Starting phenix.real_space_refine on Tue Mar 3 18:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmt_33304/03_2026/7xmt_33304.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmt_33304/03_2026/7xmt_33304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xmt_33304/03_2026/7xmt_33304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmt_33304/03_2026/7xmt_33304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xmt_33304/03_2026/7xmt_33304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmt_33304/03_2026/7xmt_33304.map" } resolution = 2.8 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5187 2.51 5 N 1381 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8137 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1955 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 4, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1723 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "S" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 265 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain: "B" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2370 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 305} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'I8B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (3 atoms not shown) pdb=" CB LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 2.07, per 1000 atoms: 0.25 Number of scatterers: 8137 At special positions: 0 Unit cell: (111.815, 108.68, 109.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1516 8.00 N 1381 7.00 C 5187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 333.4 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 46 through 74 removed outlier: 4.198A pdb=" N ILE R 50 " --> pdb=" O GLY R 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 55 " --> pdb=" O GLN R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 97 Processing helix chain 'R' and resid 99 through 109 removed outlier: 3.590A pdb=" N SER R 105 " --> pdb=" O PRO R 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 150 removed outlier: 3.553A pdb=" N VAL R 148 " --> pdb=" O ARG R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 Processing helix chain 'R' and resid 159 through 179 removed outlier: 3.586A pdb=" N TRP R 171 " --> pdb=" O ASN R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 184 removed outlier: 3.618A pdb=" N PHE R 184 " --> pdb=" O PRO R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 218 Processing helix chain 'R' and resid 220 through 245 Processing helix chain 'R' and resid 251 through 284 removed outlier: 3.657A pdb=" N VAL R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Proline residue: R 274 - end of helix removed outlier: 3.740A pdb=" N GLN R 279 " --> pdb=" O PHE R 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU R 280 " --> pdb=" O TYR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 307 removed outlier: 4.077A pdb=" N SER R 304 " --> pdb=" O SER R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 312 Processing helix chain 'R' and resid 315 through 320 removed outlier: 3.996A pdb=" N ARG R 319 " --> pdb=" O SER R 315 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG R 320 " --> pdb=" O ASP R 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 315 through 320' Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.593A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.682A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.924A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.543A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.521A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.782A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 37 through 42 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.734A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.472A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.516A pdb=" N CYS S 159 " --> pdb=" O PHE S 212 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.599A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 186 through 187 Processing sheet with id=AA7, first strand: chain 'S' and resid 189 through 190 Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.864A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.794A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.732A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.443A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 202 Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.652A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.974A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2625 1.34 - 1.46: 2034 1.46 - 1.58: 3573 1.58 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 8307 Sorted by residual: bond pdb=" C I8B R 401 " pdb=" O3 I8B R 401 " ideal model delta sigma weight residual 1.331 1.233 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" N I8B R 401 " pdb=" C I8B R 401 " ideal model delta sigma weight residual 1.263 1.324 -0.061 2.00e-02 2.50e+03 9.25e+00 bond pdb=" N3 I8B R 401 " pdb=" S I8B R 401 " ideal model delta sigma weight residual 1.656 1.615 0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C7 I8B R 401 " pdb=" C8 I8B R 401 " ideal model delta sigma weight residual 1.403 1.381 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" O1 I8B R 401 " pdb=" S I8B R 401 " ideal model delta sigma weight residual 1.453 1.432 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 8302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 11180 1.74 - 3.49: 92 3.49 - 5.23: 17 5.23 - 6.97: 3 6.97 - 8.71: 2 Bond angle restraints: 11294 Sorted by residual: angle pdb=" N I8B R 401 " pdb=" C I8B R 401 " pdb=" C1 I8B R 401 " ideal model delta sigma weight residual 125.42 116.71 8.71 3.00e+00 1.11e-01 8.44e+00 angle pdb=" N LEU A 283 " pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " ideal model delta sigma weight residual 113.65 110.15 3.50 1.47e+00 4.63e-01 5.66e+00 angle pdb=" C1 I8B R 401 " pdb=" C I8B R 401 " pdb=" O3 I8B R 401 " ideal model delta sigma weight residual 113.39 120.07 -6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" N LEU R 179 " pdb=" CA LEU R 179 " pdb=" C LEU R 179 " ideal model delta sigma weight residual 109.81 114.68 -4.87 2.21e+00 2.05e-01 4.86e+00 angle pdb=" CA VAL R 100 " pdb=" C VAL R 100 " pdb=" N PRO R 101 " ideal model delta sigma weight residual 118.88 121.97 -3.09 1.54e+00 4.22e-01 4.03e+00 ... (remaining 11289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 4664 16.61 - 33.23: 195 33.23 - 49.84: 36 49.84 - 66.45: 1 66.45 - 83.07: 3 Dihedral angle restraints: 4899 sinusoidal: 1808 harmonic: 3091 Sorted by residual: dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 198 " pdb=" CB CYS R 198 " ideal model delta sinusoidal sigma weight residual -86.00 -123.08 37.08 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " pdb=" CG ASP B 153 " pdb=" OD1 ASP B 153 " ideal model delta sinusoidal sigma weight residual -30.00 -82.34 52.34 1 2.00e+01 2.50e-03 9.34e+00 dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 69.30 23.70 1 1.00e+01 1.00e-02 8.09e+00 ... (remaining 4896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 917 0.034 - 0.068: 282 0.068 - 0.102: 78 0.102 - 0.137: 29 0.137 - 0.171: 2 Chirality restraints: 1308 Sorted by residual: chirality pdb=" C1 I8B R 401 " pdb=" C I8B R 401 " pdb=" C17 I8B R 401 " pdb=" N1 I8B R 401 " both_signs ideal model delta sigma weight residual False 2.35 2.52 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ILE B 33 " pdb=" N ILE B 33 " pdb=" C ILE B 33 " pdb=" CB ILE B 33 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1305 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 179 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO R 180 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 180 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 180 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 307 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 308 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 308 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 308 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO S 75 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.016 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2081 2.79 - 3.32: 7584 3.32 - 3.85: 13581 3.85 - 4.37: 16272 4.37 - 4.90: 27589 Nonbonded interactions: 67107 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 326 " pdb=" OG1 THR A 329 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.299 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.306 3.120 nonbonded pdb=" OG SER S 106 " pdb=" OD1 ASP S 109 " model vdw 2.310 3.040 ... (remaining 67102 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 8309 Z= 0.112 Angle : 0.470 8.714 11298 Z= 0.252 Chirality : 0.038 0.171 1308 Planarity : 0.003 0.043 1427 Dihedral : 9.399 83.066 2899 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.22), residues: 1050 helix: -3.42 (0.19), residues: 311 sheet: -1.91 (0.30), residues: 250 loop : -2.22 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 314 TYR 0.005 0.001 TYR S 102 PHE 0.005 0.001 PHE B 151 TRP 0.006 0.001 TRP R 171 HIS 0.002 0.000 HIS R 111 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8307) covalent geometry : angle 0.46996 (11294) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.84921 ( 4) hydrogen bonds : bond 0.26887 ( 341) hydrogen bonds : angle 9.12517 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.288 Fit side-chains REVERT: B 111 TYR cc_start: 0.6384 (m-80) cc_final: 0.6070 (m-80) REVERT: B 289 TYR cc_start: 0.6451 (m-10) cc_final: 0.6184 (m-10) REVERT: B 335 PHE cc_start: 0.6095 (m-10) cc_final: 0.5845 (m-10) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.4464 time to fit residues: 87.4332 Evaluate side-chains 116 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 88 ASN R 167 ASN R 248 GLN A 213 HIS A 269 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 110 ASN B 156 GLN B 239 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.192630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154659 restraints weight = 8217.281| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.72 r_work: 0.3801 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8309 Z= 0.271 Angle : 0.758 14.271 11298 Z= 0.391 Chirality : 0.048 0.193 1308 Planarity : 0.005 0.054 1427 Dihedral : 4.940 25.465 1175 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.05 % Allowed : 11.72 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.24), residues: 1050 helix: -1.18 (0.26), residues: 327 sheet: -1.49 (0.31), residues: 269 loop : -1.62 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 38 TYR 0.020 0.003 TYR R 85 PHE 0.017 0.002 PHE R 184 TRP 0.022 0.002 TRP B 99 HIS 0.008 0.002 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 8307) covalent geometry : angle 0.75821 (11294) SS BOND : bond 0.00343 ( 2) SS BOND : angle 0.71646 ( 4) hydrogen bonds : bond 0.04427 ( 341) hydrogen bonds : angle 5.59525 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: R 110 ARG cc_start: 0.6796 (ttt-90) cc_final: 0.5927 (tpp80) REVERT: R 114 PHE cc_start: 0.5941 (m-80) cc_final: 0.5722 (m-80) REVERT: A 256 ASN cc_start: 0.7488 (p0) cc_final: 0.7261 (p0) REVERT: A 294 ASN cc_start: 0.8665 (m-40) cc_final: 0.8451 (m-40) REVERT: B 111 TYR cc_start: 0.7755 (m-80) cc_final: 0.7482 (m-80) REVERT: B 268 ASN cc_start: 0.7498 (t0) cc_final: 0.6986 (t0) outliers start: 26 outliers final: 10 residues processed: 152 average time/residue: 0.5156 time to fit residues: 83.6677 Evaluate side-chains 118 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 14 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 248 GLN R 282 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 HIS S 183 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.193494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.154666 restraints weight = 8204.568| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.70 r_work: 0.3826 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8309 Z= 0.152 Angle : 0.623 10.525 11298 Z= 0.311 Chirality : 0.043 0.249 1308 Planarity : 0.004 0.049 1427 Dihedral : 4.433 15.415 1175 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.40 % Allowed : 16.88 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.25), residues: 1050 helix: -0.08 (0.29), residues: 325 sheet: -1.33 (0.31), residues: 268 loop : -1.36 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 188 TYR 0.017 0.002 TYR R 85 PHE 0.013 0.001 PHE B 151 TRP 0.016 0.001 TRP B 99 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8307) covalent geometry : angle 0.62321 (11294) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.83265 ( 4) hydrogen bonds : bond 0.03675 ( 341) hydrogen bonds : angle 4.96523 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.321 Fit side-chains REVERT: R 243 LEU cc_start: 0.7590 (tt) cc_final: 0.7372 (tp) REVERT: A 256 ASN cc_start: 0.7276 (p0) cc_final: 0.7065 (p0) REVERT: A 294 ASN cc_start: 0.8594 (m-40) cc_final: 0.8374 (m-40) REVERT: A 306 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.6069 (tm-30) REVERT: A 308 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: C 38 MET cc_start: 0.6313 (mpp) cc_final: 0.6033 (mmp) REVERT: B 111 TYR cc_start: 0.7727 (m-80) cc_final: 0.7521 (m-80) REVERT: B 217 MET cc_start: 0.6767 (pp-130) cc_final: 0.5749 (tpp) REVERT: B 314 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6155 (ttt90) REVERT: B 315 VAL cc_start: 0.6398 (OUTLIER) cc_final: 0.6125 (m) outliers start: 29 outliers final: 13 residues processed: 129 average time/residue: 0.5764 time to fit residues: 79.1422 Evaluate side-chains 121 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 248 GLN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.194280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.155930 restraints weight = 8257.267| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.78 r_work: 0.3823 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8309 Z= 0.128 Angle : 0.593 9.730 11298 Z= 0.294 Chirality : 0.042 0.207 1308 Planarity : 0.004 0.048 1427 Dihedral : 4.264 16.038 1175 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 18.64 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.26), residues: 1050 helix: 0.45 (0.30), residues: 324 sheet: -1.21 (0.31), residues: 263 loop : -1.18 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 188 TYR 0.016 0.001 TYR R 85 PHE 0.016 0.001 PHE R 184 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8307) covalent geometry : angle 0.59247 (11294) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.81913 ( 4) hydrogen bonds : bond 0.03191 ( 341) hydrogen bonds : angle 4.73134 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.330 Fit side-chains REVERT: R 243 LEU cc_start: 0.7603 (tt) cc_final: 0.7398 (tp) REVERT: R 259 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.6240 (ttp-110) REVERT: R 263 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7051 (ttm) REVERT: A 29 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7823 (tppp) REVERT: A 256 ASN cc_start: 0.7056 (p0) cc_final: 0.6855 (p0) REVERT: B 111 TYR cc_start: 0.7693 (m-80) cc_final: 0.7459 (m-80) REVERT: B 315 VAL cc_start: 0.6377 (OUTLIER) cc_final: 0.6093 (m) REVERT: B 325 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7402 (mmm) outliers start: 26 outliers final: 12 residues processed: 133 average time/residue: 0.5515 time to fit residues: 78.1374 Evaluate side-chains 129 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 MET Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain R residue 263 MET Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 96 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 29 optimal weight: 0.0000 chunk 11 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 199 ASN A 294 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.183104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.143900 restraints weight = 8278.451| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.80 r_work: 0.3646 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8309 Z= 0.251 Angle : 0.728 11.875 11298 Z= 0.369 Chirality : 0.047 0.230 1308 Planarity : 0.004 0.049 1427 Dihedral : 5.081 19.685 1175 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.57 % Allowed : 19.46 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.26), residues: 1050 helix: 0.42 (0.30), residues: 324 sheet: -1.20 (0.31), residues: 268 loop : -1.11 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 304 TYR 0.019 0.002 TYR R 85 PHE 0.021 0.002 PHE B 222 TRP 0.023 0.002 TRP B 99 HIS 0.006 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 8307) covalent geometry : angle 0.72786 (11294) SS BOND : bond 0.00396 ( 2) SS BOND : angle 1.21171 ( 4) hydrogen bonds : bond 0.03865 ( 341) hydrogen bonds : angle 5.21892 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.284 Fit side-chains REVERT: R 86 LEU cc_start: 0.7390 (mp) cc_final: 0.7188 (mm) REVERT: R 88 ASN cc_start: 0.7174 (t0) cc_final: 0.6913 (t0) REVERT: R 259 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6395 (ttp-110) REVERT: R 263 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6943 (ttm) REVERT: A 256 ASN cc_start: 0.7508 (p0) cc_final: 0.7270 (p0) REVERT: A 305 CYS cc_start: 0.7841 (m) cc_final: 0.7482 (m) REVERT: A 308 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: A 323 PHE cc_start: 0.6691 (m-80) cc_final: 0.6460 (m-80) REVERT: S 83 MET cc_start: 0.8561 (mtm) cc_final: 0.8300 (mtp) outliers start: 39 outliers final: 15 residues processed: 161 average time/residue: 0.4854 time to fit residues: 83.8946 Evaluate side-chains 138 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain R residue 263 MET Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN R 282 ASN A 294 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.187957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147736 restraints weight = 8195.833| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.69 r_work: 0.3742 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8309 Z= 0.140 Angle : 0.628 9.562 11298 Z= 0.313 Chirality : 0.042 0.158 1308 Planarity : 0.004 0.045 1427 Dihedral : 4.617 17.893 1175 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.22 % Allowed : 21.34 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.26), residues: 1050 helix: 0.63 (0.30), residues: 327 sheet: -1.11 (0.31), residues: 265 loop : -1.11 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.018 0.001 TYR R 85 PHE 0.015 0.001 PHE R 184 TRP 0.018 0.002 TRP R 272 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8307) covalent geometry : angle 0.62807 (11294) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.92369 ( 4) hydrogen bonds : bond 0.03220 ( 341) hydrogen bonds : angle 4.80323 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.323 Fit side-chains REVERT: R 110 ARG cc_start: 0.6915 (ttt90) cc_final: 0.6333 (tpp80) REVERT: R 259 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6312 (ttp-110) REVERT: A 33 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.5785 (pp20) REVERT: A 256 ASN cc_start: 0.7036 (p0) cc_final: 0.6792 (p0) REVERT: A 305 CYS cc_start: 0.7725 (m) cc_final: 0.7432 (m) REVERT: A 308 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: B 46 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8008 (tpt170) REVERT: B 111 TYR cc_start: 0.7746 (m-80) cc_final: 0.7529 (m-80) REVERT: B 172 GLU cc_start: 0.7472 (pm20) cc_final: 0.7224 (pm20) REVERT: B 217 MET cc_start: 0.6953 (pp-130) cc_final: 0.5848 (tpp) outliers start: 36 outliers final: 11 residues processed: 148 average time/residue: 0.4886 time to fit residues: 77.6901 Evaluate side-chains 132 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 ASN ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN R 282 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.187885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148860 restraints weight = 8255.882| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.76 r_work: 0.3746 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8309 Z= 0.149 Angle : 0.650 11.726 11298 Z= 0.317 Chirality : 0.044 0.346 1308 Planarity : 0.004 0.044 1427 Dihedral : 4.570 18.724 1175 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.46 % Allowed : 23.09 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1050 helix: 0.76 (0.30), residues: 325 sheet: -1.05 (0.30), residues: 268 loop : -0.98 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 159 TYR 0.015 0.001 TYR R 85 PHE 0.013 0.001 PHE B 222 TRP 0.015 0.002 TRP R 272 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8307) covalent geometry : angle 0.64957 (11294) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.94224 ( 4) hydrogen bonds : bond 0.03245 ( 341) hydrogen bonds : angle 4.82015 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.340 Fit side-chains REVERT: R 97 MET cc_start: 0.3997 (mtt) cc_final: 0.3414 (mmp) REVERT: R 110 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6338 (tpp80) REVERT: R 259 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6329 (ttp-110) REVERT: A 33 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.5745 (pp20) REVERT: A 305 CYS cc_start: 0.7634 (m) cc_final: 0.7238 (m) REVERT: A 308 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: B 46 ARG cc_start: 0.8370 (mmm160) cc_final: 0.7948 (tpt170) REVERT: B 111 TYR cc_start: 0.7714 (m-80) cc_final: 0.7490 (m-80) REVERT: B 176 GLN cc_start: 0.8242 (mt0) cc_final: 0.7939 (tt0) outliers start: 21 outliers final: 10 residues processed: 146 average time/residue: 0.5186 time to fit residues: 80.7827 Evaluate side-chains 132 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN R 282 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.187047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148383 restraints weight = 8300.432| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.78 r_work: 0.3729 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8309 Z= 0.156 Angle : 0.643 9.294 11298 Z= 0.321 Chirality : 0.044 0.328 1308 Planarity : 0.004 0.044 1427 Dihedral : 4.649 18.977 1175 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.40 % Allowed : 23.09 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.26), residues: 1050 helix: 0.77 (0.30), residues: 327 sheet: -1.04 (0.31), residues: 264 loop : -0.92 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 159 TYR 0.013 0.001 TYR R 85 PHE 0.013 0.002 PHE B 222 TRP 0.017 0.002 TRP R 272 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8307) covalent geometry : angle 0.64280 (11294) SS BOND : bond 0.00337 ( 2) SS BOND : angle 0.90586 ( 4) hydrogen bonds : bond 0.03247 ( 341) hydrogen bonds : angle 4.85086 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.237 Fit side-chains REVERT: R 97 MET cc_start: 0.3926 (mtt) cc_final: 0.3349 (mmp) REVERT: R 110 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6413 (tpp80) REVERT: R 130 MET cc_start: 0.6545 (ptt) cc_final: 0.6226 (ppp) REVERT: R 159 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6722 (mtt-85) REVERT: R 259 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6353 (ttp-110) REVERT: A 33 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.5933 (pp20) REVERT: A 305 CYS cc_start: 0.7767 (m) cc_final: 0.7336 (m) REVERT: A 308 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: B 46 ARG cc_start: 0.8500 (mmm160) cc_final: 0.8076 (tpt90) REVERT: B 111 TYR cc_start: 0.7735 (m-80) cc_final: 0.7518 (m-80) REVERT: B 217 MET cc_start: 0.6838 (pp-130) cc_final: 0.6117 (tpp) REVERT: B 219 ARG cc_start: 0.7365 (mtp180) cc_final: 0.7047 (mmm160) outliers start: 29 outliers final: 17 residues processed: 142 average time/residue: 0.5574 time to fit residues: 84.2225 Evaluate side-chains 140 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 129 ASN Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 0.0970 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.188638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.151109 restraints weight = 8279.655| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.79 r_work: 0.3760 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8309 Z= 0.142 Angle : 0.656 13.678 11298 Z= 0.322 Chirality : 0.043 0.316 1308 Planarity : 0.004 0.044 1427 Dihedral : 4.569 18.159 1175 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.93 % Allowed : 23.92 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.26), residues: 1050 helix: 0.86 (0.31), residues: 326 sheet: -1.02 (0.30), residues: 268 loop : -0.85 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 159 TYR 0.012 0.001 TYR R 85 PHE 0.011 0.001 PHE B 222 TRP 0.014 0.002 TRP R 272 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8307) covalent geometry : angle 0.65564 (11294) SS BOND : bond 0.00376 ( 2) SS BOND : angle 0.94451 ( 4) hydrogen bonds : bond 0.03221 ( 341) hydrogen bonds : angle 4.79810 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.350 Fit side-chains REVERT: R 97 MET cc_start: 0.3996 (mtt) cc_final: 0.3355 (mmp) REVERT: R 110 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6368 (tpp80) REVERT: R 159 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6724 (mtt-85) REVERT: R 259 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6324 (ttp-110) REVERT: A 33 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.5921 (pp20) REVERT: A 198 MET cc_start: 0.7779 (ttp) cc_final: 0.7553 (mtp) REVERT: A 305 CYS cc_start: 0.7759 (m) cc_final: 0.7363 (m) REVERT: A 308 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: B 46 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8083 (tpt170) REVERT: B 111 TYR cc_start: 0.7719 (m-80) cc_final: 0.7505 (m-80) REVERT: B 172 GLU cc_start: 0.7583 (pm20) cc_final: 0.7206 (pm20) REVERT: B 217 MET cc_start: 0.6863 (pp-130) cc_final: 0.5879 (tpp) outliers start: 25 outliers final: 13 residues processed: 125 average time/residue: 0.4849 time to fit residues: 64.7483 Evaluate side-chains 125 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 87 optimal weight: 4.9990 chunk 52 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 overall best weight: 0.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 167 ASN A 294 ASN A 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.191736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.153756 restraints weight = 8266.182| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.75 r_work: 0.3809 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8309 Z= 0.121 Angle : 0.619 9.690 11298 Z= 0.307 Chirality : 0.042 0.314 1308 Planarity : 0.004 0.043 1427 Dihedral : 4.397 17.106 1175 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.34 % Allowed : 24.38 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.26), residues: 1050 helix: 0.92 (0.31), residues: 326 sheet: -0.93 (0.31), residues: 266 loop : -0.87 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 159 TYR 0.013 0.001 TYR B 59 PHE 0.011 0.001 PHE R 184 TRP 0.014 0.001 TRP R 272 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8307) covalent geometry : angle 0.61928 (11294) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.73833 ( 4) hydrogen bonds : bond 0.03037 ( 341) hydrogen bonds : angle 4.69033 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.319 Fit side-chains REVERT: R 86 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6769 (mp) REVERT: R 97 MET cc_start: 0.4021 (mtt) cc_final: 0.3358 (mmp) REVERT: R 110 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6521 (ttt180) REVERT: R 259 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6308 (ttp-110) REVERT: A 33 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.5979 (pp20) REVERT: A 252 SER cc_start: 0.8811 (t) cc_final: 0.8415 (p) REVERT: A 305 CYS cc_start: 0.7747 (m) cc_final: 0.7404 (m) REVERT: A 308 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: S 220 GLU cc_start: 0.7685 (mp0) cc_final: 0.7211 (mp0) REVERT: B 46 ARG cc_start: 0.8310 (mmm160) cc_final: 0.8071 (tpt170) REVERT: B 50 THR cc_start: 0.7740 (t) cc_final: 0.7502 (m) REVERT: B 111 TYR cc_start: 0.7643 (m-80) cc_final: 0.7319 (m-80) REVERT: B 152 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7975 (mm) REVERT: B 172 GLU cc_start: 0.7456 (pm20) cc_final: 0.7139 (pm20) REVERT: B 197 ARG cc_start: 0.7974 (ptp-110) cc_final: 0.7588 (ptm160) REVERT: B 217 MET cc_start: 0.6858 (pp-130) cc_final: 0.5931 (tpp) outliers start: 20 outliers final: 7 residues processed: 125 average time/residue: 0.5230 time to fit residues: 69.8940 Evaluate side-chains 118 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 28 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN A 294 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.187957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150074 restraints weight = 8312.437| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.67 r_work: 0.3759 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8309 Z= 0.155 Angle : 0.669 13.130 11298 Z= 0.326 Chirality : 0.044 0.319 1308 Planarity : 0.004 0.043 1427 Dihedral : 4.587 17.730 1175 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.58 % Allowed : 24.38 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.26), residues: 1050 helix: 0.94 (0.31), residues: 326 sheet: -1.08 (0.29), residues: 282 loop : -0.81 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 159 TYR 0.010 0.001 TYR S 94 PHE 0.012 0.001 PHE B 222 TRP 0.023 0.002 TRP R 272 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8307) covalent geometry : angle 0.66904 (11294) SS BOND : bond 0.00369 ( 2) SS BOND : angle 0.70091 ( 4) hydrogen bonds : bond 0.03193 ( 341) hydrogen bonds : angle 4.78005 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6185.24 seconds wall clock time: 105 minutes 22.55 seconds (6322.55 seconds total)