Starting phenix.real_space_refine on Fri Sep 11 11:03:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tuz_26136/09_2026/7tuz_26136.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tuz_26136/09_2026/7tuz_26136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tuz_26136/09_2026/7tuz_26136.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tuz_26136/09_2026/7tuz_26136.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tuz_26136/09_2026/7tuz_26136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tuz_26136/09_2026/7tuz_26136.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tuz_26136/09_2026/7tuz_26136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tuz_26136/09_2026/7tuz_26136.map" } resolution = 3.12 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= 0.002 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 68 5.16 5 C 5681 2.51 5 N 1504 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8910 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2214 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1823 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.86, per 1000 atoms: 0.21 Number of scatterers: 8910 At special positions: 0 Unit cell: (104.125, 119.119, 110.789, 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 68 16.00 O 1657 8.00 N 1504 7.00 C 5681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 181 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 244.3 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 38.0% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 26 through 59 removed outlier: 3.988A pdb=" N ILE R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) Proline residue: R 35 - end of helix removed outlier: 3.562A pdb=" N LEU R 51 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 88 Proline residue: R 85 - end of helix Processing helix chain 'R' and resid 102 through 134 removed outlier: 4.236A pdb=" N ILE R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR R 115 " --> pdb=" O PHE R 111 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR R 116 " --> pdb=" O TYR R 112 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER R 126 " --> pdb=" O MET R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 142 Processing helix chain 'R' and resid 144 through 168 Proline residue: R 165 - end of helix removed outlier: 3.827A pdb=" N ILE R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 188 Processing helix chain 'R' and resid 192 through 230 removed outlier: 4.620A pdb=" N LEU R 198 " --> pdb=" O PRO R 194 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY R 199 " --> pdb=" O TRP R 195 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU R 207 " --> pdb=" O ILE R 203 " (cutoff:3.500A) Proline residue: R 208 - end of helix Processing helix chain 'R' and resid 230 through 237 removed outlier: 3.647A pdb=" N GLU R 234 " --> pdb=" O ASN R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 274 removed outlier: 4.593A pdb=" N LYS R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Proline residue: R 259 - end of helix Processing helix chain 'R' and resid 281 through 312 removed outlier: 4.151A pdb=" N CYS R 295 " --> pdb=" O HIS R 291 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N CYS R 301 " --> pdb=" O MET R 297 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS R 302 " --> pdb=" O ASN R 298 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET R 303 " --> pdb=" O PHE R 299 " (cutoff:3.500A) Proline residue: R 305 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.614A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.877A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.502A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.890A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.507A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.540A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.742A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.293A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.974A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.899A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.994A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.294A 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: 6.733A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.685A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.438A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.879A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.050A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.715A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1278 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: 1.38 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1448 1.27 - 1.41: 2296 1.41 - 1.54: 5205 1.54 - 1.68: 46 1.68 - 1.82: 100 Bond restraints: 9095 Sorted by residual: bond pdb=" C05 KJX R 401 " pdb=" C06 KJX R 401 " ideal model delta sigma weight residual 1.522 1.131 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" C04 KJX R 401 " pdb=" C09 KJX R 401 " ideal model delta sigma weight residual 1.528 1.193 0.335 2.00e-02 2.50e+03 2.80e+02 bond pdb=" C06 KJX R 401 " pdb=" C14 KJX R 401 " ideal model delta sigma weight residual 1.526 1.257 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C10 KJX R 401 " pdb=" C17 KJX R 401 " ideal model delta sigma weight residual 1.519 1.251 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C09 KJX R 401 " pdb=" C12 KJX R 401 " ideal model delta sigma weight residual 1.528 1.279 0.249 2.00e-02 2.50e+03 1.55e+02 ... (remaining 9090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 12092 2.13 - 4.26: 192 4.26 - 6.39: 38 6.39 - 8.51: 7 8.51 - 10.64: 1 Bond angle restraints: 12330 Sorted by residual: angle pdb=" C ALA R 102 " pdb=" N LEU R 103 " pdb=" CA LEU R 103 " ideal model delta sigma weight residual 120.38 125.62 -5.24 1.46e+00 4.69e-01 1.29e+01 angle pdb=" C14 KJX R 401 " pdb=" C19 KJX R 401 " pdb=" C17 KJX R 401 " ideal model delta sigma weight residual 125.07 114.43 10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.08 126.65 -4.57 1.47e+00 4.63e-01 9.65e+00 angle pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 122.46 126.77 -4.31 1.41e+00 5.03e-01 9.36e+00 angle pdb=" N LEU R 84 " pdb=" CA LEU R 84 " pdb=" C LEU R 84 " ideal model delta sigma weight residual 109.81 116.39 -6.58 2.21e+00 2.05e-01 8.87e+00 ... (remaining 12325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4921 17.31 - 34.61: 404 34.61 - 51.92: 62 51.92 - 69.22: 7 69.22 - 86.53: 4 Dihedral angle restraints: 5398 sinusoidal: 2081 harmonic: 3317 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PHE R 111 " pdb=" C PHE R 111 " pdb=" N TYR R 112 " pdb=" CA TYR R 112 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ILE R 113 " pdb=" C ILE R 113 " pdb=" N ASN R 114 " pdb=" CA ASN R 114 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 1410 0.280 - 0.559: 2 0.559 - 0.839: 1 0.839 - 1.119: 0 1.119 - 1.398: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" C06 KJX R 401 " pdb=" C05 KJX R 401 " pdb=" C07 KJX R 401 " pdb=" C14 KJX R 401 " both_signs ideal model delta sigma weight residual False -2.58 -1.19 -1.40 2.00e-01 2.50e+01 4.89e+01 chirality pdb=" C04 KJX R 401 " pdb=" C05 KJX R 401 " pdb=" C08 KJX R 401 " pdb=" C09 KJX R 401 " both_signs ideal model delta sigma weight residual False -2.94 -2.15 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C08 KJX R 401 " pdb=" C04 KJX R 401 " pdb=" C13 KJX R 401 " pdb=" C15 KJX R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.98 -0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 1411 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 KJX R 401 " 0.091 2.00e-02 2.50e+03 1.23e-01 1.90e+02 pdb=" C14 KJX R 401 " -0.119 2.00e-02 2.50e+03 pdb=" C17 KJX R 401 " -0.107 2.00e-02 2.50e+03 pdb=" C19 KJX R 401 " 0.196 2.00e-02 2.50e+03 pdb=" C21 KJX R 401 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 236 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 184 " 0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO R 185 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 185 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 185 " 0.026 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 324 2.71 - 3.26: 8764 3.26 - 3.80: 14198 3.80 - 4.35: 17914 4.35 - 4.90: 30664 Nonbonded interactions: 71864 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.161 3.040 nonbonded pdb=" O THR R 123 " pdb=" OG SER R 126 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.216 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.255 3.040 ... (remaining 71859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.040 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 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 : 0.011 0.391 9098 Z= 0.555 Angle : 0.734 10.643 12336 Z= 0.404 Chirality : 0.066 1.398 1414 Planarity : 0.005 0.123 1554 Dihedral : 12.679 86.527 3247 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % 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: -2.23 (0.22), residues: 1123 helix: -0.54 (0.24), residues: 406 sheet: -1.68 (0.26), residues: 309 loop : -2.09 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 98 TYR 0.016 0.002 TYR R 90 PHE 0.017 0.002 PHE B 199 TRP 0.018 0.002 TRP B 211 HIS 0.012 0.001 HIS R 37 Details of bonding type rmsd/Z covalent geometry : bond 0.01144 / 0.56 ( 9095) covalent geometry : angle 0.73305 / 0.40 (12330) SS BOND : bond 0.00883 / 0.44 ( 3) SS BOND : angle 1.69445 / 0.81 ( 6) hydrogen bonds : bond 0.12993 / 9.48 ( 450) hydrogen bonds : angle 5.88264 / 4.13 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7449 (mmm) cc_final: 0.6953 (mmm) REVERT: R 87 ARG cc_start: 0.6850 (tpp80) cc_final: 0.6489 (tpt-90) REVERT: R 149 LYS cc_start: 0.7782 (tppt) cc_final: 0.7109 (tptt) REVERT: R 160 PHE cc_start: 0.7758 (m-10) cc_final: 0.7489 (m-80) REVERT: R 225 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7593 (ttm110) REVERT: B 3 GLU cc_start: 0.9081 (tp30) cc_final: 0.8768 (tp30) REVERT: B 10 GLU cc_start: 0.9182 (tp30) cc_final: 0.8546 (tp30) REVERT: B 23 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8717 (tmmt) REVERT: B 217 MET cc_start: 0.8398 (ptm) cc_final: 0.8080 (ptm) REVERT: C 17 GLU cc_start: 0.8985 (tp30) cc_final: 0.8553 (tp30) REVERT: E 153 GLU cc_start: 0.8340 (pt0) cc_final: 0.7822 (pt0) REVERT: E 220 GLU cc_start: 0.8171 (mp0) cc_final: 0.7771 (mp0) REVERT: E 223 ASP cc_start: 0.8220 (m-30) cc_final: 0.7757 (m-30) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1261 time to fit residues: 29.1411 Evaluate side-chains 131 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN R 282 GLN ** R 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS B 88 ASN B 91 HIS B 119 ASN B 259 GLN E 232 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.068523 restraints weight = 17400.413| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.83 r_work: 0.2846 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9098 Z= 0.129 Angle : 0.544 8.724 12336 Z= 0.287 Chirality : 0.042 0.147 1414 Planarity : 0.004 0.044 1554 Dihedral : 5.041 63.281 1239 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.25 % Allowed : 9.03 % Favored : 89.72 % 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: -1.06 (0.24), residues: 1123 helix: 0.78 (0.26), residues: 410 sheet: -1.29 (0.27), residues: 302 loop : -1.64 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.018 0.001 TYR E 190 PHE 0.009 0.001 PHE B 199 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9095) covalent geometry : angle 0.54292 / 0.29 (12330) SS BOND : bond 0.00418 / 0.21 ( 3) SS BOND : angle 1.33523 / 0.64 ( 6) hydrogen bonds : bond 0.03648 / 2.55 ( 450) hydrogen bonds : angle 4.58386 / 3.25 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7640 (mmm) cc_final: 0.6990 (mmm) REVERT: R 149 LYS cc_start: 0.7703 (tppt) cc_final: 0.7069 (tptt) REVERT: R 225 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7489 (ttm110) REVERT: R 287 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8489 (tm-30) REVERT: B 3 GLU cc_start: 0.9100 (tp30) cc_final: 0.8755 (tp30) REVERT: B 10 GLU cc_start: 0.9261 (tp30) cc_final: 0.8593 (tp30) REVERT: B 23 LYS cc_start: 0.8953 (ttpp) cc_final: 0.8715 (tmmt) REVERT: B 59 TYR cc_start: 0.9227 (m-80) cc_final: 0.8839 (m-80) REVERT: B 254 ASP cc_start: 0.8412 (t70) cc_final: 0.8052 (t0) REVERT: C 17 GLU cc_start: 0.9190 (tp30) cc_final: 0.8889 (tp30) REVERT: C 20 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8415 (mttp) REVERT: E 220 GLU cc_start: 0.8180 (mp0) cc_final: 0.7623 (mp0) REVERT: E 223 ASP cc_start: 0.8754 (m-30) cc_final: 0.8028 (m-30) outliers start: 12 outliers final: 6 residues processed: 152 average time/residue: 0.1124 time to fit residues: 22.5800 Evaluate side-chains 138 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS A 204 GLN B 36 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.067421 restraints weight = 17000.426| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.99 r_work: 0.2825 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9098 Z= 0.222 Angle : 0.563 6.424 12336 Z= 0.302 Chirality : 0.043 0.148 1414 Planarity : 0.004 0.045 1554 Dihedral : 4.982 63.845 1239 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.39 % Allowed : 10.28 % Favored : 87.33 % 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: -0.69 (0.25), residues: 1123 helix: 1.11 (0.26), residues: 420 sheet: -1.09 (0.28), residues: 298 loop : -1.53 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.016 0.002 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 ( 9095) covalent geometry : angle 0.56262 / 0.30 (12330) SS BOND : bond 0.00441 / 0.22 ( 3) SS BOND : angle 1.43355 / 0.62 ( 6) hydrogen bonds : bond 0.03788 / 2.63 ( 450) hydrogen bonds : angle 4.50632 / 3.21 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7691 (mmm) cc_final: 0.6852 (mmm) REVERT: R 147 HIS cc_start: 0.7271 (m-70) cc_final: 0.6360 (t-170) REVERT: R 149 LYS cc_start: 0.7714 (tppt) cc_final: 0.7124 (tptt) REVERT: R 225 ARG cc_start: 0.7713 (ttm110) cc_final: 0.7448 (ttm110) REVERT: B 3 GLU cc_start: 0.9084 (tp30) cc_final: 0.8722 (tp30) REVERT: B 10 GLU cc_start: 0.9256 (tp30) cc_final: 0.8734 (tp30) REVERT: B 23 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8686 (tmmt) REVERT: B 254 ASP cc_start: 0.8510 (t70) cc_final: 0.7988 (t0) REVERT: C 17 GLU cc_start: 0.9183 (tp30) cc_final: 0.8779 (tp30) REVERT: E 220 GLU cc_start: 0.7968 (mp0) cc_final: 0.7256 (mp0) REVERT: E 223 ASP cc_start: 0.8697 (m-30) cc_final: 0.7295 (m-30) outliers start: 23 outliers final: 17 residues processed: 150 average time/residue: 0.1002 time to fit residues: 19.9874 Evaluate side-chains 145 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 36 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.071210 restraints weight = 16511.443| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.09 r_work: 0.2884 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9098 Z= 0.120 Angle : 0.510 8.376 12336 Z= 0.272 Chirality : 0.041 0.146 1414 Planarity : 0.003 0.042 1554 Dihedral : 4.925 76.659 1239 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.28 % Allowed : 12.56 % Favored : 85.15 % 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: -0.35 (0.25), residues: 1123 helix: 1.33 (0.27), residues: 421 sheet: -0.82 (0.28), residues: 296 loop : -1.38 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.016 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.015 0.001 TRP B 211 HIS 0.014 0.001 HIS R 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9095) covalent geometry : angle 0.51008 / 0.27 (12330) SS BOND : bond 0.00350 / 0.17 ( 3) SS BOND : angle 0.86731 / 0.39 ( 6) hydrogen bonds : bond 0.03294 / 2.29 ( 450) hydrogen bonds : angle 4.33829 / 3.08 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 HIS cc_start: 0.7272 (m-70) cc_final: 0.6301 (t-170) REVERT: R 149 LYS cc_start: 0.7696 (tppt) cc_final: 0.7131 (tptt) REVERT: A 296 TYR cc_start: 0.8528 (t80) cc_final: 0.8302 (t80) REVERT: B 3 GLU cc_start: 0.9044 (tp30) cc_final: 0.8676 (tp30) REVERT: B 10 GLU cc_start: 0.9220 (tp30) cc_final: 0.8689 (tp30) REVERT: B 23 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8614 (tmmt) REVERT: B 215 GLU cc_start: 0.8602 (mp0) cc_final: 0.8340 (mp0) REVERT: B 254 ASP cc_start: 0.8463 (t70) cc_final: 0.7884 (t0) REVERT: B 262 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8919 (tpp) REVERT: B 294 CYS cc_start: 0.8638 (m) cc_final: 0.8367 (t) REVERT: C 15 LEU cc_start: 0.8836 (tp) cc_final: 0.8482 (tt) REVERT: C 17 GLU cc_start: 0.9158 (tp30) cc_final: 0.8829 (tp30) REVERT: C 20 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8208 (mttp) REVERT: E 43 LYS cc_start: 0.8874 (mmtp) cc_final: 0.8509 (mmmt) REVERT: E 51 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8003 (tp) REVERT: E 220 GLU cc_start: 0.7931 (mp0) cc_final: 0.7367 (mp0) REVERT: E 223 ASP cc_start: 0.8753 (m-30) cc_final: 0.7544 (m-30) outliers start: 22 outliers final: 15 residues processed: 157 average time/residue: 0.1008 time to fit residues: 20.9513 Evaluate side-chains 152 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 268 ASN C 18 GLN E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.068427 restraints weight = 17187.029| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.95 r_work: 0.2823 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9098 Z= 0.129 Angle : 0.509 8.063 12336 Z= 0.272 Chirality : 0.041 0.204 1414 Planarity : 0.003 0.041 1554 Dihedral : 4.780 77.023 1239 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.60 % Allowed : 13.08 % Favored : 84.32 % 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: -0.03 (0.25), residues: 1123 helix: 1.64 (0.27), residues: 413 sheet: -0.57 (0.29), residues: 291 loop : -1.25 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.015 0.001 TYR E 190 PHE 0.015 0.001 PHE R 299 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9095) covalent geometry : angle 0.50800 / 0.27 (12330) SS BOND : bond 0.00251 / 0.13 ( 3) SS BOND : angle 1.54763 / 0.80 ( 6) hydrogen bonds : bond 0.03228 / 2.24 ( 450) hydrogen bonds : angle 4.26739 / 3.04 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 HIS cc_start: 0.7300 (m-70) cc_final: 0.6363 (t-170) REVERT: R 149 LYS cc_start: 0.7767 (tppt) cc_final: 0.7185 (tptt) REVERT: R 299 PHE cc_start: 0.8591 (t80) cc_final: 0.8339 (t80) REVERT: B 3 GLU cc_start: 0.9087 (tp30) cc_final: 0.8723 (tp30) REVERT: B 10 GLU cc_start: 0.9248 (tp30) cc_final: 0.8709 (tp30) REVERT: B 23 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8663 (tmmt) REVERT: B 254 ASP cc_start: 0.8457 (t70) cc_final: 0.7950 (t0) REVERT: B 262 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8844 (tpp) REVERT: C 15 LEU cc_start: 0.8924 (tp) cc_final: 0.8556 (tt) REVERT: C 17 GLU cc_start: 0.9187 (tp30) cc_final: 0.8826 (tp30) REVERT: E 43 LYS cc_start: 0.8886 (mmtp) cc_final: 0.8559 (mmmt) REVERT: E 51 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8117 (tp) REVERT: E 220 GLU cc_start: 0.7997 (mp0) cc_final: 0.7526 (mp0) REVERT: E 223 ASP cc_start: 0.8775 (m-30) cc_final: 0.7763 (m-30) outliers start: 25 outliers final: 17 residues processed: 158 average time/residue: 0.1070 time to fit residues: 22.6155 Evaluate side-chains 155 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 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 = 0.3552 r_free = 0.3552 target = 0.100735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.069126 restraints weight = 17226.919| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.95 r_work: 0.2853 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9098 Z= 0.115 Angle : 0.505 9.377 12336 Z= 0.268 Chirality : 0.041 0.259 1414 Planarity : 0.003 0.041 1554 Dihedral : 4.663 77.506 1239 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.80 % Allowed : 13.91 % Favored : 83.28 % 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: 0.14 (0.25), residues: 1123 helix: 1.74 (0.27), residues: 413 sheet: -0.50 (0.29), residues: 287 loop : -1.10 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.014 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 9095) covalent geometry : angle 0.50431 / 0.27 (12330) SS BOND : bond 0.00281 / 0.14 ( 3) SS BOND : angle 1.30649 / 0.62 ( 6) hydrogen bonds : bond 0.03087 / 2.13 ( 450) hydrogen bonds : angle 4.18477 / 2.98 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 144 ARG cc_start: 0.5707 (mmp-170) cc_final: 0.5444 (mmp-170) REVERT: R 147 HIS cc_start: 0.7263 (m-70) cc_final: 0.6324 (t-170) REVERT: R 149 LYS cc_start: 0.7749 (tppt) cc_final: 0.7172 (tptt) REVERT: A 317 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6839 (ttpt) REVERT: B 3 GLU cc_start: 0.9044 (tp30) cc_final: 0.8678 (tp30) REVERT: B 10 GLU cc_start: 0.9237 (tp30) cc_final: 0.8693 (tp30) REVERT: B 23 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8646 (tmmt) REVERT: B 254 ASP cc_start: 0.8380 (t70) cc_final: 0.7881 (t0) REVERT: C 15 LEU cc_start: 0.8915 (tp) cc_final: 0.8580 (tt) REVERT: C 17 GLU cc_start: 0.9169 (tp30) cc_final: 0.8865 (tp30) REVERT: C 20 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8340 (mttp) REVERT: E 43 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8559 (mmmt) REVERT: E 51 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8075 (tp) REVERT: E 73 ASP cc_start: 0.8373 (m-30) cc_final: 0.8018 (t0) REVERT: E 220 GLU cc_start: 0.7941 (mp0) cc_final: 0.7491 (mp0) REVERT: E 223 ASP cc_start: 0.8779 (m-30) cc_final: 0.7677 (m-30) outliers start: 27 outliers final: 19 residues processed: 163 average time/residue: 0.1047 time to fit residues: 22.6991 Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN E 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.071574 restraints weight = 16563.961| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.09 r_work: 0.2894 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9098 Z= 0.133 Angle : 0.509 6.668 12336 Z= 0.274 Chirality : 0.042 0.233 1414 Planarity : 0.003 0.041 1554 Dihedral : 4.663 77.660 1239 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.01 % Allowed : 14.33 % Favored : 82.66 % 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: 0.21 (0.26), residues: 1123 helix: 1.83 (0.27), residues: 414 sheet: -0.39 (0.29), residues: 284 loop : -1.14 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.014 0.001 TYR E 190 PHE 0.020 0.001 PHE R 154 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9095) covalent geometry : angle 0.50825 / 0.27 (12330) SS BOND : bond 0.00311 / 0.15 ( 3) SS BOND : angle 1.20496 / 0.54 ( 6) hydrogen bonds : bond 0.03108 / 2.14 ( 450) hydrogen bonds : angle 4.14936 / 2.97 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 144 ARG cc_start: 0.5724 (mmp-170) cc_final: 0.5456 (mmp-170) REVERT: R 147 HIS cc_start: 0.7246 (m-70) cc_final: 0.6316 (t-170) REVERT: R 149 LYS cc_start: 0.7732 (tppt) cc_final: 0.7163 (tptt) REVERT: A 317 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6868 (ttpt) REVERT: B 3 GLU cc_start: 0.9022 (tp30) cc_final: 0.8661 (tp30) REVERT: B 10 GLU cc_start: 0.9217 (tp30) cc_final: 0.8678 (tp30) REVERT: B 23 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8604 (tmmt) REVERT: B 254 ASP cc_start: 0.8370 (t70) cc_final: 0.7818 (t0) REVERT: C 15 LEU cc_start: 0.8827 (tp) cc_final: 0.8499 (tt) REVERT: C 17 GLU cc_start: 0.9149 (tp30) cc_final: 0.8827 (tp30) REVERT: C 20 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8224 (mttp) REVERT: E 43 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8514 (mmmt) REVERT: E 51 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8009 (tp) REVERT: E 73 ASP cc_start: 0.8377 (m-30) cc_final: 0.7975 (t0) REVERT: E 140 MET cc_start: 0.9088 (mmm) cc_final: 0.8730 (mmm) REVERT: E 220 GLU cc_start: 0.7815 (mp0) cc_final: 0.7360 (mp0) REVERT: E 223 ASP cc_start: 0.8730 (m-30) cc_final: 0.7516 (m-30) outliers start: 29 outliers final: 20 residues processed: 161 average time/residue: 0.0995 time to fit residues: 21.3873 Evaluate side-chains 155 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 4.9990 chunk 80 optimal weight: 0.0870 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072698 restraints weight = 16488.125| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.10 r_work: 0.2914 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9098 Z= 0.112 Angle : 0.512 10.124 12336 Z= 0.269 Chirality : 0.041 0.228 1414 Planarity : 0.003 0.041 1554 Dihedral : 4.593 79.266 1239 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.28 % Allowed : 15.37 % Favored : 82.35 % 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: 0.34 (0.26), residues: 1123 helix: 1.94 (0.27), residues: 413 sheet: -0.31 (0.30), residues: 274 loop : -1.06 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.014 0.001 TYR E 190 PHE 0.021 0.001 PHE R 299 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9095) covalent geometry : angle 0.51128 / 0.27 (12330) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 1.00467 / 0.47 ( 6) hydrogen bonds : bond 0.02951 / 2.04 ( 450) hydrogen bonds : angle 4.08453 / 2.93 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 144 ARG cc_start: 0.5768 (mmp-170) cc_final: 0.5545 (mmp-170) REVERT: R 147 HIS cc_start: 0.7251 (m-70) cc_final: 0.6334 (t-170) REVERT: R 149 LYS cc_start: 0.7742 (tppt) cc_final: 0.7198 (tptt) REVERT: R 160 PHE cc_start: 0.7618 (m-10) cc_final: 0.7268 (m-80) REVERT: A 317 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6732 (ttpt) REVERT: B 3 GLU cc_start: 0.8987 (tp30) cc_final: 0.8621 (tp30) REVERT: B 23 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8594 (tmmt) REVERT: B 146 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 254 ASP cc_start: 0.8336 (t70) cc_final: 0.7804 (t0) REVERT: B 327 VAL cc_start: 0.8871 (t) cc_final: 0.8613 (p) REVERT: C 15 LEU cc_start: 0.8822 (tp) cc_final: 0.8519 (tt) REVERT: C 17 GLU cc_start: 0.9147 (tp30) cc_final: 0.8783 (tp30) REVERT: E 43 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8512 (mmmt) REVERT: E 51 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7987 (tp) REVERT: E 73 ASP cc_start: 0.8374 (m-30) cc_final: 0.7977 (t0) REVERT: E 140 MET cc_start: 0.9071 (mmm) cc_final: 0.8698 (mmm) REVERT: E 220 GLU cc_start: 0.7794 (mp0) cc_final: 0.7362 (mp0) REVERT: E 223 ASP cc_start: 0.8755 (m-30) cc_final: 0.7391 (m-30) outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 0.0966 time to fit residues: 20.3465 Evaluate side-chains 151 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.0040 chunk 98 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.108268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074506 restraints weight = 16262.121| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.09 r_work: 0.2944 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9098 Z= 0.101 Angle : 0.507 7.270 12336 Z= 0.268 Chirality : 0.041 0.230 1414 Planarity : 0.003 0.043 1554 Dihedral : 4.505 78.450 1239 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.28 % Allowed : 15.68 % Favored : 82.04 % 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: 0.44 (0.26), residues: 1123 helix: 1.95 (0.27), residues: 412 sheet: -0.15 (0.30), residues: 273 loop : -1.00 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 32 TYR 0.014 0.001 TYR E 190 PHE 0.033 0.001 PHE R 299 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9095) covalent geometry : angle 0.50668 / 0.27 (12330) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 0.85706 / 0.43 ( 6) hydrogen bonds : bond 0.02871 / 2.00 ( 450) hydrogen bonds : angle 4.05719 / 2.91 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: R 144 ARG cc_start: 0.5901 (mmp-170) cc_final: 0.5651 (mmp-170) REVERT: R 147 HIS cc_start: 0.7238 (m-70) cc_final: 0.6327 (t-170) REVERT: R 149 LYS cc_start: 0.7755 (tppt) cc_final: 0.7219 (tptt) REVERT: R 160 PHE cc_start: 0.7627 (m-10) cc_final: 0.7272 (m-80) REVERT: R 299 PHE cc_start: 0.8358 (t80) cc_final: 0.8000 (t80) REVERT: A 317 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6560 (ttpt) REVERT: B 3 GLU cc_start: 0.8988 (tp30) cc_final: 0.8632 (tp30) REVERT: B 23 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8557 (tmmt) REVERT: B 146 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 254 ASP cc_start: 0.8263 (t70) cc_final: 0.7734 (t0) REVERT: B 327 VAL cc_start: 0.8784 (t) cc_final: 0.8579 (p) REVERT: C 15 LEU cc_start: 0.8839 (tp) cc_final: 0.8529 (tt) REVERT: C 17 GLU cc_start: 0.9143 (tp30) cc_final: 0.8825 (tp30) REVERT: C 20 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8203 (mttp) REVERT: C 58 GLU cc_start: 0.8598 (mp0) cc_final: 0.8044 (pm20) REVERT: E 43 LYS cc_start: 0.8841 (mmtp) cc_final: 0.8491 (mmmt) REVERT: E 51 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7937 (tp) REVERT: E 73 ASP cc_start: 0.8377 (m-30) cc_final: 0.7973 (t0) REVERT: E 140 MET cc_start: 0.9063 (mmm) cc_final: 0.8721 (mmm) REVERT: E 220 GLU cc_start: 0.7744 (mp0) cc_final: 0.7315 (mp0) REVERT: E 222 GLU cc_start: 0.8768 (pm20) cc_final: 0.8520 (pm20) REVERT: E 223 ASP cc_start: 0.8737 (m-30) cc_final: 0.7371 (m-30) outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 0.1040 time to fit residues: 22.0986 Evaluate side-chains 156 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 0.1980 chunk 43 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 106 optimal weight: 0.1980 chunk 98 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.108721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074857 restraints weight = 16291.995| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.10 r_work: 0.2950 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9098 Z= 0.101 Angle : 0.531 8.156 12336 Z= 0.275 Chirality : 0.041 0.183 1414 Planarity : 0.003 0.056 1554 Dihedral : 4.481 78.773 1239 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.66 % Allowed : 16.41 % Favored : 81.93 % 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: 1123 helix: 2.04 (0.27), residues: 412 sheet: -0.13 (0.30), residues: 278 loop : -0.84 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 32 TYR 0.014 0.001 TYR E 190 PHE 0.034 0.001 PHE R 299 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9095) covalent geometry : angle 0.53061 / 0.28 (12330) SS BOND : bond 0.00243 / 0.12 ( 3) SS BOND : angle 0.82578 / 0.42 ( 6) hydrogen bonds : bond 0.02801 / 1.96 ( 450) hydrogen bonds : angle 4.03689 / 2.89 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 144 ARG cc_start: 0.5860 (mmp-170) cc_final: 0.5606 (mmp-170) REVERT: R 147 HIS cc_start: 0.7197 (m-70) cc_final: 0.6298 (t-170) REVERT: R 149 LYS cc_start: 0.7798 (tppt) cc_final: 0.7218 (tptt) REVERT: R 160 PHE cc_start: 0.7656 (m-10) cc_final: 0.7316 (m-80) REVERT: R 299 PHE cc_start: 0.8175 (t80) cc_final: 0.7719 (t80) REVERT: A 317 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6486 (ttpt) REVERT: B 3 GLU cc_start: 0.9001 (tp30) cc_final: 0.8641 (tp30) REVERT: B 23 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8544 (tmmt) REVERT: B 146 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8421 (tt) REVERT: B 254 ASP cc_start: 0.8173 (t70) cc_final: 0.7655 (t0) REVERT: C 15 LEU cc_start: 0.8804 (tp) cc_final: 0.8518 (tt) REVERT: C 17 GLU cc_start: 0.9141 (tp30) cc_final: 0.8833 (tp30) REVERT: C 20 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8173 (mttp) REVERT: C 58 GLU cc_start: 0.8577 (mp0) cc_final: 0.8049 (pm20) REVERT: E 43 LYS cc_start: 0.8856 (mmtp) cc_final: 0.8497 (mmmt) REVERT: E 51 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7921 (tp) REVERT: E 73 ASP cc_start: 0.8336 (m-30) cc_final: 0.7937 (t0) REVERT: E 89 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8738 (pt0) REVERT: E 140 MET cc_start: 0.9052 (mmm) cc_final: 0.8705 (mmm) REVERT: E 220 GLU cc_start: 0.7536 (mp0) cc_final: 0.7173 (mp0) REVERT: E 222 GLU cc_start: 0.8724 (pm20) cc_final: 0.8460 (pm20) REVERT: E 223 ASP cc_start: 0.8693 (m-30) cc_final: 0.7583 (m-30) outliers start: 16 outliers final: 11 residues processed: 159 average time/residue: 0.1087 time to fit residues: 22.7558 Evaluate side-chains 152 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.074503 restraints weight = 16250.823| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.08 r_work: 0.2946 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9098 Z= 0.109 Angle : 0.537 10.553 12336 Z= 0.278 Chirality : 0.042 0.288 1414 Planarity : 0.004 0.059 1554 Dihedral : 4.481 78.754 1239 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.97 % Allowed : 16.72 % Favored : 81.31 % 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: 0.67 (0.26), residues: 1123 helix: 2.06 (0.27), residues: 413 sheet: 0.05 (0.30), residues: 272 loop : -0.84 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 32 TYR 0.014 0.001 TYR E 190 PHE 0.035 0.001 PHE R 299 TRP 0.012 0.001 TRP B 211 HIS 0.014 0.001 HIS R 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9095) covalent geometry : angle 0.53714 / 0.28 (12330) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 0.89531 / 0.44 ( 6) hydrogen bonds : bond 0.02882 / 2.00 ( 450) hydrogen bonds : angle 4.00128 / 2.87 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.18 seconds wall clock time: 37 minutes 40.87 seconds (2260.87 seconds total)