Starting phenix.real_space_refine on Sun May 18 15:39:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4n_36887/05_2025/8k4n_36887_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4n_36887/05_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_36887/05_2025/8k4n_36887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4n_36887/05_2025/8k4n_36887.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4n_36887/05_2025/8k4n_36887_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4n_36887/05_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-5687/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: 9.38, per 1000 atoms: 0.55 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: 4.32 Conformation dependent library (CDL) restraints added in 1.6 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: 1.55 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: 7.48 Time building geometry restraints manager: 5.19 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: 3.530 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: 0.320 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 41.240 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.100 ------------------------------------------------------------------------------- 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 : 1.182 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: 2.4449 time to fit residues: 423.3817 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 : 1.228 ------------------------------------------------------------------------------- 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 = 0.114662 restraints weight = 29743.853| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.30 r_work: 0.3224 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 7.676 107.575 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 5.12022 ( 972) SS BOND : bond 0.00667 ( 3) SS BOND : angle 1.08929 ( 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 : 1.175 Fit side-chains revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7036 (m-70) cc_final: 0.6820 (m-70) REVERT: B 46 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7397 (mtp-110) REVERT: B 258 ASP cc_start: 0.8008 (m-30) cc_final: 0.7723 (m-30) REVERT: B 340 ASN cc_start: 0.7952 (t0) cc_final: 0.7664 (t0) REVERT: C 27 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7943 (mtt-85) REVERT: E 43 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7393 (ttpt) REVERT: E 151 LYS cc_start: 0.7880 (tttt) cc_final: 0.7654 (tttp) REVERT: D 169 LYS cc_start: 0.7268 (tptp) cc_final: 0.6639 (tptt) REVERT: D 195 LYS cc_start: 0.4270 (mmtp) cc_final: 0.3318 (ptpp) outliers start: 11 outliers final: 5 residues processed: 150 average time/residue: 2.1226 time to fit residues: 343.0028 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 : 1.355 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 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: 0.4980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.149222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107349 restraints weight = 30017.869| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.23 r_work: 0.3181 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8836 Z= 0.149 Angle : 0.547 6.798 11964 Z= 0.294 Chirality : 0.042 0.153 1374 Planarity : 0.004 0.046 1492 Dihedral : 7.214 121.688 1242 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.42 % Allowed : 14.97 % Favored : 83.61 % 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: -2.46 (0.23), residues: 1101 helix: -1.62 (0.26), residues: 346 sheet: -0.18 (0.31), residues: 282 loop : -2.53 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.014 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 0.04014 ( 339) hydrogen bonds : angle 4.79342 ( 972) SS BOND : bond 0.00688 ( 3) SS BOND : angle 2.80098 ( 6) covalent geometry : bond 0.00351 ( 8833) covalent geometry : angle 0.54328 (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 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7033 (m-70) cc_final: 0.6799 (m-70) REVERT: B 58 ILE cc_start: 0.8251 (pt) cc_final: 0.8029 (mt) REVERT: B 212 ASP cc_start: 0.8263 (t0) cc_final: 0.8022 (t0) REVERT: B 258 ASP cc_start: 0.7969 (m-30) cc_final: 0.7694 (m-30) REVERT: B 260 GLU cc_start: 0.8134 (pt0) cc_final: 0.7811 (tt0) REVERT: B 268 ASN cc_start: 0.8390 (p0) cc_final: 0.8178 (p0) REVERT: C 27 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7906 (mtt-85) REVERT: E 151 LYS cc_start: 0.7808 (tttt) cc_final: 0.7556 (tttp) REVERT: D 153 TYR cc_start: 0.8214 (t80) cc_final: 0.7844 (t80) REVERT: D 195 LYS cc_start: 0.4419 (mmtp) cc_final: 0.3679 (ptmm) REVERT: D 247 ARG cc_start: 0.6194 (ptp-170) cc_final: 0.5983 (ptt-90) REVERT: D 319 ASN cc_start: 0.8254 (t0) cc_final: 0.7920 (t0) outliers start: 13 outliers final: 7 residues processed: 149 average time/residue: 2.4370 time to fit residues: 387.7367 Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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: 4.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.147620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105482 restraints weight = 30142.112| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.23 r_work: 0.3157 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8836 Z= 0.157 Angle : 0.535 5.287 11964 Z= 0.289 Chirality : 0.042 0.135 1374 Planarity : 0.003 0.036 1492 Dihedral : 6.928 124.546 1242 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.97 % Allowed : 16.50 % Favored : 81.53 % 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: -2.07 (0.24), residues: 1101 helix: -1.27 (0.27), residues: 349 sheet: -0.04 (0.31), residues: 284 loop : -2.27 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.014 0.001 TYR D 207 ARG 0.002 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 339) hydrogen bonds : angle 4.63552 ( 972) SS BOND : bond 0.00977 ( 3) SS BOND : angle 1.62597 ( 6) covalent geometry : bond 0.00373 ( 8833) covalent geometry : angle 0.53438 (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 161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7062 (m-70) cc_final: 0.6828 (m-70) REVERT: B 58 ILE cc_start: 0.8302 (pt) cc_final: 0.7984 (mt) REVERT: B 70 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8461 (pt) REVERT: B 123 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 212 ASP cc_start: 0.8345 (t0) cc_final: 0.8098 (t0) REVERT: B 258 ASP cc_start: 0.8066 (m-30) cc_final: 0.7774 (m-30) REVERT: C 27 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7982 (mtt-85) REVERT: E 151 LYS cc_start: 0.7845 (tttt) cc_final: 0.7620 (tttm) REVERT: D 109 PHE cc_start: 0.7095 (m-80) cc_final: 0.6653 (m-10) REVERT: D 110 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6787 (tpt-90) REVERT: D 195 LYS cc_start: 0.4478 (mmtp) cc_final: 0.3796 (ptmm) REVERT: D 319 ASN cc_start: 0.8264 (t0) cc_final: 0.7934 (t0) outliers start: 18 outliers final: 11 residues processed: 152 average time/residue: 2.4026 time to fit residues: 391.5053 Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.146284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103938 restraints weight = 30478.895| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.24 r_work: 0.3136 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8836 Z= 0.178 Angle : 0.548 5.375 11964 Z= 0.296 Chirality : 0.042 0.134 1374 Planarity : 0.004 0.042 1492 Dihedral : 6.983 126.399 1242 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.84 % Allowed : 17.81 % Favored : 79.34 % 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: -1.85 (0.24), residues: 1101 helix: -1.04 (0.27), residues: 349 sheet: -0.03 (0.31), residues: 284 loop : -2.10 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.04094 ( 339) hydrogen bonds : angle 4.63353 ( 972) SS BOND : bond 0.00746 ( 3) SS BOND : angle 1.00923 ( 6) covalent geometry : bond 0.00427 ( 8833) covalent geometry : angle 0.54768 (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 163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7188 (m-70) cc_final: 0.6915 (m-70) REVERT: A 225 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 70 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8507 (pt) REVERT: B 123 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 212 ASP cc_start: 0.8470 (t0) cc_final: 0.8179 (t0) REVERT: E 151 LYS cc_start: 0.7830 (tttt) cc_final: 0.7621 (tttm) REVERT: D 109 PHE cc_start: 0.7022 (m-80) cc_final: 0.6674 (m-10) REVERT: D 169 LYS cc_start: 0.7242 (tmtt) cc_final: 0.6791 (tptt) REVERT: D 195 LYS cc_start: 0.4541 (mmtp) cc_final: 0.3870 (ptmm) REVERT: D 319 ASN cc_start: 0.8231 (t0) cc_final: 0.7901 (t0) outliers start: 26 outliers final: 12 residues processed: 153 average time/residue: 2.1556 time to fit residues: 354.9561 Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 B residue 323 ASP 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: 0.8980 chunk 63 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.146751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105142 restraints weight = 30068.119| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.12 r_work: 0.3109 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8836 Z= 0.139 Angle : 0.515 5.255 11964 Z= 0.278 Chirality : 0.041 0.134 1374 Planarity : 0.003 0.040 1492 Dihedral : 6.790 125.488 1242 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.08 % Allowed : 19.13 % Favored : 78.80 % 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: -1.66 (0.24), residues: 1101 helix: -0.88 (0.27), residues: 353 sheet: 0.03 (0.32), residues: 284 loop : -1.94 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE D 227 TYR 0.011 0.001 TYR E 178 ARG 0.005 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 339) hydrogen bonds : angle 4.52485 ( 972) SS BOND : bond 0.00707 ( 3) SS BOND : angle 0.84293 ( 6) covalent geometry : bond 0.00329 ( 8833) covalent geometry : angle 0.51518 (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 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7399 (m-70) cc_final: 0.7161 (m-70) REVERT: A 225 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8148 (p) REVERT: B 70 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8697 (pt) REVERT: B 123 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8644 (mp) REVERT: D 109 PHE cc_start: 0.7245 (m-80) cc_final: 0.6951 (m-10) REVERT: D 153 TYR cc_start: 0.8430 (t80) cc_final: 0.8172 (t80) REVERT: D 169 LYS cc_start: 0.7374 (tmtt) cc_final: 0.7103 (tptt) REVERT: D 195 LYS cc_start: 0.4736 (mmtp) cc_final: 0.4013 (ptmm) outliers start: 19 outliers final: 10 residues processed: 150 average time/residue: 2.2456 time to fit residues: 363.0047 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 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: 0.5980 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.147646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106208 restraints weight = 29972.024| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.13 r_work: 0.3144 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3390 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= 0.113 Angle : 0.497 5.582 11964 Z= 0.268 Chirality : 0.041 0.136 1374 Planarity : 0.003 0.035 1492 Dihedral : 6.582 124.396 1242 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: -1.45 (0.25), residues: 1101 helix: -0.63 (0.28), residues: 353 sheet: 0.13 (0.32), residues: 282 loop : -1.88 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.004 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 339) hydrogen bonds : angle 4.41020 ( 972) SS BOND : bond 0.00652 ( 3) SS BOND : angle 0.73119 ( 6) covalent geometry : bond 0.00267 ( 8833) covalent geometry : angle 0.49735 (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 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 HIS cc_start: 0.7393 (m-70) cc_final: 0.7153 (m-70) REVERT: B 70 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8614 (pt) REVERT: B 268 ASN cc_start: 0.8025 (p0) cc_final: 0.7786 (p0) REVERT: D 109 PHE cc_start: 0.7204 (m-80) cc_final: 0.6969 (m-10) REVERT: D 153 TYR cc_start: 0.8355 (t80) cc_final: 0.8095 (t80) REVERT: D 169 LYS cc_start: 0.7392 (tmtt) cc_final: 0.7101 (tptt) REVERT: D 195 LYS cc_start: 0.4719 (mmtp) cc_final: 0.3966 (ptmm) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 2.0905 time to fit residues: 331.2225 Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.108849 restraints weight = 30031.187| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.23 r_work: 0.3107 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8836 Z= 0.131 Angle : 0.507 5.363 11964 Z= 0.273 Chirality : 0.041 0.134 1374 Planarity : 0.003 0.044 1492 Dihedral : 6.596 124.919 1242 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.08 % Allowed : 20.44 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.35 (0.25), residues: 1101 helix: -0.50 (0.28), residues: 353 sheet: 0.15 (0.32), residues: 282 loop : -1.83 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE D 227 TYR 0.011 0.001 TYR E 178 ARG 0.007 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 339) hydrogen bonds : angle 4.40892 ( 972) SS BOND : bond 0.00666 ( 3) SS BOND : angle 0.73746 ( 6) covalent geometry : bond 0.00312 ( 8833) covalent geometry : angle 0.50644 (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 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.348 Fit side-chains REVERT: A 195 HIS cc_start: 0.7500 (m-70) cc_final: 0.7271 (m-70) REVERT: A 225 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 354 PHE cc_start: 0.4238 (p90) cc_final: 0.3763 (p90) REVERT: B 70 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8721 (pt) REVERT: C 27 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8150 (mtt-85) REVERT: E 43 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8118 (mmmt) REVERT: D 153 TYR cc_start: 0.8416 (t80) cc_final: 0.8171 (t80) REVERT: D 169 LYS cc_start: 0.7417 (tmtt) cc_final: 0.7112 (tptt) REVERT: D 180 MET cc_start: 0.5193 (ptt) cc_final: 0.4921 (mpp) REVERT: D 195 LYS cc_start: 0.4765 (mmtp) cc_final: 0.3995 (ptmm) REVERT: D 203 MET cc_start: 0.5677 (mtt) cc_final: 0.5420 (mtt) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 2.2219 time to fit residues: 351.8320 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.147521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109475 restraints weight = 29971.186| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.18 r_work: 0.3114 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8836 Z= 0.120 Angle : 0.516 6.176 11964 Z= 0.277 Chirality : 0.041 0.132 1374 Planarity : 0.003 0.052 1492 Dihedral : 6.566 124.471 1242 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.75 % Allowed : 20.98 % Favored : 77.27 % 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: -1.27 (0.25), residues: 1101 helix: -0.44 (0.28), residues: 355 sheet: 0.18 (0.32), residues: 282 loop : -1.77 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.03440 ( 339) hydrogen bonds : angle 4.35477 ( 972) SS BOND : bond 0.00864 ( 3) SS BOND : angle 2.64973 ( 6) covalent geometry : bond 0.00285 ( 8833) covalent geometry : angle 0.51319 (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 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.310 Fit side-chains REVERT: A 195 HIS cc_start: 0.7457 (m-70) cc_final: 0.7229 (m-70) REVERT: A 209 LYS cc_start: 0.8152 (pttm) cc_final: 0.7853 (pmtt) REVERT: A 225 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 22 ARG cc_start: 0.6675 (ptp-170) cc_final: 0.6403 (ptp90) REVERT: B 70 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8703 (pt) REVERT: C 27 ARG cc_start: 0.8424 (mtt-85) cc_final: 0.8204 (mtt-85) REVERT: D 153 TYR cc_start: 0.8407 (t80) cc_final: 0.8156 (t80) REVERT: D 169 LYS cc_start: 0.7414 (tmtt) cc_final: 0.7105 (tptt) REVERT: D 180 MET cc_start: 0.5195 (ptt) cc_final: 0.4942 (mpp) REVERT: D 195 LYS cc_start: 0.4762 (mmtp) cc_final: 0.3995 (ptmm) REVERT: D 251 ARG cc_start: 0.6862 (ttp80) cc_final: 0.6219 (mtp-110) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 2.3104 time to fit residues: 361.7313 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN C 59 ASN E 113 GLN D 72 ASN D 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108484 restraints weight = 30000.834| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.19 r_work: 0.3101 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8836 Z= 0.148 Angle : 0.534 5.631 11964 Z= 0.286 Chirality : 0.041 0.133 1374 Planarity : 0.003 0.037 1492 Dihedral : 6.678 125.563 1242 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.86 % Allowed : 20.77 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.29 (0.25), residues: 1101 helix: -0.44 (0.28), residues: 354 sheet: 0.12 (0.32), residues: 283 loop : -1.77 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.015 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 0.03693 ( 339) hydrogen bonds : angle 4.41011 ( 972) SS BOND : bond 0.00851 ( 3) SS BOND : angle 2.12280 ( 6) covalent geometry : bond 0.00355 ( 8833) covalent geometry : angle 0.53162 (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 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.319 Fit side-chains REVERT: A 195 HIS cc_start: 0.7403 (m-70) cc_final: 0.7165 (m-70) REVERT: A 209 LYS cc_start: 0.8153 (pttm) cc_final: 0.7837 (pmtt) REVERT: A 225 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8213 (p) REVERT: B 22 ARG cc_start: 0.6666 (ptp-170) cc_final: 0.6366 (ptp90) REVERT: B 70 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8700 (pt) REVERT: B 123 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8627 (mp) REVERT: D 153 TYR cc_start: 0.8409 (t80) cc_final: 0.8144 (t80) REVERT: D 169 LYS cc_start: 0.7403 (tmtt) cc_final: 0.7088 (tptt) REVERT: D 180 MET cc_start: 0.5182 (ptt) cc_final: 0.4922 (mpp) REVERT: D 195 LYS cc_start: 0.4699 (mmtp) cc_final: 0.3942 (ptmm) outliers start: 17 outliers final: 13 residues processed: 146 average time/residue: 2.2823 time to fit residues: 357.6402 Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.0670 chunk 98 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.148473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110658 restraints weight = 29786.407| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.20 r_work: 0.3158 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8836 Z= 0.100 Angle : 0.502 5.528 11964 Z= 0.267 Chirality : 0.040 0.134 1374 Planarity : 0.003 0.039 1492 Dihedral : 6.431 123.061 1242 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.53 % Allowed : 21.75 % Favored : 76.72 % 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: -1.11 (0.25), residues: 1101 helix: -0.22 (0.29), residues: 350 sheet: 0.22 (0.32), residues: 281 loop : -1.71 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS D 283 PHE 0.014 0.001 PHE D 227 TYR 0.010 0.001 TYR E 178 ARG 0.006 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 339) hydrogen bonds : angle 4.29420 ( 972) SS BOND : bond 0.00665 ( 3) SS BOND : angle 1.66748 ( 6) covalent geometry : bond 0.00233 ( 8833) covalent geometry : angle 0.50072 (11958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12825.45 seconds wall clock time: 220 minutes 13.91 seconds (13213.91 seconds total)