Starting phenix.real_space_refine on Sat Oct 11 19:30:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4n_36887/10_2025/8k4n_36887_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4n_36887/10_2025/8k4n_36887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k4n_36887/10_2025/8k4n_36887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4n_36887/10_2025/8k4n_36887.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4n_36887/10_2025/8k4n_36887_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4n_36887/10_2025/8k4n_36887_trim.cif" } resolution = 2.83 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= 0.032 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 60 5.16 5 C 5543 2.51 5 N 1481 2.21 5 O 1571 1.98 5 H 8511 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17167 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3310 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 4984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 4984 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 759 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3417 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4666 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 4, 'TRANS': 274} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'VF0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.02, per 1000 atoms: 0.18 Number of scatterers: 17167 At special positions: 0 Unit cell: (91.8, 119.85, 132.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 1 15.00 O 1571 8.00 N 1481 7.00 C 5543 6.00 H 8511 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 467.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 30.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.598A pdb=" N MET A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.576A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.405A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 280' Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.414A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.581A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 22 removed outlier: 3.739A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.575A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.580A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.520A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.533A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.902A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 81 removed outlier: 4.186A pdb=" N THR D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 106 Processing helix chain 'D' and resid 108 through 116 removed outlier: 3.915A pdb=" N MET D 112 " --> pdb=" O PRO D 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR D 113 " --> pdb=" O PHE D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 143 through 155 removed outlier: 4.254A pdb=" N SER D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 194 removed outlier: 4.152A pdb=" N TYR D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 174 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP D 179 " --> pdb=" O CYS D 175 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU D 183 " --> pdb=" O TRP D 179 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 239 removed outlier: 3.561A pdb=" N PHE D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 232 " --> pdb=" O TRP D 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 269 through 280 removed outlier: 3.964A pdb=" N PHE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.534A pdb=" N SER D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 318 removed outlier: 4.083A pdb=" N HIS D 306 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.563A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.813A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.722A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.993A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.789A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.748A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.749A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.797A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'E' and resid 182 through 183 removed outlier: 3.541A pdb=" N ASN E 182 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 183 removed outlier: 3.541A pdb=" N ASN E 182 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 972 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: 4.05 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8484 1.03 - 1.23: 32 1.23 - 1.42: 3729 1.42 - 1.62: 5010 1.62 - 1.81: 89 Bond restraints: 17344 Sorted by residual: bond pdb=" C09 VF0 D 401 " pdb=" C10 VF0 D 401 " ideal model delta sigma weight residual 1.330 1.525 -0.195 2.00e-02 2.50e+03 9.51e+01 bond pdb=" C18 VF0 D 401 " pdb=" O20 VF0 D 401 " ideal model delta sigma weight residual 1.333 1.398 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CB ARG E 38 " pdb=" CG ARG E 38 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.54e+00 bond pdb=" CB ILE B 232 " pdb=" CG2 ILE B 232 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" O27 VF0 D 401 " pdb=" P26 VF0 D 401 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.92e+00 ... (remaining 17339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 31153 3.99 - 7.98: 29 7.98 - 11.97: 2 11.97 - 15.95: 2 15.95 - 19.94: 2 Bond angle restraints: 31188 Sorted by residual: angle pdb=" O27 VF0 D 401 " pdb=" P26 VF0 D 401 " pdb=" O28 VF0 D 401 " ideal model delta sigma weight residual 121.16 101.22 19.94 3.00e+00 1.11e-01 4.42e+01 angle pdb=" N VAL D 124 " pdb=" CA VAL D 124 " pdb=" C VAL D 124 " ideal model delta sigma weight residual 113.71 108.45 5.26 9.50e-01 1.11e+00 3.07e+01 angle pdb=" C09 VF0 D 401 " pdb=" C10 VF0 D 401 " pdb=" C11 VF0 D 401 " ideal model delta sigma weight residual 125.54 109.37 16.17 3.00e+00 1.11e-01 2.91e+01 angle pdb=" C08 VF0 D 401 " pdb=" C09 VF0 D 401 " pdb=" C10 VF0 D 401 " ideal model delta sigma weight residual 125.21 110.63 14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O25 VF0 D 401 " pdb=" P26 VF0 D 401 " pdb=" O29 VF0 D 401 " ideal model delta sigma weight residual 98.23 110.86 -12.63 3.00e+00 1.11e-01 1.77e+01 ... (remaining 31183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7340 17.93 - 35.85: 686 35.85 - 53.78: 159 53.78 - 71.71: 27 71.71 - 89.63: 6 Dihedral angle restraints: 8218 sinusoidal: 4338 harmonic: 3880 Sorted by residual: dihedral pdb=" CA SER D 292 " pdb=" C SER D 292 " pdb=" N GLN D 293 " pdb=" CA GLN D 293 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " pdb=" SG CYS D 204 " pdb=" CB CYS D 204 " ideal model delta sinusoidal sigma weight residual 93.00 131.66 -38.66 1 1.00e+01 1.00e-02 2.10e+01 ... (remaining 8215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 798 0.038 - 0.075: 411 0.075 - 0.113: 142 0.113 - 0.151: 20 0.151 - 0.188: 3 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CB VAL A 218 " pdb=" CA VAL A 218 " pdb=" CG1 VAL A 218 " pdb=" CG2 VAL A 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CB VAL A 34 " pdb=" CA VAL A 34 " pdb=" CG1 VAL A 34 " pdb=" CG2 VAL A 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB VAL B 112 " pdb=" CA VAL B 112 " pdb=" CG1 VAL B 112 " pdb=" CG2 VAL B 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1371 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 VF0 D 401 " 0.307 2.00e-02 2.50e+03 3.01e-01 9.08e+02 pdb=" C09 VF0 D 401 " -0.324 2.00e-02 2.50e+03 pdb=" C10 VF0 D 401 " -0.277 2.00e-02 2.50e+03 pdb=" C11 VF0 D 401 " 0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO E 107 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 107 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO D 108 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 108 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 108 " -0.019 5.00e-02 4.00e+02 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 438 2.11 - 2.73: 30325 2.73 - 3.36: 44822 3.36 - 3.98: 59895 3.98 - 4.60: 96217 Nonbonded interactions: 231697 Sorted by model distance: nonbonded pdb=" O THR B 29 " pdb=" H GLN B 32 " model vdw 1.488 2.450 nonbonded pdb=" OE1 GLU E 6 " pdb=" H GLY E 114 " model vdw 1.610 2.450 nonbonded pdb=" HG1 THR B 34 " pdb=" O LEU B 300 " model vdw 1.631 2.450 nonbonded pdb=" O GLY D 68 " pdb="HD21 ASN D 72 " model vdw 1.641 2.450 nonbonded pdb=" O LYS B 57 " pdb=" HG SER B 74 " model vdw 1.651 2.450 ... (remaining 231692 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: 4.220 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: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.009 0.195 8836 Z= 0.360 Angle : 0.757 19.943 11964 Z= 0.396 Chirality : 0.047 0.188 1374 Planarity : 0.009 0.301 1492 Dihedral : 14.321 89.632 3140 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.19 (0.21), residues: 1101 helix: -3.40 (0.21), residues: 343 sheet: -0.93 (0.30), residues: 282 loop : -3.42 (0.21), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 67 TYR 0.023 0.002 TYR E 178 PHE 0.018 0.002 PHE B 151 TRP 0.016 0.002 TRP E 47 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00920 ( 8833) covalent geometry : angle 0.75674 (11958) SS BOND : bond 0.00667 ( 3) SS BOND : angle 1.50929 ( 6) hydrogen bonds : bond 0.14962 ( 339) hydrogen bonds : angle 7.07474 ( 972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASP cc_start: 0.6902 (p0) cc_final: 0.6653 (p0) REVERT: B 325 MET cc_start: 0.7449 (mmt) cc_final: 0.7193 (mmt) REVERT: E 43 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7719 (ttpt) REVERT: D 195 LYS cc_start: 0.4766 (mmtp) cc_final: 0.4195 (ptpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.2257 time to fit residues: 211.1629 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 175 GLN B 266 HIS D 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113009 restraints weight = 29917.750| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.30 r_work: 0.3200 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8836 Z= 0.135 Angle : 0.546 5.581 11964 Z= 0.295 Chirality : 0.042 0.141 1374 Planarity : 0.004 0.041 1492 Dihedral : 7.771 112.761 1242 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.31 % Allowed : 14.86 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.23), residues: 1101 helix: -2.30 (0.24), residues: 354 sheet: -0.40 (0.31), residues: 282 loop : -2.85 (0.23), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.011 0.001 TYR E 178 PHE 0.013 0.001 PHE D 227 TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8833) covalent geometry : angle 0.54532 (11958) SS BOND : bond 0.00714 ( 3) SS BOND : angle 1.14511 ( 6) hydrogen bonds : bond 0.04108 ( 339) hydrogen bonds : angle 5.12130 ( 972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7127 (m-70) cc_final: 0.6877 (m-70) REVERT: A 341 ASP cc_start: 0.7919 (t70) cc_final: 0.7705 (t0) REVERT: B 46 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7414 (mtp-110) REVERT: B 258 ASP cc_start: 0.8008 (m-30) cc_final: 0.7747 (m-30) REVERT: C 27 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7954 (mtt-85) REVERT: E 43 LYS cc_start: 0.8418 (mmtt) cc_final: 0.7430 (ttpt) REVERT: D 169 LYS cc_start: 0.7262 (tptp) cc_final: 0.6640 (tptt) REVERT: D 195 LYS cc_start: 0.4273 (mmtp) cc_final: 0.3319 (ptpp) outliers start: 12 outliers final: 6 residues processed: 151 average time/residue: 1.0790 time to fit residues: 174.0800 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 156 GLN E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107547 restraints weight = 30334.594| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.24 r_work: 0.3176 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8836 Z= 0.143 Angle : 0.549 9.089 11964 Z= 0.295 Chirality : 0.041 0.137 1374 Planarity : 0.003 0.044 1492 Dihedral : 7.214 119.005 1242 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.42 % Allowed : 15.41 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.23), residues: 1101 helix: -1.64 (0.26), residues: 345 sheet: -0.20 (0.31), residues: 282 loop : -2.57 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.013 0.001 TYR D 207 PHE 0.015 0.001 PHE D 227 TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8833) covalent geometry : angle 0.54399 (11958) SS BOND : bond 0.00717 ( 3) SS BOND : angle 3.46132 ( 6) hydrogen bonds : bond 0.03966 ( 339) hydrogen bonds : angle 4.81484 ( 972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7017 (m-70) cc_final: 0.6785 (m-70) REVERT: B 58 ILE cc_start: 0.8261 (pt) cc_final: 0.7943 (mt) REVERT: B 212 ASP cc_start: 0.8261 (t0) cc_final: 0.8017 (t0) REVERT: B 258 ASP cc_start: 0.7959 (m-30) cc_final: 0.7599 (m-30) REVERT: C 27 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.7910 (mtt-85) REVERT: D 153 TYR cc_start: 0.8199 (t80) cc_final: 0.7832 (t80) REVERT: D 195 LYS cc_start: 0.4382 (mmtp) cc_final: 0.3649 (ptmm) REVERT: D 319 ASN cc_start: 0.8239 (t0) cc_final: 0.7904 (t0) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 1.0910 time to fit residues: 166.7691 Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105792 restraints weight = 30126.245| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.23 r_work: 0.3144 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8836 Z= 0.149 Angle : 0.531 6.049 11964 Z= 0.287 Chirality : 0.042 0.134 1374 Planarity : 0.003 0.042 1492 Dihedral : 7.106 123.562 1242 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.53 % Allowed : 16.72 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.24), residues: 1101 helix: -1.29 (0.27), residues: 349 sheet: -0.02 (0.31), residues: 284 loop : -2.31 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.013 0.001 TYR D 207 PHE 0.014 0.001 PHE D 227 TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8833) covalent geometry : angle 0.52951 (11958) SS BOND : bond 0.00907 ( 3) SS BOND : angle 1.67052 ( 6) hydrogen bonds : bond 0.03824 ( 339) hydrogen bonds : angle 4.66294 ( 972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7013 (m-70) cc_final: 0.6777 (m-70) REVERT: B 58 ILE cc_start: 0.8269 (pt) cc_final: 0.7949 (mt) REVERT: B 70 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8374 (pt) REVERT: B 123 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8288 (mp) REVERT: B 212 ASP cc_start: 0.8303 (t0) cc_final: 0.8006 (t0) REVERT: B 258 ASP cc_start: 0.8000 (m-30) cc_final: 0.7678 (m-30) REVERT: B 260 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: C 27 ARG cc_start: 0.8207 (mtt-85) cc_final: 0.7932 (mtt-85) REVERT: D 169 LYS cc_start: 0.7226 (tmtt) cc_final: 0.6763 (tptt) REVERT: D 195 LYS cc_start: 0.4423 (mmtp) cc_final: 0.3744 (ptmm) REVERT: D 319 ASN cc_start: 0.8221 (t0) cc_final: 0.7887 (t0) outliers start: 14 outliers final: 8 residues processed: 149 average time/residue: 1.1348 time to fit residues: 180.4519 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN D 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105566 restraints weight = 30149.557| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.23 r_work: 0.3145 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8836 Z= 0.139 Angle : 0.517 4.836 11964 Z= 0.279 Chirality : 0.041 0.134 1374 Planarity : 0.003 0.052 1492 Dihedral : 6.995 122.052 1242 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.86 % Allowed : 18.58 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.24), residues: 1101 helix: -1.01 (0.27), residues: 349 sheet: 0.02 (0.32), residues: 284 loop : -2.08 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.011 0.001 TYR E 178 PHE 0.014 0.001 PHE D 227 TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8833) covalent geometry : angle 0.51688 (11958) SS BOND : bond 0.00740 ( 3) SS BOND : angle 0.98449 ( 6) hydrogen bonds : bond 0.03714 ( 339) hydrogen bonds : angle 4.54744 ( 972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7098 (m-70) cc_final: 0.6823 (m-70) REVERT: B 58 ILE cc_start: 0.8269 (pt) cc_final: 0.7947 (mt) REVERT: B 70 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8367 (pt) REVERT: B 123 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 212 ASP cc_start: 0.8368 (t0) cc_final: 0.8081 (t0) REVERT: B 258 ASP cc_start: 0.8010 (m-30) cc_final: 0.7641 (m-30) REVERT: B 260 GLU cc_start: 0.8041 (pt0) cc_final: 0.7809 (tt0) REVERT: B 322 ASP cc_start: 0.7734 (m-30) cc_final: 0.7417 (m-30) REVERT: D 169 LYS cc_start: 0.7192 (tmtt) cc_final: 0.6908 (tptt) REVERT: D 195 LYS cc_start: 0.4527 (mmtp) cc_final: 0.3824 (ptmm) REVERT: D 319 ASN cc_start: 0.8227 (t0) cc_final: 0.7874 (t0) outliers start: 17 outliers final: 10 residues processed: 145 average time/residue: 1.0499 time to fit residues: 163.2127 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN E 113 GLN D 72 ASN D 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109359 restraints weight = 29863.217| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.21 r_work: 0.3114 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8836 Z= 0.124 Angle : 0.502 5.442 11964 Z= 0.270 Chirality : 0.041 0.133 1374 Planarity : 0.003 0.038 1492 Dihedral : 6.667 122.463 1242 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.30 % Allowed : 19.13 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.24), residues: 1101 helix: -0.79 (0.28), residues: 352 sheet: 0.11 (0.32), residues: 282 loop : -1.91 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 251 TYR 0.011 0.001 TYR E 178 PHE 0.013 0.001 PHE D 227 TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8833) covalent geometry : angle 0.50191 (11958) SS BOND : bond 0.00720 ( 3) SS BOND : angle 0.83995 ( 6) hydrogen bonds : bond 0.03539 ( 339) hydrogen bonds : angle 4.46376 ( 972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7473 (m-70) cc_final: 0.7244 (m-70) REVERT: A 225 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8238 (p) REVERT: B 70 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8669 (pt) REVERT: B 123 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8689 (mp) REVERT: B 258 ASP cc_start: 0.8320 (m-30) cc_final: 0.8086 (m-30) REVERT: D 153 TYR cc_start: 0.8457 (t80) cc_final: 0.8216 (t80) REVERT: D 169 LYS cc_start: 0.7363 (tmtt) cc_final: 0.6967 (tptt) REVERT: D 195 LYS cc_start: 0.4753 (mmtp) cc_final: 0.4024 (ptmm) outliers start: 21 outliers final: 8 residues processed: 150 average time/residue: 1.0484 time to fit residues: 168.7585 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN C 59 ASN E 113 GLN D 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105587 restraints weight = 29929.276| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.11 r_work: 0.3134 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8836 Z= 0.136 Angle : 0.513 5.981 11964 Z= 0.276 Chirality : 0.041 0.132 1374 Planarity : 0.003 0.042 1492 Dihedral : 6.649 124.322 1242 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.97 % Allowed : 20.00 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.25), residues: 1101 helix: -0.69 (0.28), residues: 354 sheet: 0.12 (0.32), residues: 283 loop : -1.87 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 251 TYR 0.011 0.001 TYR E 178 PHE 0.015 0.001 PHE D 227 TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8833) covalent geometry : angle 0.51304 (11958) SS BOND : bond 0.00692 ( 3) SS BOND : angle 0.75334 ( 6) hydrogen bonds : bond 0.03641 ( 339) hydrogen bonds : angle 4.45293 ( 972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7388 (m-70) cc_final: 0.7141 (m-70) REVERT: A 225 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 70 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8649 (pt) REVERT: B 123 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8590 (mp) REVERT: B 268 ASN cc_start: 0.8059 (p0) cc_final: 0.7847 (p0) REVERT: D 153 TYR cc_start: 0.8398 (t80) cc_final: 0.8144 (t80) REVERT: D 169 LYS cc_start: 0.7367 (tmtt) cc_final: 0.6950 (tptt) REVERT: D 195 LYS cc_start: 0.4705 (mmtp) cc_final: 0.3954 (ptmm) outliers start: 18 outliers final: 10 residues processed: 147 average time/residue: 1.1032 time to fit residues: 173.9418 Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN D 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107442 restraints weight = 29951.064| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.22 r_work: 0.3086 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8836 Z= 0.173 Angle : 0.542 6.485 11964 Z= 0.291 Chirality : 0.042 0.134 1374 Planarity : 0.004 0.044 1492 Dihedral : 6.832 126.301 1242 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.30 % Allowed : 20.00 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.24), residues: 1101 helix: -0.65 (0.28), residues: 352 sheet: 0.06 (0.32), residues: 284 loop : -1.90 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.012 0.001 TYR E 178 PHE 0.015 0.001 PHE D 227 TRP 0.012 0.001 TRP E 47 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8833) covalent geometry : angle 0.54162 (11958) SS BOND : bond 0.00762 ( 3) SS BOND : angle 0.78563 ( 6) hydrogen bonds : bond 0.03946 ( 339) hydrogen bonds : angle 4.53724 ( 972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7494 (m-70) cc_final: 0.7261 (m-70) REVERT: A 225 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 354 PHE cc_start: 0.4294 (p90) cc_final: 0.3792 (p90) REVERT: B 70 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8802 (pt) REVERT: B 123 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8718 (mp) REVERT: C 27 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.8107 (mtt-85) REVERT: E 43 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8103 (mmmt) REVERT: D 153 TYR cc_start: 0.8467 (t80) cc_final: 0.8216 (t80) REVERT: D 169 LYS cc_start: 0.7398 (tmtt) cc_final: 0.6874 (tptt) REVERT: D 195 LYS cc_start: 0.4713 (mmtp) cc_final: 0.3938 (ptmm) REVERT: D 203 MET cc_start: 0.5744 (mtt) cc_final: 0.5501 (mtt) outliers start: 21 outliers final: 13 residues processed: 146 average time/residue: 1.0745 time to fit residues: 168.2597 Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN E 113 GLN D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105465 restraints weight = 30045.209| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.10 r_work: 0.3132 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8836 Z= 0.128 Angle : 0.513 5.510 11964 Z= 0.275 Chirality : 0.041 0.133 1374 Planarity : 0.003 0.043 1492 Dihedral : 6.653 124.526 1242 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.86 % Allowed : 20.77 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.25), residues: 1101 helix: -0.47 (0.28), residues: 352 sheet: 0.13 (0.32), residues: 284 loop : -1.81 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 251 TYR 0.011 0.001 TYR E 178 PHE 0.014 0.001 PHE D 227 TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8833) covalent geometry : angle 0.51257 (11958) SS BOND : bond 0.00712 ( 3) SS BOND : angle 0.69580 ( 6) hydrogen bonds : bond 0.03559 ( 339) hydrogen bonds : angle 4.43579 ( 972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7358 (m-70) cc_final: 0.7115 (m-70) REVERT: A 209 LYS cc_start: 0.8105 (pttm) cc_final: 0.7783 (pmtt) REVERT: A 225 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 70 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8681 (pt) REVERT: B 123 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8598 (mp) REVERT: C 27 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.8063 (mtt-85) REVERT: D 153 TYR cc_start: 0.8393 (t80) cc_final: 0.8131 (t80) REVERT: D 169 LYS cc_start: 0.7390 (tmtt) cc_final: 0.6860 (tptt) REVERT: D 180 MET cc_start: 0.5148 (ptt) cc_final: 0.4875 (mpp) REVERT: D 195 LYS cc_start: 0.4675 (mmtp) cc_final: 0.3905 (ptmm) REVERT: D 203 MET cc_start: 0.5711 (mtt) cc_final: 0.5481 (mtt) REVERT: D 251 ARG cc_start: 0.6983 (ttp80) cc_final: 0.6242 (mtp-110) outliers start: 17 outliers final: 10 residues processed: 145 average time/residue: 1.1154 time to fit residues: 172.9207 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN D 72 ASN D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105658 restraints weight = 29606.238| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.19 r_work: 0.3132 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8836 Z= 0.114 Angle : 0.515 6.118 11964 Z= 0.276 Chirality : 0.041 0.136 1374 Planarity : 0.003 0.039 1492 Dihedral : 6.559 124.795 1242 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.64 % Allowed : 20.87 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.25), residues: 1101 helix: -0.35 (0.29), residues: 352 sheet: 0.18 (0.32), residues: 282 loop : -1.77 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 251 TYR 0.011 0.001 TYR E 178 PHE 0.015 0.001 PHE D 227 TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8833) covalent geometry : angle 0.51130 (11958) SS BOND : bond 0.00933 ( 3) SS BOND : angle 2.63531 ( 6) hydrogen bonds : bond 0.03387 ( 339) hydrogen bonds : angle 4.38717 ( 972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7320 (m-70) cc_final: 0.7067 (m-70) REVERT: A 209 LYS cc_start: 0.8060 (pttm) cc_final: 0.7723 (pmtt) REVERT: A 225 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8174 (p) REVERT: B 22 ARG cc_start: 0.6659 (ptp-170) cc_final: 0.5980 (ptp90) REVERT: B 70 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8585 (pt) REVERT: C 27 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.7993 (mtt-85) REVERT: D 153 TYR cc_start: 0.8312 (t80) cc_final: 0.8038 (t80) REVERT: D 169 LYS cc_start: 0.7387 (tmtt) cc_final: 0.6775 (tptt) REVERT: D 180 MET cc_start: 0.5134 (ptt) cc_final: 0.4871 (mpp) REVERT: D 195 LYS cc_start: 0.4626 (mmtp) cc_final: 0.3845 (ptmm) outliers start: 15 outliers final: 11 residues processed: 147 average time/residue: 1.0768 time to fit residues: 169.9009 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.0470 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.148258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109765 restraints weight = 29870.898| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.30 r_work: 0.3141 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8836 Z= 0.101 Angle : 0.500 5.143 11964 Z= 0.267 Chirality : 0.040 0.132 1374 Planarity : 0.003 0.037 1492 Dihedral : 6.395 122.904 1242 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.20 % Allowed : 21.75 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.25), residues: 1101 helix: -0.16 (0.29), residues: 349 sheet: 0.19 (0.32), residues: 281 loop : -1.72 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 251 TYR 0.010 0.001 TYR E 178 PHE 0.014 0.001 PHE D 227 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8833) covalent geometry : angle 0.49786 (11958) SS BOND : bond 0.00737 ( 3) SS BOND : angle 2.02431 ( 6) hydrogen bonds : bond 0.03174 ( 339) hydrogen bonds : angle 4.31957 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6695.14 seconds wall clock time: 113 minutes 57.34 seconds (6837.34 seconds total)