Starting phenix.real_space_refine on Thu Sep 18 06:00:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eea_47953/09_2025/9eea_47953.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eea_47953/09_2025/9eea_47953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eea_47953/09_2025/9eea_47953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eea_47953/09_2025/9eea_47953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eea_47953/09_2025/9eea_47953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eea_47953/09_2025/9eea_47953.map" } resolution = 3.36 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= 0.010 sd= 0.225 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 48 5.16 5 C 4819 2.51 5 N 1306 2.21 5 O 1377 1.98 5 H 7098 0.53 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14648 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4064 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 4724 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 594 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3408 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 7, 'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "E" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1839 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.72, per 1000 atoms: 0.19 Number of scatterers: 14648 At special positions: 0 Unit cell: (75.15, 98.53, 128.59, 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) S 48 16.00 O 1377 8.00 N 1306 7.00 C 4819 6.00 H 7098 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 262 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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: 1.14 Conformation dependent library (CDL) restraints added in 446.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 42.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 39 through 69 removed outlier: 4.111A pdb=" N PHE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.886A pdb=" N GLY A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 108 Processing helix chain 'A' and resid 108 through 116 removed outlier: 4.171A pdb=" N ASN A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 137 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.802A pdb=" N VAL A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 210 Processing helix chain 'A' and resid 224 through 259 removed outlier: 3.557A pdb=" N GLU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 266 through 288 Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.711A pdb=" N ILE A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.752A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'D' and resid 12 through 40 removed outlier: 3.619A pdb=" N GLU D 16 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 252 through 269 removed outlier: 4.130A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 273 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 297 through 302 removed outlier: 4.245A pdb=" N TYR D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.046A pdb=" N TYR D 308 " --> pdb=" O PHE D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 342 removed outlier: 4.511A pdb=" N SER D 342 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 381 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.510A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.881A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.661A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.887A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.592A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.521A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.521A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.840A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.720A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AA9, first strand: chain 'D' and resid 208 through 213 removed outlier: 7.164A pdb=" N ARG D 42 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE D 245 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 44 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL D 247 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU D 46 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASP D 249 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE D 244 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE D 280 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE D 246 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN D 282 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL D 248 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.927A pdb=" N GLN E 5 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.296A pdb=" N GLY E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E 124 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 92 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 38 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.530A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1047 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: 2.27 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7074 1.04 - 1.24: 1038 1.24 - 1.44: 2364 1.44 - 1.64: 4268 1.64 - 1.84: 66 Bond restraints: 14810 Sorted by residual: bond pdb=" CB PRO A 266 " pdb=" CG PRO A 266 " ideal model delta sigma weight residual 1.492 1.601 -0.109 5.00e-02 4.00e+02 4.78e+00 bond pdb=" N GLN C 11 " pdb=" CA GLN C 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N ASP B 5 " pdb=" CA ASP B 5 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N GLU D 10 " pdb=" CA GLU D 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 ... (remaining 14805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.31: 26541 11.31 - 22.63: 3 22.63 - 33.94: 3 33.94 - 45.26: 1 45.26 - 56.57: 4 Bond angle restraints: 26552 Sorted by residual: angle pdb=" CA GLY A 76 " pdb=" N GLY A 76 " pdb=" H GLY A 76 " ideal model delta sigma weight residual 114.88 58.31 56.57 3.00e+00 1.11e-01 3.56e+02 angle pdb=" C HIS A 75 " pdb=" N GLY A 76 " pdb=" H GLY A 76 " ideal model delta sigma weight residual 125.18 68.77 56.41 3.00e+00 1.11e-01 3.54e+02 angle pdb=" C ILE A 287 " pdb=" N TYR A 288 " pdb=" H TYR A 288 " ideal model delta sigma weight residual 124.06 73.01 51.05 3.00e+00 1.11e-01 2.90e+02 angle pdb=" CA TYR A 288 " pdb=" N TYR A 288 " pdb=" H TYR A 288 " ideal model delta sigma weight residual 113.76 63.10 50.67 3.00e+00 1.11e-01 2.85e+02 angle pdb=" HG2 PRO A 266 " pdb=" CG PRO A 266 " pdb=" HG3 PRO A 266 " ideal model delta sigma weight residual 110.00 74.67 35.33 3.00e+00 1.11e-01 1.39e+02 ... (remaining 26547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6280 17.88 - 35.76: 566 35.76 - 53.64: 199 53.64 - 71.52: 37 71.52 - 89.39: 18 Dihedral angle restraints: 7100 sinusoidal: 3615 harmonic: 3485 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -42.69 -43.31 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA CYS E 99 " pdb=" C CYS E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta harmonic sigma weight residual -180.00 -154.99 -25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ALA A 184 " pdb=" C ALA A 184 " pdb=" N CYS A 185 " pdb=" CA CYS A 185 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1014 0.048 - 0.096: 165 0.096 - 0.144: 50 0.144 - 0.192: 1 0.192 - 0.240: 1 Chirality restraints: 1231 Sorted by residual: chirality pdb=" C2' ADN A 400 " pdb=" C1' ADN A 400 " pdb=" C3' ADN A 400 " pdb=" O2' ADN A 400 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C3' ADN A 400 " pdb=" C2' ADN A 400 " pdb=" C4' ADN A 400 " pdb=" O3' ADN A 400 " both_signs ideal model delta sigma weight residual False -2.56 -2.73 0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1228 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 53 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE A 53 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE A 53 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 54 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 189 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C PRO A 189 " 0.032 2.00e-02 2.50e+03 pdb=" O PRO A 189 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 190 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 172 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO A 173 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " 0.023 5.00e-02 4.00e+02 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 435 2.13 - 2.74: 26003 2.74 - 3.36: 40483 3.36 - 3.98: 49530 3.98 - 4.60: 77796 Nonbonded interactions: 194247 Sorted by model distance: nonbonded pdb=" H TYR A 288 " pdb=" HA TYR A 288 " model vdw 1.507 1.816 nonbonded pdb=" H GLY A 76 " pdb=" HA2 GLY A 76 " model vdw 1.584 1.816 nonbonded pdb=" HG1 THR B 164 " pdb=" O HIS B 183 " model vdw 1.597 2.450 nonbonded pdb=" O ASP B 186 " pdb=" H CYS B 204 " model vdw 1.602 2.450 nonbonded pdb=" H MET B 101 " pdb=" O GLY B 115 " model vdw 1.603 2.450 ... (remaining 194242 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 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 : 0.003 0.109 7716 Z= 0.144 Angle : 0.589 14.287 10527 Z= 0.326 Chirality : 0.040 0.240 1231 Planarity : 0.003 0.041 1339 Dihedral : 17.732 89.394 2611 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.40 % Allowed : 30.42 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.27), residues: 995 helix: 1.06 (0.28), residues: 379 sheet: -1.12 (0.36), residues: 210 loop : -1.61 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.008 0.001 TYR A 288 PHE 0.017 0.001 PHE A 182 TRP 0.015 0.001 TRP A 268 HIS 0.002 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7712) covalent geometry : angle 0.58667 (10519) SS BOND : bond 0.00430 ( 4) SS BOND : angle 1.84816 ( 8) hydrogen bonds : bond 0.17047 ( 372) hydrogen bonds : angle 6.76103 ( 1047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 308 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.8290 (t) cc_final: 0.8033 (t) REVERT: B 215 GLU cc_start: 0.8136 (tt0) cc_final: 0.7757 (tm-30) REVERT: B 308 LEU cc_start: 0.7576 (mp) cc_final: 0.6930 (mp) outliers start: 3 outliers final: 2 residues processed: 309 average time/residue: 0.1941 time to fit residues: 80.1608 Evaluate side-chains 223 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 80 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN B 311 HIS D 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.095091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.084354 restraints weight = 108852.621| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 6.30 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 7716 Z= 0.210 Angle : 0.659 13.966 10527 Z= 0.363 Chirality : 0.040 0.159 1231 Planarity : 0.004 0.043 1339 Dihedral : 7.863 83.985 1110 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.23 % Allowed : 30.55 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.03 (0.26), residues: 995 helix: 0.82 (0.27), residues: 380 sheet: -1.07 (0.35), residues: 207 loop : -1.90 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 314 TYR 0.017 0.001 TYR B 264 PHE 0.017 0.002 PHE E 103 TRP 0.011 0.002 TRP A 268 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7712) covalent geometry : angle 0.65763 (10519) SS BOND : bond 0.00526 ( 4) SS BOND : angle 1.82826 ( 8) hydrogen bonds : bond 0.05010 ( 372) hydrogen bonds : angle 5.76756 ( 1047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 PHE cc_start: 0.7552 (m-80) cc_final: 0.7235 (m-10) outliers start: 24 outliers final: 19 residues processed: 232 average time/residue: 0.1975 time to fit residues: 61.8141 Evaluate side-chains 224 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 6.9990 chunk 87 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 overall best weight: 1.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 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 = 0.3930 r_free = 0.3930 target = 0.094974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.083911 restraints weight = 106310.239| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 6.31 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 7716 Z= 0.152 Angle : 0.618 13.840 10527 Z= 0.337 Chirality : 0.039 0.149 1231 Planarity : 0.004 0.042 1339 Dihedral : 7.262 81.516 1110 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.90 % Allowed : 29.48 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.77 (0.27), residues: 995 helix: 1.02 (0.27), residues: 380 sheet: -0.81 (0.36), residues: 206 loop : -1.81 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 375 TYR 0.013 0.001 TYR A 288 PHE 0.017 0.001 PHE B 199 TRP 0.011 0.001 TRP B 63 HIS 0.045 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7712) covalent geometry : angle 0.61702 (10519) SS BOND : bond 0.00406 ( 4) SS BOND : angle 1.54317 ( 8) hydrogen bonds : bond 0.04682 ( 372) hydrogen bonds : angle 5.39045 ( 1047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 PHE cc_start: 0.7732 (m-80) cc_final: 0.7432 (m-10) REVERT: B 335 PHE cc_start: 0.8006 (m-80) cc_final: 0.7714 (m-80) outliers start: 29 outliers final: 21 residues processed: 237 average time/residue: 0.2013 time to fit residues: 64.1191 Evaluate side-chains 229 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 44 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 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 = 0.3920 r_free = 0.3920 target = 0.094157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.083220 restraints weight = 105843.496| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 6.27 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 7716 Z= 0.141 Angle : 0.619 13.938 10527 Z= 0.332 Chirality : 0.039 0.194 1231 Planarity : 0.004 0.047 1339 Dihedral : 7.014 81.505 1110 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.50 % Allowed : 30.69 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.65 (0.27), residues: 995 helix: 1.04 (0.27), residues: 381 sheet: -0.69 (0.35), residues: 213 loop : -1.71 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.012 0.001 TYR A 288 PHE 0.020 0.001 PHE B 199 TRP 0.010 0.001 TRP B 63 HIS 0.014 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7712) covalent geometry : angle 0.61746 (10519) SS BOND : bond 0.00189 ( 4) SS BOND : angle 1.51984 ( 8) hydrogen bonds : bond 0.04494 ( 372) hydrogen bonds : angle 5.29998 ( 1047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 PHE cc_start: 0.7763 (m-80) cc_final: 0.7467 (m-10) REVERT: D 29 GLN cc_start: 0.8900 (mm110) cc_final: 0.8562 (mp10) REVERT: E 38 ARG cc_start: 0.8285 (ptp90) cc_final: 0.7999 (ptp-170) outliers start: 26 outliers final: 24 residues processed: 226 average time/residue: 0.2010 time to fit residues: 61.2016 Evaluate side-chains 230 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 292 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.093785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.083001 restraints weight = 107860.482| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 6.25 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 7716 Z= 0.137 Angle : 0.610 13.879 10527 Z= 0.328 Chirality : 0.039 0.150 1231 Planarity : 0.004 0.046 1339 Dihedral : 6.905 82.160 1110 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.04 % Allowed : 31.49 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.54 (0.27), residues: 995 helix: 1.13 (0.27), residues: 381 sheet: -0.69 (0.35), residues: 213 loop : -1.61 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 22 TYR 0.012 0.001 TYR A 288 PHE 0.021 0.001 PHE B 199 TRP 0.011 0.001 TRP B 63 HIS 0.007 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7712) covalent geometry : angle 0.60931 (10519) SS BOND : bond 0.00339 ( 4) SS BOND : angle 1.43719 ( 8) hydrogen bonds : bond 0.04425 ( 372) hydrogen bonds : angle 5.20608 ( 1047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8736 (tt) REVERT: D 29 GLN cc_start: 0.8885 (mm110) cc_final: 0.8558 (mp10) REVERT: D 252 ASP cc_start: 0.8149 (t0) cc_final: 0.7909 (t0) REVERT: E 38 ARG cc_start: 0.8274 (ptp90) cc_final: 0.8026 (ptp-170) outliers start: 30 outliers final: 24 residues processed: 223 average time/residue: 0.1963 time to fit residues: 59.3293 Evaluate side-chains 234 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 292 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 10.0000 chunk 84 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 2.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 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 = 0.3899 r_free = 0.3899 target = 0.092306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.081738 restraints weight = 107696.003| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 6.12 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 7716 Z= 0.156 Angle : 0.617 14.003 10527 Z= 0.332 Chirality : 0.039 0.147 1231 Planarity : 0.004 0.047 1339 Dihedral : 6.922 82.033 1110 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.44 % Allowed : 30.69 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.58 (0.27), residues: 995 helix: 1.03 (0.27), residues: 387 sheet: -0.73 (0.35), residues: 213 loop : -1.59 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 22 TYR 0.013 0.002 TYR A 288 PHE 0.023 0.001 PHE B 199 TRP 0.013 0.001 TRP B 63 HIS 0.007 0.001 HIS D 377 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7712) covalent geometry : angle 0.61610 (10519) SS BOND : bond 0.00363 ( 4) SS BOND : angle 1.37715 ( 8) hydrogen bonds : bond 0.04408 ( 372) hydrogen bonds : angle 5.21608 ( 1047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8776 (tt) REVERT: D 29 GLN cc_start: 0.8864 (mm110) cc_final: 0.8509 (mp10) REVERT: D 252 ASP cc_start: 0.8077 (t0) cc_final: 0.7862 (t0) outliers start: 33 outliers final: 31 residues processed: 224 average time/residue: 0.1947 time to fit residues: 59.1324 Evaluate side-chains 225 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN D 380 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.093819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.082984 restraints weight = 103868.884| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 6.17 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 7716 Z= 0.115 Angle : 0.599 13.898 10527 Z= 0.319 Chirality : 0.039 0.145 1231 Planarity : 0.003 0.044 1339 Dihedral : 6.863 85.252 1110 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.31 % Allowed : 30.69 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.29 (0.28), residues: 995 helix: 1.34 (0.28), residues: 386 sheet: -0.78 (0.34), residues: 218 loop : -1.38 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.012 0.001 TYR E 80 PHE 0.022 0.001 PHE B 199 TRP 0.021 0.001 TRP B 63 HIS 0.004 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7712) covalent geometry : angle 0.59804 (10519) SS BOND : bond 0.00276 ( 4) SS BOND : angle 1.32436 ( 8) hydrogen bonds : bond 0.04255 ( 372) hydrogen bonds : angle 4.93712 ( 1047) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8791 (tt) REVERT: B 314 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.6925 (mmm-85) REVERT: D 29 GLN cc_start: 0.8812 (mm110) cc_final: 0.8502 (mp10) REVERT: D 219 PHE cc_start: 0.8592 (m-80) cc_final: 0.8357 (m-80) REVERT: D 252 ASP cc_start: 0.7936 (t0) cc_final: 0.7716 (t0) outliers start: 32 outliers final: 27 residues processed: 222 average time/residue: 0.1932 time to fit residues: 58.2125 Evaluate side-chains 218 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.093619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.082891 restraints weight = 108018.478| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 6.29 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 7716 Z= 0.115 Angle : 0.604 13.885 10527 Z= 0.321 Chirality : 0.039 0.144 1231 Planarity : 0.004 0.043 1339 Dihedral : 6.813 85.033 1110 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.50 % Allowed : 31.22 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.19 (0.28), residues: 995 helix: 1.41 (0.28), residues: 386 sheet: -0.74 (0.34), residues: 218 loop : -1.28 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 332 TYR 0.011 0.001 TYR D 329 PHE 0.023 0.001 PHE B 199 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7712) covalent geometry : angle 0.60319 (10519) SS BOND : bond 0.00184 ( 4) SS BOND : angle 1.31183 ( 8) hydrogen bonds : bond 0.04234 ( 372) hydrogen bonds : angle 4.88921 ( 1047) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8824 (tt) REVERT: D 29 GLN cc_start: 0.8817 (mm110) cc_final: 0.8509 (mp10) REVERT: D 219 PHE cc_start: 0.8591 (m-80) cc_final: 0.8358 (m-80) REVERT: D 252 ASP cc_start: 0.7899 (t0) cc_final: 0.7696 (t0) REVERT: E 38 ARG cc_start: 0.8206 (ptp90) cc_final: 0.7974 (ptp-170) outliers start: 26 outliers final: 25 residues processed: 212 average time/residue: 0.1861 time to fit residues: 53.4199 Evaluate side-chains 215 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 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 = 0.3929 r_free = 0.3929 target = 0.093743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.083211 restraints weight = 108081.669| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 6.19 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 7716 Z= 0.114 Angle : 0.605 13.902 10527 Z= 0.321 Chirality : 0.039 0.143 1231 Planarity : 0.004 0.043 1339 Dihedral : 6.785 85.145 1110 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.63 % Allowed : 31.36 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.16 (0.28), residues: 995 helix: 1.42 (0.28), residues: 386 sheet: -0.72 (0.34), residues: 219 loop : -1.27 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 332 TYR 0.011 0.001 TYR E 80 PHE 0.024 0.001 PHE B 199 TRP 0.020 0.001 TRP B 63 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7712) covalent geometry : angle 0.60409 (10519) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.25015 ( 8) hydrogen bonds : bond 0.04114 ( 372) hydrogen bonds : angle 4.85408 ( 1047) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8816 (tt) REVERT: B 93 ILE cc_start: 0.8578 (mm) cc_final: 0.8301 (tp) REVERT: D 29 GLN cc_start: 0.8818 (mm110) cc_final: 0.8525 (mp10) REVERT: D 380 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8683 (tm-30) outliers start: 27 outliers final: 26 residues processed: 214 average time/residue: 0.1894 time to fit residues: 55.2999 Evaluate side-chains 220 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 380 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 = 0.3883 r_free = 0.3883 target = 0.090819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.080737 restraints weight = 113139.959| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 6.09 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 7716 Z= 0.208 Angle : 0.660 14.025 10527 Z= 0.360 Chirality : 0.040 0.139 1231 Planarity : 0.004 0.045 1339 Dihedral : 6.932 81.750 1110 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.31 % Allowed : 31.09 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.57 (0.27), residues: 995 helix: 1.05 (0.27), residues: 388 sheet: -0.82 (0.33), residues: 228 loop : -1.54 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.013 0.002 TYR B 289 PHE 0.022 0.002 PHE B 199 TRP 0.024 0.002 TRP B 63 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 7712) covalent geometry : angle 0.65882 (10519) SS BOND : bond 0.00425 ( 4) SS BOND : angle 1.42474 ( 8) hydrogen bonds : bond 0.04399 ( 372) hydrogen bonds : angle 5.20471 ( 1047) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8847 (tt) REVERT: D 380 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8731 (tm-30) outliers start: 32 outliers final: 30 residues processed: 202 average time/residue: 0.1787 time to fit residues: 50.1068 Evaluate side-chains 211 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 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 = 0.3899 r_free = 0.3899 target = 0.091765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.081605 restraints weight = 111404.352| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 6.09 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 7716 Z= 0.139 Angle : 0.639 13.917 10527 Z= 0.341 Chirality : 0.040 0.140 1231 Planarity : 0.004 0.043 1339 Dihedral : 6.917 83.549 1110 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.17 % Allowed : 31.63 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.47 (0.27), residues: 995 helix: 1.09 (0.27), residues: 389 sheet: -0.83 (0.34), residues: 225 loop : -1.40 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 375 TYR 0.011 0.001 TYR A 288 PHE 0.023 0.001 PHE B 199 TRP 0.023 0.001 TRP B 63 HIS 0.004 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7712) covalent geometry : angle 0.63786 (10519) SS BOND : bond 0.00231 ( 4) SS BOND : angle 1.34607 ( 8) hydrogen bonds : bond 0.04285 ( 372) hydrogen bonds : angle 5.03964 ( 1047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.08 seconds wall clock time: 52 minutes 4.80 seconds (3124.80 seconds total)