Starting phenix.real_space_refine on Wed Aug 5 06:50:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pa1_71429/08_2026/9pa1_71429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pa1_71429/08_2026/9pa1_71429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pa1_71429/08_2026/9pa1_71429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pa1_71429/08_2026/9pa1_71429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pa1_71429/08_2026/9pa1_71429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pa1_71429/08_2026/9pa1_71429.map" } resolution = 2.63 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= 0.024 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 62 5.16 5 C 5554 2.51 5 N 1462 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 8716 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2118 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'TYR:plan': 2, 'ASP:plan': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2600 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 414 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1779 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1787 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'1PC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.22 Number of scatterers: 8716 At special positions: 0 Unit cell: (87.768, 123.372, 125.856, 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 62 16.00 O 1638 8.00 N 1462 7.00 C 5554 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=2.03 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: 0.66 Conformation dependent library (CDL) restraints added in 412.3 milliseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 39.9% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 58 through 87 Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 127 through 162 Processing helix chain 'A' and resid 162 through 170 removed outlier: 4.377A pdb=" N ASP A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 196 Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 263 through 298 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 304 Processing helix chain 'A' and resid 305 through 331 Proline residue: A 327 - end of helix Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.529A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.791A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.502A pdb=" N ASP E 211 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 212' Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.612A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 removed outlier: 4.312A pdb=" N ASP B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 260 removed outlier: 4.207A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.116A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 Processing helix chain 'B' and resid 327 through 352 removed outlier: 3.774A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.420A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.575A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.046A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.698A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.948A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.062A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.621A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 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: 6.487A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.487A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.681A pdb=" N ALA E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 174 through 177 removed outlier: 5.700A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 190 removed outlier: 3.631A pdb=" N PHE B 189 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1353 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: 1.25 Time building geometry restraints manager: 0.89 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: 2793 1.34 - 1.46: 2045 1.46 - 1.58: 3966 1.58 - 1.70: 0 1.70 - 1.81: 90 Bond restraints: 8894 Sorted by residual: bond pdb=" CG 1PC A 401 " pdb=" NM 1PC A 401 " ideal model delta sigma weight residual 1.461 1.559 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" CI 1PC A 401 " pdb=" CJ 1PC A 401 " ideal model delta sigma weight residual 1.525 1.481 0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" CR 1PC A 401 " pdb=" NM 1PC A 401 " ideal model delta sigma weight residual 1.450 1.488 -0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.10e-02 2.27e+03 3.01e+00 bond pdb=" CJ 1PC A 401 " pdb=" CK 1PC A 401 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.52e+00 ... (remaining 8889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 11973 2.96 - 5.91: 76 5.91 - 8.87: 14 8.87 - 11.82: 4 11.82 - 14.78: 1 Bond angle restraints: 12068 Sorted by residual: angle pdb=" N ILE A 58 " pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 111.00 121.87 -10.87 2.80e+00 1.28e-01 1.51e+01 angle pdb=" CA LEU A 259 " pdb=" CB LEU A 259 " pdb=" CG LEU A 259 " ideal model delta sigma weight residual 116.30 127.99 -11.69 3.50e+00 8.16e-02 1.12e+01 angle pdb=" C ASP C 195 " pdb=" N THR C 196 " pdb=" CA THR C 196 " ideal model delta sigma weight residual 122.61 127.80 -5.19 1.56e+00 4.11e-01 1.11e+01 angle pdb=" CA 1PC A 401 " pdb=" CG 1PC A 401 " pdb=" NM 1PC A 401 " ideal model delta sigma weight residual 115.06 105.12 9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA ILE A 58 " pdb=" C ILE A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 116.90 121.38 -4.48 1.50e+00 4.44e-01 8.94e+00 ... (remaining 12063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 4818 23.67 - 47.34: 406 47.34 - 71.01: 39 71.01 - 94.68: 5 94.68 - 118.35: 7 Dihedral angle restraints: 5275 sinusoidal: 1990 harmonic: 3285 Sorted by residual: dihedral pdb=" CH 1PC A 401 " pdb=" CI 1PC A 401 " pdb=" CJ 1PC A 401 " pdb=" CK 1PC A 401 " ideal model delta sinusoidal sigma weight residual -52.72 65.63 -118.35 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CI 1PC A 401 " pdb=" CJ 1PC A 401 " pdb=" CK 1PC A 401 " pdb=" CL 1PC A 401 " ideal model delta sinusoidal sigma weight residual 52.66 -58.25 110.91 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" CG 1PC A 401 " pdb=" CH 1PC A 401 " pdb=" CI 1PC A 401 " pdb=" CJ 1PC A 401 " ideal model delta sinusoidal sigma weight residual 58.08 -51.72 109.80 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 5272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 941 0.039 - 0.078: 330 0.078 - 0.117: 101 0.117 - 0.156: 21 0.156 - 0.195: 2 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CB ILE E 177 " pdb=" CA ILE E 177 " pdb=" CG1 ILE E 177 " pdb=" CG2 ILE E 177 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CB ILE E 100 " pdb=" CA ILE E 100 " pdb=" CG1 ILE E 100 " pdb=" CG2 ILE E 100 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA THR C 196 " pdb=" N THR C 196 " pdb=" C THR C 196 " pdb=" CB THR C 196 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1392 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO C 236 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 228 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" CG ASP C 228 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP C 228 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP C 228 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 171 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 172 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " 0.021 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 379 2.72 - 3.27: 8337 3.27 - 3.81: 15141 3.81 - 4.36: 18549 4.36 - 4.90: 31567 Nonbonded interactions: 73973 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.176 3.040 nonbonded pdb=" O VAL A 284 " pdb=" OG1 THR A 288 " model vdw 2.176 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.272 3.040 nonbonded pdb=" O PHE B 336 " pdb=" OG1 THR B 340 " model vdw 2.294 3.040 nonbonded pdb=" OG SER D 57 " pdb=" OE1 GLU D 58 " model vdw 2.295 3.040 ... (remaining 73968 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: 1.440 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.430 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 0.098 8896 Z= 0.179 Angle : 0.687 14.775 12072 Z= 0.340 Chirality : 0.044 0.195 1395 Planarity : 0.005 0.055 1519 Dihedral : 16.787 118.354 3147 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.19 % Allowed : 18.83 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.07 (0.24), residues: 1116 helix: 1.24 (0.25), residues: 395 sheet: 0.01 (0.31), residues: 255 loop : -0.93 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 197 TYR 0.021 0.002 TYR A 140 PHE 0.023 0.002 PHE B 274 TRP 0.010 0.002 TRP A 183 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 8894) covalent geometry : angle 0.68753 / 0.34 (12068) SS BOND : bond 0.00039 / 0.02 ( 2) SS BOND : angle 0.24063 / 0.12 ( 4) hydrogen bonds : bond 0.17366 / 12.01 ( 467) hydrogen bonds : angle 6.75075 / 4.91 ( 1353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.220 Fit side-chains outliers start: 30 outliers final: 23 residues processed: 178 average time/residue: 0.4112 time to fit residues: 79.0568 Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 332 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.0040 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.0980 chunk 106 optimal weight: 0.6980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 162 HIS C 295 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.174424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151143 restraints weight = 10823.903| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.32 r_work: 0.3741 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8896 Z= 0.123 Angle : 0.573 12.915 12072 Z= 0.289 Chirality : 0.041 0.147 1395 Planarity : 0.004 0.047 1519 Dihedral : 10.915 114.812 1267 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.15 % Allowed : 17.66 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1116 helix: 2.04 (0.26), residues: 397 sheet: 0.18 (0.30), residues: 263 loop : -0.81 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.020 0.001 TYR A 140 PHE 0.011 0.001 PHE C 199 TRP 0.017 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 8894) covalent geometry : angle 0.57314 / 0.29 (12068) SS BOND : bond 0.00231 / 0.12 ( 2) SS BOND : angle 0.38537 / 0.21 ( 4) hydrogen bonds : bond 0.04166 / 2.84 ( 467) hydrogen bonds : angle 5.00878 / 3.64 ( 1353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.333 Fit side-chains REVERT: A 185 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6410 (mt) outliers start: 39 outliers final: 24 residues processed: 183 average time/residue: 0.4276 time to fit residues: 84.6394 Evaluate side-chains 172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 332 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.0000 chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS C 156 GLN C 295 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.173082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149780 restraints weight = 10656.284| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.31 r_work: 0.3716 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8896 Z= 0.153 Angle : 0.587 13.692 12072 Z= 0.294 Chirality : 0.042 0.144 1395 Planarity : 0.004 0.044 1519 Dihedral : 9.306 103.392 1252 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.47 % Allowed : 17.77 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.72 (0.24), residues: 1116 helix: 2.20 (0.25), residues: 398 sheet: 0.09 (0.29), residues: 260 loop : -0.82 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.022 0.002 TYR E 178 PHE 0.013 0.001 PHE C 199 TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8894) covalent geometry : angle 0.58741 / 0.29 (12068) SS BOND : bond 0.00144 / 0.08 ( 2) SS BOND : angle 0.35783 / 0.19 ( 4) hydrogen bonds : bond 0.04144 / 2.82 ( 467) hydrogen bonds : angle 4.84816 / 3.52 ( 1353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.314 Fit side-chains REVERT: E 95 TYR cc_start: 0.8233 (m-80) cc_final: 0.7700 (m-80) REVERT: E 177 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 225 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7797 (m) outliers start: 42 outliers final: 26 residues processed: 175 average time/residue: 0.4335 time to fit residues: 82.1367 Evaluate side-chains 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.6980 chunk 107 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 65 optimal weight: 0.0050 chunk 92 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS C 156 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.173397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149990 restraints weight = 10898.409| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.34 r_work: 0.3718 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8896 Z= 0.140 Angle : 0.565 13.628 12072 Z= 0.284 Chirality : 0.042 0.143 1395 Planarity : 0.004 0.044 1519 Dihedral : 7.822 93.536 1247 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.36 % Allowed : 18.30 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.78 (0.24), residues: 1116 helix: 2.30 (0.26), residues: 398 sheet: 0.12 (0.29), residues: 259 loop : -0.85 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 32 TYR 0.022 0.002 TYR E 178 PHE 0.012 0.001 PHE C 199 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8894) covalent geometry : angle 0.56492 / 0.28 (12068) SS BOND : bond 0.00162 / 0.08 ( 2) SS BOND : angle 0.38295 / 0.22 ( 4) hydrogen bonds : bond 0.03925 / 2.66 ( 467) hydrogen bonds : angle 4.73456 / 3.44 ( 1353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.307 Fit side-chains REVERT: A 185 LEU cc_start: 0.6663 (mm) cc_final: 0.6402 (mt) REVERT: E 57 THR cc_start: 0.7647 (m) cc_final: 0.7252 (m) REVERT: E 95 TYR cc_start: 0.8203 (m-80) cc_final: 0.7659 (m-80) REVERT: E 177 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7758 (mp) REVERT: B 225 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7818 (m) REVERT: B 345 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7227 (ttmt) outliers start: 41 outliers final: 25 residues processed: 179 average time/residue: 0.4262 time to fit residues: 82.7602 Evaluate side-chains 175 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 162 HIS C 156 GLN C 295 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147696 restraints weight = 10692.982| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.48 r_work: 0.3658 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8896 Z= 0.275 Angle : 0.698 14.721 12072 Z= 0.351 Chirality : 0.047 0.182 1395 Planarity : 0.005 0.050 1519 Dihedral : 7.572 71.135 1244 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.53 % Allowed : 18.09 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.51 (0.24), residues: 1116 helix: 1.88 (0.25), residues: 402 sheet: 0.04 (0.28), residues: 265 loop : -0.89 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.031 0.003 TYR E 178 PHE 0.017 0.002 PHE C 292 TRP 0.011 0.002 TRP C 63 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.28 ( 8894) covalent geometry : angle 0.69781 / 0.35 (12068) SS BOND : bond 0.00271 / 0.13 ( 2) SS BOND : angle 0.41866 / 0.19 ( 4) hydrogen bonds : bond 0.04870 / 3.30 ( 467) hydrogen bonds : angle 5.05686 / 3.69 ( 1353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.233 Fit side-chains REVERT: A 185 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6360 (mt) REVERT: A 239 VAL cc_start: 0.6961 (OUTLIER) cc_final: 0.6585 (t) REVERT: C 217 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6845 (ppp) REVERT: E 177 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7845 (mp) REVERT: B 345 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7257 (ttmt) outliers start: 52 outliers final: 32 residues processed: 188 average time/residue: 0.3389 time to fit residues: 69.1536 Evaluate side-chains 188 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 162 HIS C 156 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.172307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.149931 restraints weight = 10762.424| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.49 r_work: 0.3692 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8896 Z= 0.148 Angle : 0.596 13.292 12072 Z= 0.298 Chirality : 0.042 0.144 1395 Planarity : 0.004 0.048 1519 Dihedral : 7.152 78.296 1240 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.47 % Allowed : 20.21 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.63 (0.24), residues: 1116 helix: 2.13 (0.26), residues: 397 sheet: 0.10 (0.29), residues: 264 loop : -0.92 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 32 TYR 0.025 0.002 TYR E 178 PHE 0.014 0.001 PHE A 99 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8894) covalent geometry : angle 0.59655 / 0.30 (12068) SS BOND : bond 0.00170 / 0.09 ( 2) SS BOND : angle 0.42111 / 0.23 ( 4) hydrogen bonds : bond 0.04016 / 2.72 ( 467) hydrogen bonds : angle 4.80575 / 3.51 ( 1353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.187 Fit side-chains REVERT: E 57 THR cc_start: 0.7666 (m) cc_final: 0.7244 (m) REVERT: E 95 TYR cc_start: 0.8240 (m-80) cc_final: 0.7724 (m-80) REVERT: E 177 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7736 (mp) REVERT: B 345 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7209 (ttmt) outliers start: 42 outliers final: 31 residues processed: 185 average time/residue: 0.3796 time to fit residues: 75.9889 Evaluate side-chains 184 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 162 HIS C 156 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.172081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149824 restraints weight = 10758.496| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.49 r_work: 0.3687 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8896 Z= 0.167 Angle : 0.612 13.477 12072 Z= 0.306 Chirality : 0.043 0.147 1395 Planarity : 0.004 0.053 1519 Dihedral : 7.170 79.718 1240 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.79 % Allowed : 19.79 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1116 helix: 2.09 (0.26), residues: 396 sheet: 0.06 (0.29), residues: 264 loop : -0.93 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 32 TYR 0.025 0.002 TYR E 178 PHE 0.015 0.002 PHE B 199 TRP 0.014 0.002 TRP C 82 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 8894) covalent geometry : angle 0.61185 / 0.31 (12068) SS BOND : bond 0.00156 / 0.08 ( 2) SS BOND : angle 0.42797 / 0.22 ( 4) hydrogen bonds : bond 0.04118 / 2.80 ( 467) hydrogen bonds : angle 4.78612 / 3.50 ( 1353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.261 Fit side-chains REVERT: E 57 THR cc_start: 0.7660 (m) cc_final: 0.7246 (m) REVERT: E 95 TYR cc_start: 0.8232 (m-80) cc_final: 0.7699 (m-80) REVERT: E 177 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7778 (mp) outliers start: 45 outliers final: 34 residues processed: 183 average time/residue: 0.3948 time to fit residues: 78.0478 Evaluate side-chains 184 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 332 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 162 HIS C 156 GLN C 340 ASN E 39 GLN E 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.173057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150675 restraints weight = 10733.288| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.49 r_work: 0.3712 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8896 Z= 0.127 Angle : 0.579 13.096 12072 Z= 0.289 Chirality : 0.041 0.144 1395 Planarity : 0.004 0.055 1519 Dihedral : 7.066 81.392 1240 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.72 % Allowed : 21.28 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1116 helix: 2.19 (0.26), residues: 398 sheet: 0.10 (0.29), residues: 264 loop : -0.92 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 32 TYR 0.023 0.002 TYR E 178 PHE 0.015 0.001 PHE A 99 TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 8894) covalent geometry : angle 0.57881 / 0.29 (12068) SS BOND : bond 0.00152 / 0.08 ( 2) SS BOND : angle 0.45260 / 0.22 ( 4) hydrogen bonds : bond 0.03804 / 2.58 ( 467) hydrogen bonds : angle 4.66871 / 3.42 ( 1353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.317 Fit side-chains REVERT: E 57 THR cc_start: 0.7584 (m) cc_final: 0.7130 (m) REVERT: E 95 TYR cc_start: 0.8192 (m-80) cc_final: 0.7689 (m-80) REVERT: E 177 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7745 (mp) REVERT: E 190 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6806 (mtm110) outliers start: 35 outliers final: 29 residues processed: 172 average time/residue: 0.4168 time to fit residues: 77.6335 Evaluate side-chains 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 332 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 104 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 162 HIS C 156 GLN E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.172598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.149916 restraints weight = 10687.180| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.41 r_work: 0.3698 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8896 Z= 0.155 Angle : 0.602 13.257 12072 Z= 0.300 Chirality : 0.042 0.144 1395 Planarity : 0.004 0.064 1519 Dihedral : 7.014 81.074 1238 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.04 % Allowed : 20.74 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1116 helix: 2.16 (0.25), residues: 398 sheet: 0.10 (0.29), residues: 264 loop : -0.90 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 32 TYR 0.024 0.002 TYR E 178 PHE 0.018 0.001 PHE B 199 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 8894) covalent geometry : angle 0.60166 / 0.30 (12068) SS BOND : bond 0.00149 / 0.08 ( 2) SS BOND : angle 0.44977 / 0.22 ( 4) hydrogen bonds : bond 0.03950 / 2.67 ( 467) hydrogen bonds : angle 4.69952 / 3.44 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.276 Fit side-chains REVERT: C 308 LEU cc_start: 0.7490 (mp) cc_final: 0.7233 (mt) REVERT: C 325 MET cc_start: 0.7259 (mmm) cc_final: 0.6901 (mmm) REVERT: E 57 THR cc_start: 0.7576 (m) cc_final: 0.7136 (m) REVERT: E 95 TYR cc_start: 0.8200 (m-80) cc_final: 0.7669 (m-80) REVERT: E 177 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7773 (mp) outliers start: 38 outliers final: 31 residues processed: 175 average time/residue: 0.4276 time to fit residues: 80.5934 Evaluate side-chains 181 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 85 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 162 HIS C 156 GLN E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.172359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150148 restraints weight = 10661.715| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.41 r_work: 0.3694 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 0.039 8896 Z= 0.162 Angle : 0.613 13.350 12072 Z= 0.305 Chirality : 0.043 0.146 1395 Planarity : 0.004 0.066 1519 Dihedral : 7.035 81.292 1238 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.94 % Allowed : 21.06 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.65 (0.25), residues: 1116 helix: 2.13 (0.26), residues: 397 sheet: 0.10 (0.29), residues: 264 loop : -0.89 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 32 TYR 0.024 0.002 TYR E 178 PHE 0.017 0.002 PHE B 199 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8894) covalent geometry : angle 0.61345 / 0.31 (12068) SS BOND : bond 0.00154 / 0.08 ( 2) SS BOND : angle 0.45538 / 0.22 ( 4) hydrogen bonds : bond 0.04013 / 2.72 ( 467) hydrogen bonds : angle 4.72072 / 3.46 ( 1353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.197 Fit side-chains REVERT: C 308 LEU cc_start: 0.7476 (mp) cc_final: 0.7230 (mt) REVERT: C 325 MET cc_start: 0.7284 (mmm) cc_final: 0.6942 (mmm) REVERT: E 57 THR cc_start: 0.7577 (m) cc_final: 0.7127 (m) REVERT: E 95 TYR cc_start: 0.8215 (m-80) cc_final: 0.7666 (m-80) REVERT: E 177 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7774 (mp) outliers start: 37 outliers final: 33 residues processed: 173 average time/residue: 0.4235 time to fit residues: 79.0341 Evaluate side-chains 180 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 42 optimal weight: 0.0770 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN C 156 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 = 0.4128 r_free = 0.4128 target = 0.173037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.150849 restraints weight = 10654.317| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.43 r_work: 0.3696 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8896 Z= 0.137 Angle : 0.594 13.094 12072 Z= 0.296 Chirality : 0.042 0.142 1395 Planarity : 0.004 0.066 1519 Dihedral : 6.845 82.023 1236 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.04 % Allowed : 21.06 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1116 helix: 2.18 (0.26), residues: 397 sheet: 0.12 (0.29), residues: 264 loop : -0.89 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 32 TYR 0.023 0.002 TYR E 178 PHE 0.016 0.001 PHE B 199 TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8894) covalent geometry : angle 0.59422 / 0.30 (12068) SS BOND : bond 0.00150 / 0.08 ( 2) SS BOND : angle 0.46307 / 0.24 ( 4) hydrogen bonds : bond 0.03829 / 2.60 ( 467) hydrogen bonds : angle 4.66508 / 3.42 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.99 seconds wall clock time: 57 minutes 3.23 seconds (3423.23 seconds total)