86e+00 bond pdb=" N ASP C 170 " pdb=" CA ASP C 170 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.23e-02 6.61e+03 2.65e+00 bond pdb=" C16 U9I A 401 " pdb=" C17 U9I A 401 " ideal model delta sigma weight residual 1.548 1.521 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C ASP C 170 " pdb=" N ILE C 171 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.26e-02 6.30e+03 1.69e+00 bond pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.42e+00 ... (remaining 8095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10655 1.64 - 3.29: 311 3.29 - 4.93: 40 4.93 - 6.58: 15 6.58 - 8.22: 8 Bond angle restraints: 11029 Sorted by residual: angle pdb=" N PRO A 56 " pdb=" CA PRO A 56 " pdb=" CB PRO A 56 " ideal model delta sigma weight residual 103.00 110.47 -7.47 1.10e+00 8.26e-01 4.61e+01 angle pdb=" N ASP C 170 " pdb=" CA ASP C 170 " pdb=" C ASP C 170 " ideal model delta sigma weight residual 108.96 101.81 7.15 1.59e+00 3.96e-01 2.02e+01 angle pdb=" N SER C 161 " pdb=" CA SER C 161 " pdb=" C SER C 161 " ideal model delta sigma weight residual 108.74 113.37 -4.63 1.38e+00 5.25e-01 1.13e+01 angle pdb=" N ASP C 170 " pdb=" CA ASP C 170 " pdb=" CB ASP C 170 " ideal model delta sigma weight residual 110.17 115.01 -4.84 1.68e+00 3.54e-01 8.31e+00 angle pdb=" C VAL A 80 " pdb=" N MET A 81 " pdb=" CA MET A 81 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.15e+00 ... (remaining 11024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4361 17.54 - 35.09: 328 35.09 - 52.63: 44 52.63 - 70.18: 6 70.18 - 87.72: 9 Dihedral angle restraints: 4748 sinusoidal: 1639 harmonic: 3109 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 172.73 -79.73 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CA TYR E 178 " pdb=" C TYR E 178 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1009 0.052 - 0.104: 249 0.104 - 0.156: 57 0.156 - 0.208: 1 0.208 - 0.260: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CB THR E 160 " pdb=" CA THR E 160 " pdb=" OG1 THR E 160 " pdb=" CG2 THR E 160 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASP C 170 " pdb=" N ASP C 170 " pdb=" C ASP C 170 " pdb=" CB ASP C 170 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 56 " pdb=" N PRO A 56 " pdb=" C PRO A 56 " pdb=" CB PRO A 56 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1317 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 199 " 0.010 2.00e-02 2.50e+03 1.59e-02 4.43e+00 pdb=" CG PHE B 199 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 199 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 199 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 199 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 199 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 199 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 171 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 172 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO C 236 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.024 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1184 2.76 - 3.29: 7447 3.29 - 3.83: 13291 3.83 - 4.36: 15264 4.36 - 4.90: 27292 Nonbonded interactions: 64478 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.224 3.040 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.268 3.040 nonbonded pdb=" O VAL A 284 " pdb=" OG1 THR A 288 " model vdw 2.286 3.040 nonbonded pdb=" O THR A 111 " pdb=" OH TYR A 320 " model vdw 2.292 3.040 nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.293 3.120 ... (remaining 64473 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: 1.800 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 0.050 8102 Z= 0.169 Angle : 0.683 8.223 11033 Z= 0.365 Chirality : 0.048 0.260 1320 Planarity : 0.004 0.044 1374 Dihedral : 12.943 87.720 2730 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.09 (0.25), residues: 1045 helix: 1.15 (0.27), residues: 345 sheet: 0.49 (0.30), residues: 294 loop : -1.56 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 67 TYR 0.023 0.002 TYR C 59 PHE 0.034 0.002 PHE B 199 TRP 0.014 0.002 TRP C 82 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8100) covalent geometry : angle 0.68308 (11029) SS BOND : bond 0.00388 ( 2) SS BOND : angle 0.92588 ( 4) hydrogen bonds : bond 0.12963 ( 423) hydrogen bonds : angle 5.72958 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.277 Fit side-chains REVERT: A 288 THR cc_start: 0.7351 (m) cc_final: 0.7091 (m) REVERT: B 18 MET cc_start: 0.7284 (mmm) cc_final: 0.6942 (mmm) REVERT: B 323 MET cc_start: 0.6589 (mpp) cc_final: 0.5984 (mpp) REVERT: E 95 TYR cc_start: 0.8540 (m-80) cc_final: 0.8287 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.4057 time to fit residues: 74.6461 Evaluate side-chains 157 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131881 restraints weight = 11263.833| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.85 r_work: 0.3696 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8102 Z= 0.185 Angle : 0.586 8.684 11033 Z= 0.308 Chirality : 0.043 0.162 1320 Planarity : 0.004 0.039 1374 Dihedral : 4.912 25.791 1166 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.24 % Allowed : 10.97 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.32 (0.26), residues: 1045 helix: 1.76 (0.28), residues: 347 sheet: 0.69 (0.30), residues: 280 loop : -1.51 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.026 0.002 TYR E 178 PHE 0.020 0.002 PHE A 126 TRP 0.017 0.002 TRP C 169 HIS 0.006 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8100) covalent geometry : angle 0.58553 (11029) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.51020 ( 4) hydrogen bonds : bond 0.04527 ( 423) hydrogen bonds : angle 4.77405 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.195 Fit side-chains REVERT: A 211 SER cc_start: 0.8459 (p) cc_final: 0.8179 (m) REVERT: A 318 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7418 (mp) REVERT: B 323 MET cc_start: 0.7236 (mpp) cc_final: 0.6595 (mpp) REVERT: C 132 ASN cc_start: 0.8275 (p0) cc_final: 0.7950 (p0) REVERT: C 170 ASP cc_start: 0.7906 (t70) cc_final: 0.7691 (t0) REVERT: C 262 MET cc_start: 0.7694 (ttm) cc_final: 0.7187 (mtt) outliers start: 18 outliers final: 10 residues processed: 166 average time/residue: 0.3911 time to fit residues: 69.9738 Evaluate side-chains 169 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.152015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132286 restraints weight = 11244.907| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.86 r_work: 0.3700 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8102 Z= 0.150 Angle : 0.552 8.813 11033 Z= 0.290 Chirality : 0.042 0.141 1320 Planarity : 0.003 0.039 1374 Dihedral : 4.662 22.086 1166 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.49 % Allowed : 15.09 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.50 (0.26), residues: 1045 helix: 2.01 (0.28), residues: 346 sheet: 0.80 (0.30), residues: 287 loop : -1.54 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.025 0.002 TYR E 178 PHE 0.013 0.001 PHE B 196 TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8100) covalent geometry : angle 0.55228 (11029) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.48828 ( 4) hydrogen bonds : bond 0.04157 ( 423) hydrogen bonds : angle 4.57625 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.210 Fit side-chains REVERT: A 107 LEU cc_start: 0.8372 (mp) cc_final: 0.8165 (mp) REVERT: A 143 PHE cc_start: 0.7720 (m-80) cc_final: 0.7486 (m-80) REVERT: A 211 SER cc_start: 0.8480 (p) cc_final: 0.8209 (m) REVERT: A 318 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7424 (mp) REVERT: B 323 MET cc_start: 0.7165 (mpp) cc_final: 0.6516 (mpp) REVERT: B 327 THR cc_start: 0.7610 (p) cc_final: 0.7301 (p) REVERT: C 132 ASN cc_start: 0.8281 (p0) cc_final: 0.7940 (p0) REVERT: C 262 MET cc_start: 0.7662 (ttm) cc_final: 0.7239 (mtt) REVERT: C 323 ASP cc_start: 0.7445 (p0) cc_final: 0.7173 (p0) outliers start: 20 outliers final: 11 residues processed: 169 average time/residue: 0.3569 time to fit residues: 65.2347 Evaluate side-chains 171 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.151132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131227 restraints weight = 11378.883| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.88 r_work: 0.3687 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8102 Z= 0.176 Angle : 0.574 9.103 11033 Z= 0.300 Chirality : 0.043 0.147 1320 Planarity : 0.004 0.037 1374 Dihedral : 4.733 25.082 1166 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.24 % Allowed : 16.33 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.52 (0.26), residues: 1045 helix: 2.10 (0.28), residues: 345 sheet: 0.80 (0.30), residues: 282 loop : -1.58 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.029 0.002 TYR E 178 PHE 0.016 0.002 PHE B 196 TRP 0.015 0.002 TRP C 211 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8100) covalent geometry : angle 0.57366 (11029) SS BOND : bond 0.00228 ( 2) SS BOND : angle 0.50966 ( 4) hydrogen bonds : bond 0.04286 ( 423) hydrogen bonds : angle 4.56783 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.231 Fit side-chains REVERT: A 211 SER cc_start: 0.8477 (p) cc_final: 0.8169 (m) REVERT: A 226 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6453 (tpp) REVERT: A 318 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7406 (mp) REVERT: A 328 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6904 (mp) REVERT: B 323 MET cc_start: 0.7222 (mpp) cc_final: 0.6573 (mpp) REVERT: B 327 THR cc_start: 0.7623 (p) cc_final: 0.7318 (p) REVERT: C 132 ASN cc_start: 0.8341 (p0) cc_final: 0.7999 (p0) REVERT: C 314 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7841 (ptm160) REVERT: C 323 ASP cc_start: 0.7464 (p0) cc_final: 0.7190 (p0) outliers start: 26 outliers final: 16 residues processed: 171 average time/residue: 0.3802 time to fit residues: 70.4086 Evaluate side-chains 178 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 53 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.151522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131781 restraints weight = 11341.706| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.86 r_work: 0.3695 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8102 Z= 0.151 Angle : 0.561 9.148 11033 Z= 0.293 Chirality : 0.042 0.150 1320 Planarity : 0.003 0.037 1374 Dihedral : 4.590 19.411 1166 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.37 % Allowed : 17.71 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.62 (0.27), residues: 1045 helix: 2.16 (0.28), residues: 350 sheet: 0.87 (0.30), residues: 287 loop : -1.57 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 219 TYR 0.025 0.002 TYR E 178 PHE 0.014 0.001 PHE B 196 TRP 0.014 0.002 TRP C 82 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8100) covalent geometry : angle 0.56105 (11029) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.52377 ( 4) hydrogen bonds : bond 0.04069 ( 423) hydrogen bonds : angle 4.49367 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8367 (mp) cc_final: 0.8158 (mp) REVERT: A 209 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: A 250 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7793 (mp) REVERT: A 318 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7379 (mp) REVERT: A 328 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6875 (mp) REVERT: B 323 MET cc_start: 0.7229 (mpp) cc_final: 0.6578 (mpp) REVERT: B 327 THR cc_start: 0.7626 (p) cc_final: 0.7315 (p) REVERT: C 76 ASP cc_start: 0.8071 (p0) cc_final: 0.7839 (p0) REVERT: C 132 ASN cc_start: 0.8327 (p0) cc_final: 0.7978 (p0) REVERT: C 314 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7826 (ptm160) REVERT: C 315 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7702 (t) REVERT: C 323 ASP cc_start: 0.7437 (p0) cc_final: 0.7178 (p0) outliers start: 27 outliers final: 15 residues processed: 183 average time/residue: 0.3615 time to fit residues: 71.8398 Evaluate side-chains 183 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 70 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132940 restraints weight = 11324.640| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.86 r_work: 0.3708 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8102 Z= 0.125 Angle : 0.549 8.940 11033 Z= 0.285 Chirality : 0.042 0.150 1320 Planarity : 0.003 0.038 1374 Dihedral : 4.411 18.463 1166 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.24 % Allowed : 18.45 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.74 (0.27), residues: 1045 helix: 2.41 (0.28), residues: 345 sheet: 0.81 (0.30), residues: 293 loop : -1.53 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.022 0.002 TYR E 178 PHE 0.014 0.001 PHE B 199 TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8100) covalent geometry : angle 0.54942 (11029) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.48416 ( 4) hydrogen bonds : bond 0.03722 ( 423) hydrogen bonds : angle 4.40775 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6242 (tm-30) REVERT: A 318 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7336 (mp) REVERT: A 328 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6780 (mp) REVERT: B 323 MET cc_start: 0.7115 (mpp) cc_final: 0.6445 (mpp) REVERT: B 327 THR cc_start: 0.7639 (p) cc_final: 0.7337 (p) REVERT: C 132 ASN cc_start: 0.8245 (p0) cc_final: 0.7895 (p0) REVERT: C 315 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7668 (t) REVERT: C 323 ASP cc_start: 0.7410 (p0) cc_final: 0.7162 (p0) outliers start: 26 outliers final: 13 residues processed: 177 average time/residue: 0.3929 time to fit residues: 75.0109 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.151245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.131397 restraints weight = 11225.570| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.85 r_work: 0.3685 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8102 Z= 0.176 Angle : 0.597 9.657 11033 Z= 0.308 Chirality : 0.044 0.245 1320 Planarity : 0.004 0.037 1374 Dihedral : 4.630 22.055 1166 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.62 % Allowed : 18.95 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.58 (0.26), residues: 1045 helix: 2.15 (0.28), residues: 352 sheet: 0.88 (0.31), residues: 282 loop : -1.63 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.026 0.002 TYR E 178 PHE 0.016 0.002 PHE B 196 TRP 0.016 0.002 TRP C 211 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8100) covalent geometry : angle 0.59726 (11029) SS BOND : bond 0.00199 ( 2) SS BOND : angle 0.51310 ( 4) hydrogen bonds : bond 0.04194 ( 423) hydrogen bonds : angle 4.49256 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6234 (tm-30) REVERT: A 250 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7842 (mp) REVERT: A 318 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7336 (mp) REVERT: A 328 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6892 (mp) REVERT: B 323 MET cc_start: 0.7191 (mpp) cc_final: 0.6520 (mpp) REVERT: B 327 THR cc_start: 0.7649 (p) cc_final: 0.7343 (p) REVERT: C 132 ASN cc_start: 0.8329 (p0) cc_final: 0.7970 (p0) REVERT: C 315 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7791 (t) REVERT: C 323 ASP cc_start: 0.7430 (p0) cc_final: 0.7190 (p0) outliers start: 29 outliers final: 17 residues processed: 184 average time/residue: 0.3993 time to fit residues: 79.5389 Evaluate side-chains 186 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.150897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131137 restraints weight = 11180.806| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.84 r_work: 0.3683 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8102 Z= 0.178 Angle : 0.607 9.841 11033 Z= 0.313 Chirality : 0.044 0.210 1320 Planarity : 0.004 0.037 1374 Dihedral : 4.671 21.960 1166 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.99 % Allowed : 18.83 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.59 (0.26), residues: 1045 helix: 2.15 (0.28), residues: 352 sheet: 0.88 (0.31), residues: 282 loop : -1.63 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.029 0.002 TYR E 178 PHE 0.017 0.002 PHE B 199 TRP 0.016 0.002 TRP C 211 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8100) covalent geometry : angle 0.60654 (11029) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.56777 ( 4) hydrogen bonds : bond 0.04217 ( 423) hydrogen bonds : angle 4.52688 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8312 (mt) cc_final: 0.8083 (mt) REVERT: A 209 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: A 250 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 318 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7382 (mp) REVERT: A 328 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6950 (mp) REVERT: B 323 MET cc_start: 0.7235 (mpp) cc_final: 0.6551 (mpp) REVERT: B 327 THR cc_start: 0.7665 (p) cc_final: 0.7360 (p) REVERT: C 132 ASN cc_start: 0.8359 (p0) cc_final: 0.8011 (p0) REVERT: C 315 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7797 (t) REVERT: C 323 ASP cc_start: 0.7444 (p0) cc_final: 0.7206 (p0) outliers start: 32 outliers final: 21 residues processed: 182 average time/residue: 0.3767 time to fit residues: 74.3495 Evaluate side-chains 187 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 178 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132818 restraints weight = 11216.546| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.87 r_work: 0.3675 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8102 Z= 0.188 Angle : 0.626 10.024 11033 Z= 0.320 Chirality : 0.045 0.257 1320 Planarity : 0.004 0.037 1374 Dihedral : 4.733 22.938 1166 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.24 % Allowed : 19.70 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.56 (0.26), residues: 1045 helix: 2.12 (0.28), residues: 352 sheet: 0.87 (0.31), residues: 282 loop : -1.64 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.030 0.002 TYR E 102 PHE 0.017 0.002 PHE B 199 TRP 0.015 0.002 TRP C 211 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8100) covalent geometry : angle 0.62588 (11029) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.58740 ( 4) hydrogen bonds : bond 0.04271 ( 423) hydrogen bonds : angle 4.54982 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8308 (mt) cc_final: 0.8075 (mt) REVERT: A 209 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6186 (tm-30) REVERT: A 250 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 318 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7389 (mp) REVERT: A 328 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6992 (mp) REVERT: B 323 MET cc_start: 0.7254 (mpp) cc_final: 0.6576 (mpp) REVERT: B 327 THR cc_start: 0.7673 (p) cc_final: 0.7369 (p) REVERT: C 132 ASN cc_start: 0.8365 (p0) cc_final: 0.8018 (p0) REVERT: C 315 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7784 (t) REVERT: C 323 ASP cc_start: 0.7450 (p0) cc_final: 0.7209 (p0) outliers start: 26 outliers final: 20 residues processed: 178 average time/residue: 0.3781 time to fit residues: 73.0074 Evaluate side-chains 183 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 178 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.150749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131286 restraints weight = 11195.854| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.82 r_work: 0.3688 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8102 Z= 0.169 Angle : 0.618 9.848 11033 Z= 0.316 Chirality : 0.044 0.211 1320 Planarity : 0.004 0.038 1374 Dihedral : 4.655 21.327 1166 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.99 % Allowed : 20.45 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.58 (0.26), residues: 1045 helix: 2.15 (0.28), residues: 352 sheet: 0.87 (0.31), residues: 282 loop : -1.63 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 150 TYR 0.029 0.002 TYR E 102 PHE 0.017 0.002 PHE B 199 TRP 0.016 0.002 TRP C 211 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8100) covalent geometry : angle 0.61780 (11029) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.62887 ( 4) hydrogen bonds : bond 0.04118 ( 423) hydrogen bonds : angle 4.52472 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8295 (mt) cc_final: 0.8056 (mt) REVERT: A 209 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6205 (tm-30) REVERT: A 318 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7380 (mp) REVERT: A 328 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7029 (mt) REVERT: B 18 MET cc_start: 0.8233 (mmm) cc_final: 0.8027 (mmm) REVERT: B 323 MET cc_start: 0.7189 (mpp) cc_final: 0.6526 (mpp) REVERT: B 327 THR cc_start: 0.7693 (p) cc_final: 0.7394 (p) REVERT: C 132 ASN cc_start: 0.8335 (p0) cc_final: 0.7988 (p0) REVERT: C 315 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7731 (t) REVERT: C 323 ASP cc_start: 0.7444 (p0) cc_final: 0.7213 (p0) outliers start: 24 outliers final: 20 residues processed: 179 average time/residue: 0.3754 time to fit residues: 72.7702 Evaluate side-chains 191 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 178 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.153147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133610 restraints weight = 11247.234| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.87 r_work: 0.3687 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8102 Z= 0.160 Angle : 0.620 9.810 11033 Z= 0.317 Chirality : 0.044 0.223 1320 Planarity : 0.004 0.068 1374 Dihedral : 4.633 21.022 1166 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.24 % Allowed : 20.45 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.58 (0.26), residues: 1045 helix: 2.15 (0.28), residues: 352 sheet: 0.86 (0.31), residues: 282 loop : -1.62 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 314 TYR 0.029 0.002 TYR E 102 PHE 0.017 0.001 PHE B 199 TRP 0.014 0.002 TRP C 211 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8100) covalent geometry : angle 0.61972 (11029) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.61044 ( 4) hydrogen bonds : bond 0.04077 ( 423) hydrogen bonds : angle 4.50973 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3290.84 seconds wall clock time: 56 minutes 40.45 seconds (3400.45 seconds total)