Starting phenix.real_space_refine on Sun Jun 15 09:21:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4n_36887/06_2025/8k4n_36887_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4n_36887/06_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_36887/06_2025/8k4n_36887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4n_36887/06_2025/8k4n_36887.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4n_36887/06_2025/8k4n_36887_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4n_36887/06_2025/8k4n_36887_trim.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 7, 'ASP:plan': 6} 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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} 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: 9.09, per 1000 atoms: 0.53 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: 4.27 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.42 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: 6.55 Time building geometry restraints manager: 5.24 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: 3.990 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: 0.300 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 39.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.550 ------------------------------------------------------------------------------- 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 : 5.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP E 47 HIS 0.007 0.001 HIS E 35 PHE 0.018 0.002 PHE B 151 TYR 0.023 0.002 TYR E 178 ARG 0.008 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.14962 ( 339) hydrogen bonds : angle 7.07474 ( 972) SS BOND : bond 0.00667 ( 3) SS BOND : angle 1.50929 ( 6) covalent geometry : bond 0.00920 ( 8833) covalent geometry : angle 0.75674 (11958) *********************** 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 : 1.467 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: 0.7212 (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: 2.4303 time to fit residues: 421.7027 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 : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 175 GLN B 266 HIS E 39 GLN E 167 GLN D 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114660 restraints weight = 29743.801| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.30 r_work: 0.3181 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1824 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= 0.118 Angle : 0.530 5.316 11964 Z= 0.287 Chirality : 0.041 0.138 1374 Planarity : 0.004 0.039 1492 Dihedral : 7.676 107.576 1242 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.20 % Allowed : 13.99 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.23), residues: 1101 helix: -2.30 (0.24), residues: 354 sheet: -0.39 (0.31), residues: 282 loop : -2.86 (0.23), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS D 211 PHE 0.012 0.001 PHE D 227 TYR 0.011 0.001 TYR E 178 ARG 0.003 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 339) hydrogen bonds : angle 5.12021 ( 972) SS BOND : bond 0.00667 ( 3) SS BOND : angle 1.08930 ( 6) covalent geometry : bond 0.00267 ( 8833) covalent geometry : angle 0.52937 (11958) *********************** 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 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7075 (m-70) cc_final: 0.6862 (m-70) REVERT: B 46 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7432 (mtp-110) REVERT: B 258 ASP cc_start: 0.8037 (m-30) cc_final: 0.7761 (m-30) REVERT: B 340 ASN cc_start: 0.7954 (t0) cc_final: 0.7662 (t0) REVERT: C 27 ARG cc_start: 0.8217 (mtt-85) cc_final: 0.7988 (mtt-85) REVERT: E 43 LYS cc_start: 0.8424 (mmtt) cc_final: 0.7440 (ttpt) REVERT: E 151 LYS cc_start: 0.7931 (tttt) cc_final: 0.7707 (tttp) REVERT: D 169 LYS cc_start: 0.7294 (tptp) cc_final: 0.6662 (tptt) REVERT: D 195 LYS cc_start: 0.4305 (mmtp) cc_final: 0.3353 (ptpp) outliers start: 11 outliers final: 5 residues processed: 150 average time/residue: 2.1677 time to fit residues: 350.7110 Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105884 restraints weight = 30098.362| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.23 r_work: 0.3165 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8836 Z= 0.177 Angle : 0.567 6.068 11964 Z= 0.306 Chirality : 0.042 0.140 1374 Planarity : 0.004 0.040 1492 Dihedral : 7.416 124.623 1242 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.53 % Allowed : 15.08 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1101 helix: -1.70 (0.26), residues: 346 sheet: -0.19 (0.31), residues: 284 loop : -2.58 (0.24), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE D 227 TYR 0.013 0.001 TYR D 207 ARG 0.004 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 339) hydrogen bonds : angle 4.86731 ( 972) SS BOND : bond 0.00939 ( 3) SS BOND : angle 2.61674 ( 6) covalent geometry : bond 0.00421 ( 8833) covalent geometry : angle 0.56409 (11958) *********************** 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 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7048 (m-70) cc_final: 0.6818 (m-70) REVERT: B 58 ILE cc_start: 0.8310 (pt) cc_final: 0.8088 (mt) REVERT: B 70 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8478 (pt) REVERT: B 212 ASP cc_start: 0.8279 (t0) cc_final: 0.8014 (t0) REVERT: B 258 ASP cc_start: 0.7973 (m-30) cc_final: 0.7754 (m-30) REVERT: E 151 LYS cc_start: 0.7838 (tttt) cc_final: 0.7593 (tttp) REVERT: D 109 PHE cc_start: 0.7053 (m-80) cc_final: 0.6553 (m-10) REVERT: D 195 LYS cc_start: 0.4491 (mmtp) cc_final: 0.3791 (ptmm) REVERT: D 319 ASN cc_start: 0.8274 (t0) cc_final: 0.7948 (t0) outliers start: 14 outliers final: 8 residues processed: 150 average time/residue: 2.3919 time to fit residues: 384.5071 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 ASP 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 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 89 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.149256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107261 restraints weight = 30055.586| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.23 r_work: 0.3164 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2813 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= 0.120 Angle : 0.508 4.833 11964 Z= 0.274 Chirality : 0.041 0.135 1374 Planarity : 0.003 0.036 1492 Dihedral : 6.820 122.478 1242 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.42 % Allowed : 17.38 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.24), residues: 1101 helix: -1.26 (0.27), residues: 349 sheet: -0.06 (0.31), residues: 282 loop : -2.31 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE D 227 TYR 0.013 0.001 TYR D 207 ARG 0.003 0.000 ARG D 247 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 339) hydrogen bonds : angle 4.59780 ( 972) SS BOND : bond 0.00753 ( 3) SS BOND : angle 1.42281 ( 6) covalent geometry : bond 0.00280 ( 8833) covalent geometry : angle 0.50749 (11958) *********************** 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 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7024 (m-70) cc_final: 0.6789 (m-70) REVERT: B 58 ILE cc_start: 0.8250 (pt) cc_final: 0.7956 (mt) REVERT: B 123 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8279 (mp) REVERT: B 212 ASP cc_start: 0.8318 (t0) cc_final: 0.8053 (t0) REVERT: B 258 ASP cc_start: 0.7969 (m-30) cc_final: 0.7582 (m-30) REVERT: E 151 LYS cc_start: 0.7839 (tttt) cc_final: 0.7597 (tttm) REVERT: D 109 PHE cc_start: 0.7020 (m-80) cc_final: 0.6539 (m-10) REVERT: D 169 LYS cc_start: 0.7178 (tmtt) cc_final: 0.6777 (tptt) REVERT: D 195 LYS cc_start: 0.4427 (mmtp) cc_final: 0.3755 (ptmm) REVERT: D 319 ASN cc_start: 0.8213 (t0) cc_final: 0.7871 (t0) outliers start: 13 outliers final: 11 residues processed: 149 average time/residue: 2.3871 time to fit residues: 380.8577 Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 119 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 153 ASP 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 110 ARG Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.146174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103886 restraints weight = 30468.086| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.24 r_work: 0.3121 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8836 Z= 0.187 Angle : 0.557 5.592 11964 Z= 0.301 Chirality : 0.043 0.135 1374 Planarity : 0.004 0.043 1492 Dihedral : 7.022 127.094 1242 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.51 % Allowed : 18.03 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.24), residues: 1101 helix: -1.14 (0.27), residues: 353 sheet: -0.04 (0.31), residues: 284 loop : -2.17 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.006 0.001 HIS E 35 PHE 0.016 0.001 PHE D 227 TYR 0.012 0.001 TYR E 178 ARG 0.004 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 339) hydrogen bonds : angle 4.66354 ( 972) SS BOND : bond 0.00829 ( 3) SS BOND : angle 0.97443 ( 6) covalent geometry : bond 0.00451 ( 8833) covalent geometry : angle 0.55698 (11958) *********************** 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 160 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7130 (m-70) cc_final: 0.6858 (m-70) REVERT: A 225 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7938 (p) REVERT: B 70 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8556 (pt) REVERT: B 123 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B 212 ASP cc_start: 0.8429 (t0) cc_final: 0.8074 (t0) REVERT: E 151 LYS cc_start: 0.7843 (tttt) cc_final: 0.7633 (tttm) REVERT: D 109 PHE cc_start: 0.7073 (m-80) cc_final: 0.6765 (m-10) REVERT: D 169 LYS cc_start: 0.7213 (tmtt) cc_final: 0.6841 (tptt) REVERT: D 195 LYS cc_start: 0.4584 (mmtp) cc_final: 0.3889 (ptmm) REVERT: D 319 ASN cc_start: 0.8221 (t0) cc_final: 0.7885 (t0) outliers start: 23 outliers final: 11 residues processed: 152 average time/residue: 2.1867 time to fit residues: 358.6769 Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 298 GLU 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 D residue 291 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.147345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.105296 restraints weight = 30310.360| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.22 r_work: 0.3160 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8836 Z= 0.132 Angle : 0.513 5.158 11964 Z= 0.277 Chirality : 0.041 0.136 1374 Planarity : 0.003 0.039 1492 Dihedral : 6.782 125.072 1242 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.75 % Allowed : 19.13 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.24), residues: 1101 helix: -0.90 (0.27), residues: 352 sheet: 0.05 (0.32), residues: 283 loop : -1.97 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.011 0.001 TYR E 178 ARG 0.006 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 339) hydrogen bonds : angle 4.53411 ( 972) SS BOND : bond 0.00695 ( 3) SS BOND : angle 0.84956 ( 6) covalent geometry : bond 0.00311 ( 8833) covalent geometry : angle 0.51302 (11958) *********************** 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 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7159 (m-70) cc_final: 0.6876 (m-70) REVERT: B 70 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8525 (pt) REVERT: B 123 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8327 (mp) REVERT: B 212 ASP cc_start: 0.8466 (t0) cc_final: 0.8185 (t0) REVERT: B 322 ASP cc_start: 0.7713 (m-30) cc_final: 0.7460 (t0) REVERT: E 151 LYS cc_start: 0.7873 (tttt) cc_final: 0.7657 (tttm) REVERT: D 153 TYR cc_start: 0.8237 (t80) cc_final: 0.7951 (t80) REVERT: D 169 LYS cc_start: 0.7257 (tmtt) cc_final: 0.6854 (tptt) REVERT: D 195 LYS cc_start: 0.4600 (mmtp) cc_final: 0.3914 (ptmm) outliers start: 16 outliers final: 10 residues processed: 148 average time/residue: 2.6497 time to fit residues: 424.8693 Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 123 ILE Chi-restraints excluded: chain B residue 153 ASP 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 181 LEU Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.146348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104710 restraints weight = 30008.221| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.11 r_work: 0.3124 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3330 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= 0.155 Angle : 0.525 5.883 11964 Z= 0.284 Chirality : 0.042 0.135 1374 Planarity : 0.003 0.042 1492 Dihedral : 6.805 126.019 1242 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.19 % Allowed : 19.34 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1101 helix: -0.81 (0.28), residues: 355 sheet: 0.04 (0.32), residues: 284 loop : -1.93 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.001 PHE D 227 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 339) hydrogen bonds : angle 4.52907 ( 972) SS BOND : bond 0.00729 ( 3) SS BOND : angle 0.80186 ( 6) covalent geometry : bond 0.00372 ( 8833) covalent geometry : angle 0.52474 (11958) *********************** 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 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7391 (m-70) cc_final: 0.7148 (m-70) REVERT: A 225 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8150 (p) REVERT: B 70 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8794 (pt) REVERT: B 123 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8623 (mp) REVERT: B 212 ASP cc_start: 0.8527 (t0) cc_final: 0.8286 (t0) REVERT: B 268 ASN cc_start: 0.8103 (p0) cc_final: 0.7870 (p0) REVERT: C 27 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.8067 (mtt-85) REVERT: D 153 TYR cc_start: 0.8419 (t80) cc_final: 0.8159 (t80) REVERT: D 169 LYS cc_start: 0.7398 (tmtt) cc_final: 0.6980 (tptt) REVERT: D 195 LYS cc_start: 0.4691 (mmtp) cc_final: 0.3947 (ptmm) outliers start: 20 outliers final: 11 residues processed: 150 average time/residue: 2.2913 time to fit residues: 368.9524 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 153 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.146777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108835 restraints weight = 30007.444| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.17 r_work: 0.3108 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8836 Z= 0.136 Angle : 0.516 5.634 11964 Z= 0.277 Chirality : 0.041 0.133 1374 Planarity : 0.003 0.047 1492 Dihedral : 6.711 125.250 1242 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.19 % Allowed : 20.00 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.25), residues: 1101 helix: -0.68 (0.28), residues: 356 sheet: 0.08 (0.32), residues: 283 loop : -1.87 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.011 0.001 TYR E 178 ARG 0.006 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 339) hydrogen bonds : angle 4.47076 ( 972) SS BOND : bond 0.00698 ( 3) SS BOND : angle 0.75171 ( 6) covalent geometry : bond 0.00323 ( 8833) covalent geometry : angle 0.51581 (11958) *********************** 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 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.370 Fit side-chains REVERT: A 195 HIS cc_start: 0.7477 (m-70) cc_final: 0.7250 (m-70) REVERT: A 225 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 354 PHE cc_start: 0.4221 (p90) cc_final: 0.3749 (p90) REVERT: B 22 ARG cc_start: 0.6771 (ptp-170) cc_final: 0.6495 (ptp90) REVERT: B 70 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8827 (pt) REVERT: B 123 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8692 (mp) REVERT: C 27 ARG cc_start: 0.8374 (mtt-85) cc_final: 0.8138 (mtt-85) REVERT: D 153 TYR cc_start: 0.8439 (t80) cc_final: 0.8183 (t80) REVERT: D 169 LYS cc_start: 0.7402 (tmtt) cc_final: 0.6975 (tptt) REVERT: D 180 MET cc_start: 0.5161 (ptt) cc_final: 0.4892 (mpp) REVERT: D 195 LYS cc_start: 0.4784 (mmtp) cc_final: 0.4010 (ptmm) outliers start: 20 outliers final: 12 residues processed: 148 average time/residue: 2.1656 time to fit residues: 345.6786 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 153 ASP 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 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 69 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108606 restraints weight = 30052.803| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.23 r_work: 0.3097 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8836 Z= 0.157 Angle : 0.541 6.473 11964 Z= 0.291 Chirality : 0.042 0.134 1374 Planarity : 0.003 0.038 1492 Dihedral : 6.809 126.660 1242 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.08 % Allowed : 20.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1101 helix: -0.62 (0.28), residues: 354 sheet: 0.05 (0.32), residues: 283 loop : -1.85 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE D 227 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 339) hydrogen bonds : angle 4.50057 ( 972) SS BOND : bond 0.00754 ( 3) SS BOND : angle 2.75442 ( 6) covalent geometry : bond 0.00377 ( 8833) covalent geometry : angle 0.53747 (11958) *********************** 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 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.414 Fit side-chains REVERT: A 195 HIS cc_start: 0.7487 (m-70) cc_final: 0.7261 (m-70) REVERT: A 209 LYS cc_start: 0.8173 (pttm) cc_final: 0.7875 (pmtt) REVERT: A 225 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8206 (p) REVERT: B 22 ARG cc_start: 0.6900 (ptp-170) cc_final: 0.6179 (ptp90) REVERT: B 70 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8857 (pt) REVERT: B 123 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8705 (mp) REVERT: E 43 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8108 (mmmt) REVERT: D 153 TYR cc_start: 0.8461 (t80) cc_final: 0.8204 (t80) REVERT: D 169 LYS cc_start: 0.7430 (tmtt) cc_final: 0.6997 (tptt) REVERT: D 180 MET cc_start: 0.5254 (ptt) cc_final: 0.4985 (mpp) REVERT: D 195 LYS cc_start: 0.4749 (mmtp) cc_final: 0.3991 (ptmm) outliers start: 19 outliers final: 13 residues processed: 146 average time/residue: 2.3004 time to fit residues: 360.6905 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 153 ASP 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 154 ILE 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 33 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.147016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109071 restraints weight = 29991.641| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.19 r_work: 0.3110 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3664 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= 0.124 Angle : 0.520 5.438 11964 Z= 0.278 Chirality : 0.041 0.134 1374 Planarity : 0.003 0.040 1492 Dihedral : 6.638 124.675 1242 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.75 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1101 helix: -0.47 (0.28), residues: 354 sheet: 0.09 (0.32), residues: 283 loop : -1.79 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE D 227 TYR 0.011 0.001 TYR E 178 ARG 0.008 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 339) hydrogen bonds : angle 4.41100 ( 972) SS BOND : bond 0.00795 ( 3) SS BOND : angle 2.06336 ( 6) covalent geometry : bond 0.00294 ( 8833) covalent geometry : angle 0.51793 (11958) ********************** 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 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.376 Fit side-chains REVERT: A 195 HIS cc_start: 0.7443 (m-70) cc_final: 0.7207 (m-70) REVERT: A 209 LYS cc_start: 0.8126 (pttm) cc_final: 0.7810 (pmtt) REVERT: B 22 ARG cc_start: 0.6757 (ptp-170) cc_final: 0.6071 (ptp90) REVERT: B 123 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8627 (mp) REVERT: D 153 TYR cc_start: 0.8388 (t80) cc_final: 0.8123 (t80) REVERT: D 169 LYS cc_start: 0.7385 (tmtt) cc_final: 0.6855 (tptt) REVERT: D 180 MET cc_start: 0.5186 (ptt) cc_final: 0.4929 (mpp) REVERT: D 195 LYS cc_start: 0.4703 (mmtp) cc_final: 0.3954 (ptmm) REVERT: D 251 ARG cc_start: 0.6790 (ttp80) cc_final: 0.6185 (mtp-110) outliers start: 16 outliers final: 14 residues processed: 145 average time/residue: 2.3706 time to fit residues: 368.5189 Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 278 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 153 ASP 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 154 ILE 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 72 optimal weight: 0.0030 chunk 98 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.147856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110132 restraints weight = 29792.291| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.18 r_work: 0.3126 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8836 Z= 0.105 Angle : 0.503 5.124 11964 Z= 0.269 Chirality : 0.041 0.133 1374 Planarity : 0.003 0.037 1492 Dihedral : 6.483 123.713 1242 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.64 % Allowed : 21.42 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1101 helix: -0.32 (0.29), residues: 354 sheet: 0.15 (0.32), residues: 281 loop : -1.71 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.011 0.001 TYR E 178 ARG 0.006 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 339) hydrogen bonds : angle 4.33032 ( 972) SS BOND : bond 0.00690 ( 3) SS BOND : angle 1.62795 ( 6) covalent geometry : bond 0.00246 ( 8833) covalent geometry : angle 0.50229 (11958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14080.96 seconds wall clock time: 240 minutes 22.95 seconds (14422.95 seconds total)