Starting phenix.real_space_refine on Sun May 3 19:39:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmi_66092/05_2026/9wmi_66092.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmi_66092/05_2026/9wmi_66092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wmi_66092/05_2026/9wmi_66092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmi_66092/05_2026/9wmi_66092.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmi_66092/05_2026/9wmi_66092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmi_66092/05_2026/9wmi_66092.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 9623 2.51 5 N 2468 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14823 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1953 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain: "B" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1933 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 6, 'TRANS': 240} Chain: "C" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1945 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "D" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1945 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "E" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3463 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3476 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 7, 'TRANS': 425} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.27 Number of scatterers: 14823 At special positions: 0 Unit cell: (96.46, 125.08, 120.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 8 15.00 O 2656 8.00 N 2468 7.00 C 9623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 765.7 milliseconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 61.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 48 through 56 removed outlier: 3.662A pdb=" N LEU A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.588A pdb=" N LEU A 76 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.517A pdb=" N ALA A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 109 removed outlier: 3.650A pdb=" N ILE A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.202A pdb=" N MET A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.548A pdb=" N ILE A 138 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.760A pdb=" N GLN A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.659A pdb=" N ASN A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.050A pdb=" N PHE A 211 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'B' and resid 49 through 56 Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.539A pdb=" N ALA B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.516A pdb=" N LEU B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.771A pdb=" N MET B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.740A pdb=" N LEU B 139 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.570A pdb=" N ALA B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 196 removed outlier: 3.515A pdb=" N ASN B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.619A pdb=" N VAL B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.553A pdb=" N ALA C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.527A pdb=" N ILE C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.522A pdb=" N ASP C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 133 removed outlier: 3.678A pdb=" N MET C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.825A pdb=" N VAL C 146 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 162 removed outlier: 4.778A pdb=" N HIS C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 193 removed outlier: 3.826A pdb=" N MET C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 248 removed outlier: 3.733A pdb=" N PHE C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.534A pdb=" N LEU D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.730A pdb=" N THR D 75 " --> pdb=" O GLN D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.535A pdb=" N ARG D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.531A pdb=" N ILE D 108 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.711A pdb=" N LEU D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 134 removed outlier: 4.078A pdb=" N MET D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 129 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.983A pdb=" N LEU D 139 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 161 removed outlier: 3.804A pdb=" N ALA D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 194 Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.527A pdb=" N LEU D 241 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 244 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 12 removed outlier: 3.534A pdb=" N LEU E 12 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 40 removed outlier: 3.561A pdb=" N VAL E 29 " --> pdb=" O CYS E 25 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE E 35 " --> pdb=" O VAL E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 85 removed outlier: 3.762A pdb=" N ILE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 96 removed outlier: 3.885A pdb=" N THR E 93 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU E 94 " --> pdb=" O GLY E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 128 removed outlier: 3.614A pdb=" N GLU E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU E 112 " --> pdb=" O TYR E 108 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 137 removed outlier: 3.634A pdb=" N PHE E 132 " --> pdb=" O PHE E 128 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 160 removed outlier: 3.809A pdb=" N PHE E 155 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 175 removed outlier: 3.699A pdb=" N GLN E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 removed outlier: 3.638A pdb=" N VAL E 204 " --> pdb=" O LYS E 200 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU E 205 " --> pdb=" O TRP E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 218 removed outlier: 3.990A pdb=" N LEU E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY E 211 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 246 removed outlier: 3.533A pdb=" N LEU E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN E 246 " --> pdb=" O PHE E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 258 removed outlier: 4.040A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 264 removed outlier: 3.509A pdb=" N PHE E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 279 removed outlier: 4.446A pdb=" N VAL E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE E 276 " --> pdb=" O SER E 272 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG E 277 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.515A pdb=" N SER E 289 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N THR E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 301 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 551 removed outlier: 3.713A pdb=" N ALA E 525 " --> pdb=" O LYS E 521 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY E 543 " --> pdb=" O PHE E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 566 Processing helix chain 'E' and resid 573 through 582 Processing helix chain 'E' and resid 583 through 586 removed outlier: 3.559A pdb=" N PHE E 586 " --> pdb=" O GLY E 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 583 through 586' Processing helix chain 'E' and resid 587 through 605 removed outlier: 3.606A pdb=" N PHE E 599 " --> pdb=" O ILE E 595 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 600 " --> pdb=" O HIS E 596 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 602 " --> pdb=" O GLY E 598 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA E 603 " --> pdb=" O PHE E 599 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 604 " --> pdb=" O ALA E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 644 removed outlier: 3.843A pdb=" N ILE E 622 " --> pdb=" O ILE E 618 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR E 623 " --> pdb=" O VAL E 619 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 625 " --> pdb=" O PHE E 621 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 13 removed outlier: 4.375A pdb=" N ALA F 7 " --> pdb=" O LEU F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 40 removed outlier: 3.754A pdb=" N ALA F 28 " --> pdb=" O SER F 24 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 86 removed outlier: 3.775A pdb=" N VAL F 68 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG F 85 " --> pdb=" O PHE F 81 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS F 86 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 96 removed outlier: 3.534A pdb=" N LEU F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 131 removed outlier: 3.675A pdb=" N SER F 111 " --> pdb=" O TYR F 107 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU F 112 " --> pdb=" O TYR F 108 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 136 removed outlier: 3.701A pdb=" N MET F 136 " --> pdb=" O PHE F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 167 removed outlier: 3.678A pdb=" N VAL F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N MET F 157 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA F 160 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 161 " --> pdb=" O MET F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.751A pdb=" N ILE F 171 " --> pdb=" O GLN F 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 217 removed outlier: 3.627A pdb=" N VAL F 204 " --> pdb=" O LYS F 200 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 246 removed outlier: 3.584A pdb=" N ARG F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) Proline residue: F 231 - end of helix removed outlier: 4.201A pdb=" N LEU F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 258 removed outlier: 3.558A pdb=" N ALA F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 266 through 279 removed outlier: 4.261A pdb=" N VAL F 270 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 306 removed outlier: 3.631A pdb=" N ILE F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 552 removed outlier: 4.134A pdb=" N MET F 527 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 540 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 567 removed outlier: 4.078A pdb=" N THR F 557 " --> pdb=" O GLU F 553 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE F 567 " --> pdb=" O ALA F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 609 removed outlier: 4.545A pdb=" N ILE F 582 " --> pdb=" O LEU F 578 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU F 585 " --> pdb=" O GLN F 581 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE F 588 " --> pdb=" O PHE F 584 " (cutoff:3.500A) Proline residue: F 589 - end of helix removed outlier: 3.509A pdb=" N ILE F 595 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 602 " --> pdb=" O GLY F 598 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA F 603 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU F 608 " --> pdb=" O LEU F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 617 Processing helix chain 'F' and resid 618 through 644 removed outlier: 3.557A pdb=" N VAL F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA F 641 " --> pdb=" O ILE F 637 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 33 removed outlier: 4.872A pdb=" N PHE A 28 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N THR A 6 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET A 67 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASN A 8 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU A 65 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 14 Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.085A pdb=" N GLY A 90 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASP A 170 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 92 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE A 167 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 202 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA A 169 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 225 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS A 219 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N PHE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 32 removed outlier: 7.371A pdb=" N LEU B 30 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR B 7 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL B 32 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN B 5 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU B 9 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN B 63 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 92 removed outlier: 6.092A pdb=" N GLY B 90 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP B 170 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 92 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE B 167 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL B 202 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 169 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B 37 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL B 216 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY B 39 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE B 218 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N MET B 41 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 225 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS B 219 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 32 removed outlier: 5.327A pdb=" N PHE C 28 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 8 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 32 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 4 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N THR C 6 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET C 67 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN C 8 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU C 65 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 92 removed outlier: 5.931A pdb=" N GLY C 90 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASP C 170 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 92 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE C 167 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL C 202 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA C 169 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 38 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE C 37 " --> pdb=" O ARG C 214 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 216 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY C 39 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE C 218 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET C 41 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 225 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS C 219 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 21 through 32 removed outlier: 7.169A pdb=" N TYR D 22 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR D 14 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA D 24 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR D 12 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER D 26 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER D 10 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE D 28 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN D 8 " --> pdb=" O PHE D 28 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU D 9 " --> pdb=" O GLN D 63 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN D 63 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.584A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASP D 170 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL D 92 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE D 167 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL D 202 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA D 169 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 38 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR D 203 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE D 40 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER D 225 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYS D 219 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N PHE D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 2088 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: 2.58 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3314 1.33 - 1.46: 3491 1.46 - 1.58: 8157 1.58 - 1.70: 13 1.70 - 1.83: 120 Bond restraints: 15095 Sorted by residual: bond pdb=" CA THR A 50 " pdb=" C THR A 50 " ideal model delta sigma weight residual 1.523 1.448 0.076 1.34e-02 5.57e+03 3.18e+01 bond pdb=" CA LYS C 48 " pdb=" C LYS C 48 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.44e-02 4.82e+03 2.36e+01 bond pdb=" CA LEU A 51 " pdb=" C LEU A 51 " ideal model delta sigma weight residual 1.523 1.464 0.060 1.34e-02 5.57e+03 1.98e+01 bond pdb=" N LEU C 55 " pdb=" CA LEU C 55 " ideal model delta sigma weight residual 1.457 1.406 0.051 1.29e-02 6.01e+03 1.57e+01 bond pdb=" CA LEU C 55 " pdb=" C LEU C 55 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.34e-02 5.57e+03 1.50e+01 ... (remaining 15090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 19931 3.54 - 7.09: 353 7.09 - 10.63: 77 10.63 - 14.18: 38 14.18 - 17.72: 7 Bond angle restraints: 20406 Sorted by residual: angle pdb=" N THR C 50 " pdb=" CA THR C 50 " pdb=" C THR C 50 " ideal model delta sigma weight residual 113.37 100.90 12.47 1.38e+00 5.25e-01 8.16e+01 angle pdb=" N LEU C 55 " pdb=" CA LEU C 55 " pdb=" C LEU C 55 " ideal model delta sigma weight residual 110.80 93.71 17.09 2.13e+00 2.20e-01 6.44e+01 angle pdb=" N LYS C 48 " pdb=" CA LYS C 48 " pdb=" C LYS C 48 " ideal model delta sigma weight residual 111.37 99.82 11.55 1.65e+00 3.67e-01 4.90e+01 angle pdb=" N SER A 46 " pdb=" CA SER A 46 " pdb=" C SER A 46 " ideal model delta sigma weight residual 112.72 104.75 7.97 1.14e+00 7.69e-01 4.88e+01 angle pdb=" N LEU C 51 " pdb=" CA LEU C 51 " pdb=" C LEU C 51 " ideal model delta sigma weight residual 113.12 104.54 8.58 1.25e+00 6.40e-01 4.71e+01 ... (remaining 20401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 7996 22.90 - 45.81: 884 45.81 - 68.71: 117 68.71 - 91.62: 15 91.62 - 114.52: 4 Dihedral angle restraints: 9016 sinusoidal: 3599 harmonic: 5417 Sorted by residual: dihedral pdb=" C5' ADP D 301 " pdb=" O5' ADP D 301 " pdb=" PA ADP D 301 " pdb=" O2A ADP D 301 " ideal model delta sinusoidal sigma weight residual -60.00 54.53 -114.52 1 2.00e+01 2.50e-03 3.40e+01 dihedral pdb=" O2A ADP C 301 " pdb=" O3A ADP C 301 " pdb=" PA ADP C 301 " pdb=" PB ADP C 301 " ideal model delta sinusoidal sigma weight residual -60.00 49.11 -109.11 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" O2A ADP A 301 " pdb=" O3A ADP A 301 " pdb=" PA ADP A 301 " pdb=" PB ADP A 301 " ideal model delta sinusoidal sigma weight residual -60.00 47.89 -107.89 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 9013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1916 0.063 - 0.126: 411 0.126 - 0.189: 80 0.189 - 0.253: 13 0.253 - 0.316: 4 Chirality restraints: 2424 Sorted by residual: chirality pdb=" CB ILE E 186 " pdb=" CA ILE E 186 " pdb=" CG1 ILE E 186 " pdb=" CG2 ILE E 186 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VAL F 151 " pdb=" CA VAL F 151 " pdb=" CG1 VAL F 151 " pdb=" CG2 VAL F 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB ILE A 199 " pdb=" CA ILE A 199 " pdb=" CG1 ILE A 199 " pdb=" CG2 ILE A 199 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2421 not shown) Planarity restraints: 2511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 28 " 0.024 2.00e-02 2.50e+03 3.19e-02 1.78e+01 pdb=" CG PHE C 28 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE C 28 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE C 28 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE C 28 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 28 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 28 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 37 " 0.022 2.00e-02 2.50e+03 2.65e-02 1.23e+01 pdb=" CG PHE A 37 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 37 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 37 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 37 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 588 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO E 589 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 589 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 589 " 0.041 5.00e-02 4.00e+02 ... (remaining 2508 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3493 2.78 - 3.31: 13969 3.31 - 3.84: 25606 3.84 - 4.37: 28416 4.37 - 4.90: 47384 Nonbonded interactions: 118868 Sorted by model distance: nonbonded pdb=" OG1 THR A 103 " pdb=" O HIS A 141 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR D 49 " pdb=" O2B ADP D 301 " model vdw 2.255 3.040 nonbonded pdb=" O LEU E 285 " pdb=" OG SER E 289 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR B 12 " pdb=" OE1 GLN B 23 " model vdw 2.269 3.040 nonbonded pdb=" OG SER E 535 " pdb=" OH TYR E 623 " model vdw 2.274 3.040 ... (remaining 118863 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 248 or resid 301)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 248 or resid 301)) selection = (chain 'D' and (resid 2 through 248 or resid 301)) } ncs_group { reference = (chain 'E' and (resid 3 through 309 or resid 521 through 644)) selection = (chain 'F' and (resid 3 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 16 or (resid 17 and (name N or name CA \ or name C or name O or name CB )) or resid 18 through 644)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.520 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.005 0.076 15095 Z= 0.285 Angle : 1.264 17.724 20406 Z= 0.601 Chirality : 0.057 0.316 2424 Planarity : 0.005 0.073 2511 Dihedral : 17.961 114.523 5512 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.85 % Favored : 93.77 % Rotamer: Outliers : 1.06 % Allowed : 33.64 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.16), residues: 1845 helix: -3.29 (0.10), residues: 1042 sheet: -0.37 (0.39), residues: 177 loop : -1.33 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 120 TYR 0.036 0.002 TYR E 18 PHE 0.073 0.002 PHE C 28 TRP 0.017 0.002 TRP E 201 HIS 0.024 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00531 (15095) covalent geometry : angle 1.26395 (20406) hydrogen bonds : bond 0.28848 ( 709) hydrogen bonds : angle 9.54865 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9321 (mmt) cc_final: 0.9112 (tpp) REVERT: C 25 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8136 (tt) REVERT: C 28 PHE cc_start: 0.8820 (t80) cc_final: 0.8339 (t80) REVERT: C 51 LEU cc_start: 0.8960 (tp) cc_final: 0.8705 (tp) REVERT: E 88 GLU cc_start: 0.8352 (pm20) cc_final: 0.8144 (pm20) REVERT: E 284 MET cc_start: 0.8454 (ppp) cc_final: 0.8217 (tmm) REVERT: F 540 ILE cc_start: 0.8750 (tp) cc_final: 0.8373 (tt) outliers start: 17 outliers final: 9 residues processed: 271 average time/residue: 0.0983 time to fit residues: 42.2086 Evaluate side-chains 240 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 230 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 537 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 228 HIS D 204 HIS ** E 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.077801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064588 restraints weight = 59416.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066527 restraints weight = 32649.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067855 restraints weight = 21568.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.068797 restraints weight = 15978.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069393 restraints weight = 12772.018| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15095 Z= 0.127 Angle : 0.722 9.362 20406 Z= 0.351 Chirality : 0.041 0.196 2424 Planarity : 0.004 0.052 2511 Dihedral : 7.408 97.166 2059 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.34 % Favored : 95.45 % Rotamer: Outliers : 3.54 % Allowed : 30.16 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.19), residues: 1845 helix: -1.35 (0.14), residues: 1059 sheet: -0.46 (0.39), residues: 181 loop : -0.88 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 158 TYR 0.016 0.001 TYR D 13 PHE 0.019 0.001 PHE F 538 TRP 0.004 0.001 TRP F 201 HIS 0.007 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00261 (15095) covalent geometry : angle 0.72190 (20406) hydrogen bonds : bond 0.04779 ( 709) hydrogen bonds : angle 5.01766 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8260 (mm-30) REVERT: B 88 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: E 88 GLU cc_start: 0.8731 (pm20) cc_final: 0.8457 (pp20) REVERT: E 262 PHE cc_start: 0.8840 (t80) cc_final: 0.8634 (t80) REVERT: E 540 ILE cc_start: 0.9117 (tp) cc_final: 0.8916 (tp) REVERT: E 562 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9245 (tp) REVERT: F 162 PHE cc_start: 0.8934 (m-10) cc_final: 0.8681 (m-10) REVERT: F 545 MET cc_start: 0.8998 (ppp) cc_final: 0.8727 (ppp) outliers start: 57 outliers final: 24 residues processed: 282 average time/residue: 0.0959 time to fit residues: 43.0263 Evaluate side-chains 236 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 69 PHE Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 570 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 10 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN C 72 GLN C 162 HIS D 16 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 627 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.057564 restraints weight = 63519.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059296 restraints weight = 35358.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060469 restraints weight = 23723.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061250 restraints weight = 17797.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061852 restraints weight = 14570.560| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 15095 Z= 0.397 Angle : 0.906 13.148 20406 Z= 0.460 Chirality : 0.047 0.177 2424 Planarity : 0.005 0.056 2511 Dihedral : 7.112 96.172 2045 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.20 % Favored : 94.53 % Rotamer: Outliers : 6.16 % Allowed : 29.17 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 1845 helix: -0.56 (0.15), residues: 1089 sheet: -0.82 (0.37), residues: 202 loop : -0.78 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 87 TYR 0.027 0.002 TYR D 13 PHE 0.025 0.002 PHE F 538 TRP 0.008 0.001 TRP E 138 HIS 0.006 0.001 HIS F 41 Details of bonding type rmsd covalent geometry : bond 0.00822 (15095) covalent geometry : angle 0.90650 (20406) hydrogen bonds : bond 0.04829 ( 709) hydrogen bonds : angle 5.14572 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 186 time to evaluate : 0.552 Fit side-chains REVERT: B 88 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: B 122 MET cc_start: 0.7691 (mpt) cc_final: 0.7139 (mpt) REVERT: B 185 MET cc_start: 0.9487 (mmt) cc_final: 0.9205 (mmp) REVERT: C 41 MET cc_start: 0.8210 (tpt) cc_final: 0.7642 (tpt) REVERT: D 101 THR cc_start: 0.9650 (OUTLIER) cc_final: 0.9374 (t) REVERT: E 162 PHE cc_start: 0.9576 (OUTLIER) cc_final: 0.9003 (m-10) REVERT: E 181 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: E 252 PHE cc_start: 0.9526 (m-80) cc_final: 0.9052 (m-80) REVERT: E 264 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8786 (tmtt) REVERT: E 528 LEU cc_start: 0.9493 (tt) cc_final: 0.9006 (tp) REVERT: E 532 LEU cc_start: 0.9412 (mt) cc_final: 0.8790 (tt) REVERT: F 1 MET cc_start: 0.7797 (tmm) cc_final: 0.7104 (ttt) REVERT: F 162 PHE cc_start: 0.9082 (m-10) cc_final: 0.8781 (m-10) REVERT: F 551 PHE cc_start: 0.8536 (t80) cc_final: 0.8291 (t80) outliers start: 99 outliers final: 55 residues processed: 269 average time/residue: 0.0929 time to fit residues: 40.1303 Evaluate side-chains 234 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 633 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 171 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.061479 restraints weight = 61259.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063350 restraints weight = 33328.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.064594 restraints weight = 21957.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065476 restraints weight = 16313.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.066116 restraints weight = 13129.792| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15095 Z= 0.130 Angle : 0.712 11.396 20406 Z= 0.344 Chirality : 0.042 0.169 2424 Planarity : 0.003 0.042 2511 Dihedral : 6.389 86.398 2045 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.12 % Favored : 95.66 % Rotamer: Outliers : 4.73 % Allowed : 30.35 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1845 helix: -0.07 (0.16), residues: 1068 sheet: -0.69 (0.38), residues: 199 loop : -0.65 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.014 0.001 TYR C 144 PHE 0.016 0.001 PHE F 538 TRP 0.003 0.001 TRP F 138 HIS 0.006 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00281 (15095) covalent geometry : angle 0.71152 (20406) hydrogen bonds : bond 0.03708 ( 709) hydrogen bonds : angle 4.51429 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 224 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9236 (mm) REVERT: B 88 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: B 122 MET cc_start: 0.7587 (mpt) cc_final: 0.7095 (mpt) REVERT: B 185 MET cc_start: 0.9479 (mmt) cc_final: 0.9204 (mmp) REVERT: C 25 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8434 (tt) REVERT: C 250 ASP cc_start: 0.6587 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: D 25 LEU cc_start: 0.9642 (tp) cc_final: 0.9349 (tp) REVERT: D 101 THR cc_start: 0.9602 (OUTLIER) cc_final: 0.9288 (t) REVERT: E 88 GLU cc_start: 0.8788 (pm20) cc_final: 0.8427 (pp20) REVERT: E 252 PHE cc_start: 0.9497 (m-80) cc_final: 0.8962 (m-80) REVERT: E 528 LEU cc_start: 0.9454 (tt) cc_final: 0.9252 (tt) REVERT: E 532 LEU cc_start: 0.9330 (mt) cc_final: 0.8882 (tt) REVERT: F 1 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7197 (ttt) REVERT: F 69 PHE cc_start: 0.8038 (m-80) cc_final: 0.7792 (m-80) REVERT: F 162 PHE cc_start: 0.9022 (m-10) cc_final: 0.8689 (m-10) REVERT: F 551 PHE cc_start: 0.8470 (t80) cc_final: 0.8221 (t80) outliers start: 76 outliers final: 41 residues processed: 288 average time/residue: 0.1010 time to fit residues: 45.8296 Evaluate side-chains 249 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 113 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.0470 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 HIS ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060690 restraints weight = 61568.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.062557 restraints weight = 33626.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063808 restraints weight = 22269.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064668 restraints weight = 16583.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.065252 restraints weight = 13404.236| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15095 Z= 0.154 Angle : 0.716 11.598 20406 Z= 0.346 Chirality : 0.042 0.205 2424 Planarity : 0.003 0.039 2511 Dihedral : 6.218 89.570 2045 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.88 % Favored : 94.91 % Rotamer: Outliers : 4.85 % Allowed : 31.41 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1845 helix: 0.16 (0.16), residues: 1076 sheet: -0.68 (0.38), residues: 200 loop : -0.54 (0.28), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 158 TYR 0.014 0.001 TYR D 13 PHE 0.018 0.001 PHE F 538 TRP 0.003 0.001 TRP F 138 HIS 0.007 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00333 (15095) covalent geometry : angle 0.71629 (20406) hydrogen bonds : bond 0.03578 ( 709) hydrogen bonds : angle 4.38800 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 213 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9250 (mm) REVERT: A 217 PHE cc_start: 0.8901 (m-80) cc_final: 0.8639 (m-80) REVERT: B 88 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: B 171 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8133 (mm-30) REVERT: B 185 MET cc_start: 0.9465 (mmt) cc_final: 0.9210 (mmp) REVERT: C 25 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8403 (tt) REVERT: C 134 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8617 (tp-100) REVERT: D 25 LEU cc_start: 0.9628 (tp) cc_final: 0.9165 (tp) REVERT: D 76 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8127 (mp) REVERT: D 101 THR cc_start: 0.9645 (OUTLIER) cc_final: 0.9366 (t) REVERT: E 105 MET cc_start: 0.9131 (tmm) cc_final: 0.8906 (tmm) REVERT: E 162 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8962 (m-10) REVERT: E 252 PHE cc_start: 0.9518 (m-80) cc_final: 0.8987 (m-80) REVERT: E 572 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8559 (ptmm) REVERT: F 69 PHE cc_start: 0.8029 (m-80) cc_final: 0.7819 (m-80) REVERT: F 88 GLU cc_start: 0.8444 (mp0) cc_final: 0.8187 (mp0) REVERT: F 162 PHE cc_start: 0.9013 (m-10) cc_final: 0.8642 (m-10) REVERT: F 551 PHE cc_start: 0.8547 (t80) cc_final: 0.8274 (t80) outliers start: 78 outliers final: 52 residues processed: 277 average time/residue: 0.1017 time to fit residues: 44.1231 Evaluate side-chains 256 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 LYS Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 633 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 43 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 123 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.061945 restraints weight = 60925.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063823 restraints weight = 33241.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.065092 restraints weight = 21835.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065920 restraints weight = 16188.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066583 restraints weight = 13109.074| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15095 Z= 0.123 Angle : 0.734 10.405 20406 Z= 0.346 Chirality : 0.042 0.169 2424 Planarity : 0.003 0.037 2511 Dihedral : 5.993 88.391 2045 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.50 % Favored : 95.28 % Rotamer: Outliers : 4.17 % Allowed : 31.65 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1845 helix: 0.30 (0.16), residues: 1076 sheet: -0.63 (0.38), residues: 200 loop : -0.47 (0.28), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.011 0.001 TYR C 144 PHE 0.022 0.001 PHE A 37 TRP 0.002 0.000 TRP E 201 HIS 0.006 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00269 (15095) covalent geometry : angle 0.73447 (20406) hydrogen bonds : bond 0.03367 ( 709) hydrogen bonds : angle 4.26374 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9235 (mm) REVERT: A 59 ASP cc_start: 0.7845 (t0) cc_final: 0.7623 (t0) REVERT: A 217 PHE cc_start: 0.8893 (m-80) cc_final: 0.8608 (m-80) REVERT: B 67 MET cc_start: 0.8485 (tpp) cc_final: 0.8053 (tpp) REVERT: B 122 MET cc_start: 0.7530 (mpt) cc_final: 0.7050 (mpt) REVERT: B 171 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 185 MET cc_start: 0.9498 (mmt) cc_final: 0.9248 (mmp) REVERT: C 25 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8414 (tt) REVERT: C 84 PHE cc_start: 0.9182 (t80) cc_final: 0.8964 (t80) REVERT: D 25 LEU cc_start: 0.9643 (tp) cc_final: 0.9338 (tp) REVERT: D 76 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8219 (mp) REVERT: D 101 THR cc_start: 0.9611 (OUTLIER) cc_final: 0.9314 (t) REVERT: E 105 MET cc_start: 0.9159 (tmm) cc_final: 0.8927 (tmm) REVERT: E 162 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8918 (m-10) REVERT: E 252 PHE cc_start: 0.9531 (m-80) cc_final: 0.9005 (m-80) REVERT: E 572 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8532 (ptmm) REVERT: F 69 PHE cc_start: 0.7960 (m-80) cc_final: 0.7734 (m-80) REVERT: F 88 GLU cc_start: 0.8451 (mp0) cc_final: 0.8165 (mp0) REVERT: F 110 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8807 (tm-30) REVERT: F 274 MET cc_start: 0.8939 (mmm) cc_final: 0.8734 (mmp) REVERT: F 551 PHE cc_start: 0.8504 (t80) cc_final: 0.8264 (t80) outliers start: 67 outliers final: 44 residues processed: 277 average time/residue: 0.0977 time to fit residues: 43.1482 Evaluate side-chains 256 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 572 LYS Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 570 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 142 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059050 restraints weight = 61498.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.060850 restraints weight = 33953.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.062050 restraints weight = 22684.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062904 restraints weight = 17059.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063452 restraints weight = 13839.905| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15095 Z= 0.225 Angle : 0.778 9.712 20406 Z= 0.378 Chirality : 0.044 0.251 2424 Planarity : 0.004 0.040 2511 Dihedral : 6.169 91.594 2045 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.15 % Favored : 94.63 % Rotamer: Outliers : 5.53 % Allowed : 30.72 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1845 helix: 0.35 (0.16), residues: 1082 sheet: -0.67 (0.38), residues: 198 loop : -0.60 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 85 TYR 0.016 0.001 TYR D 13 PHE 0.020 0.002 PHE F 538 TRP 0.004 0.001 TRP F 138 HIS 0.005 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00480 (15095) covalent geometry : angle 0.77776 (20406) hydrogen bonds : bond 0.03696 ( 709) hydrogen bonds : angle 4.42886 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 200 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9273 (mm) REVERT: B 62 THR cc_start: 0.9067 (m) cc_final: 0.8682 (p) REVERT: B 67 MET cc_start: 0.8567 (tpp) cc_final: 0.8199 (tpp) REVERT: B 88 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8221 (mm-30) REVERT: B 122 MET cc_start: 0.7787 (mpt) cc_final: 0.7314 (mpt) REVERT: B 185 MET cc_start: 0.9433 (mmt) cc_final: 0.9177 (mmp) REVERT: C 25 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8463 (tt) REVERT: C 28 PHE cc_start: 0.8959 (t80) cc_final: 0.8479 (t80) REVERT: C 84 PHE cc_start: 0.9148 (t80) cc_final: 0.8927 (t80) REVERT: C 134 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8689 (tp-100) REVERT: D 25 LEU cc_start: 0.9600 (tp) cc_final: 0.9107 (tp) REVERT: D 76 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8229 (mp) REVERT: D 101 THR cc_start: 0.9670 (OUTLIER) cc_final: 0.9412 (t) REVERT: D 207 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9074 (p) REVERT: E 162 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9059 (m-10) REVERT: E 252 PHE cc_start: 0.9526 (m-80) cc_final: 0.9002 (m-80) REVERT: E 263 TYR cc_start: 0.8957 (m-10) cc_final: 0.8752 (m-10) REVERT: E 268 ILE cc_start: 0.9524 (tp) cc_final: 0.9321 (tp) REVERT: E 572 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8630 (ptmm) REVERT: F 69 PHE cc_start: 0.7935 (m-80) cc_final: 0.7683 (m-80) REVERT: F 88 GLU cc_start: 0.8538 (mp0) cc_final: 0.7992 (mp0) REVERT: F 110 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8863 (tm-30) REVERT: F 226 MET cc_start: 0.7658 (mmt) cc_final: 0.7447 (mmm) REVERT: F 274 MET cc_start: 0.8957 (mmm) cc_final: 0.8631 (mmm) REVERT: F 551 PHE cc_start: 0.8594 (t80) cc_final: 0.8273 (t80) outliers start: 89 outliers final: 64 residues processed: 273 average time/residue: 0.0942 time to fit residues: 41.1049 Evaluate side-chains 267 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 193 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 LYS Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 620 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 140 optimal weight: 0.0970 chunk 143 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061251 restraints weight = 61253.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.063145 restraints weight = 33862.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.064417 restraints weight = 22425.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065296 restraints weight = 16723.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.065909 restraints weight = 13576.081| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15095 Z= 0.126 Angle : 0.744 9.267 20406 Z= 0.350 Chirality : 0.042 0.170 2424 Planarity : 0.003 0.036 2511 Dihedral : 5.865 88.228 2045 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.44 % Favored : 95.34 % Rotamer: Outliers : 4.10 % Allowed : 32.09 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1845 helix: 0.50 (0.16), residues: 1076 sheet: -0.62 (0.39), residues: 201 loop : -0.53 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 4 TYR 0.012 0.001 TYR C 144 PHE 0.019 0.001 PHE A 37 TRP 0.003 0.000 TRP F 138 HIS 0.007 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00274 (15095) covalent geometry : angle 0.74446 (20406) hydrogen bonds : bond 0.03326 ( 709) hydrogen bonds : angle 4.21495 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 210 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9235 (mm) REVERT: A 217 PHE cc_start: 0.8948 (m-80) cc_final: 0.8370 (m-80) REVERT: B 67 MET cc_start: 0.8623 (tpp) cc_final: 0.8215 (tpp) REVERT: B 122 MET cc_start: 0.7683 (mpt) cc_final: 0.7268 (mpt) REVERT: B 185 MET cc_start: 0.9427 (mmt) cc_final: 0.9205 (mmp) REVERT: C 13 TYR cc_start: 0.9120 (m-10) cc_final: 0.8874 (m-10) REVERT: C 25 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8430 (tt) REVERT: C 28 PHE cc_start: 0.8969 (t80) cc_final: 0.8486 (t80) REVERT: C 134 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8551 (tp-100) REVERT: D 25 LEU cc_start: 0.9632 (tp) cc_final: 0.9325 (tp) REVERT: D 76 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8371 (mp) REVERT: D 101 THR cc_start: 0.9626 (OUTLIER) cc_final: 0.9358 (t) REVERT: E 50 TYR cc_start: 0.8162 (t80) cc_final: 0.7788 (t80) REVERT: E 162 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8846 (m-10) REVERT: E 181 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: E 226 MET cc_start: 0.7452 (mmt) cc_final: 0.7228 (mmm) REVERT: F 69 PHE cc_start: 0.7991 (m-80) cc_final: 0.7773 (m-80) REVERT: F 88 GLU cc_start: 0.8503 (mp0) cc_final: 0.7947 (mp0) REVERT: F 110 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8834 (tm-30) REVERT: F 134 MET cc_start: 0.8982 (tmm) cc_final: 0.8757 (tmm) REVERT: F 551 PHE cc_start: 0.8546 (t80) cc_final: 0.8268 (t80) outliers start: 66 outliers final: 46 residues processed: 265 average time/residue: 0.0931 time to fit residues: 39.5543 Evaluate side-chains 257 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 162 PHE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 570 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 69 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.071924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058742 restraints weight = 62729.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.060535 restraints weight = 34503.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061729 restraints weight = 22978.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.062590 restraints weight = 17270.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.063136 restraints weight = 13998.631| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15095 Z= 0.236 Angle : 0.806 10.096 20406 Z= 0.390 Chirality : 0.044 0.183 2424 Planarity : 0.004 0.042 2511 Dihedral : 6.095 91.604 2045 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.31 % Favored : 94.47 % Rotamer: Outliers : 4.29 % Allowed : 32.40 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1845 helix: 0.42 (0.16), residues: 1079 sheet: -0.67 (0.38), residues: 199 loop : -0.67 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 85 TYR 0.016 0.001 TYR C 144 PHE 0.020 0.002 PHE F 538 TRP 0.005 0.001 TRP F 138 HIS 0.005 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00504 (15095) covalent geometry : angle 0.80650 (20406) hydrogen bonds : bond 0.03722 ( 709) hydrogen bonds : angle 4.47199 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 195 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9301 (mm) REVERT: B 62 THR cc_start: 0.9086 (m) cc_final: 0.8709 (p) REVERT: B 122 MET cc_start: 0.7875 (mpt) cc_final: 0.7447 (mpt) REVERT: B 185 MET cc_start: 0.9436 (mmt) cc_final: 0.9189 (mmp) REVERT: C 25 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8518 (tt) REVERT: C 28 PHE cc_start: 0.9005 (t80) cc_final: 0.8597 (t80) REVERT: C 134 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8732 (tp-100) REVERT: D 25 LEU cc_start: 0.9581 (tp) cc_final: 0.9146 (tp) REVERT: D 76 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8371 (mp) REVERT: D 77 LYS cc_start: 0.8895 (tptt) cc_final: 0.8654 (tptp) REVERT: D 101 THR cc_start: 0.9664 (OUTLIER) cc_final: 0.9418 (t) REVERT: E 23 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9132 (tm) REVERT: E 50 TYR cc_start: 0.8365 (t80) cc_final: 0.8040 (t80) REVERT: E 112 LEU cc_start: 0.9100 (tt) cc_final: 0.8900 (tp) REVERT: E 162 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9078 (m-10) REVERT: E 181 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: E 252 PHE cc_start: 0.9548 (m-80) cc_final: 0.9067 (m-80) REVERT: E 545 MET cc_start: 0.8857 (ppp) cc_final: 0.8611 (ppp) REVERT: F 69 PHE cc_start: 0.8088 (m-80) cc_final: 0.7843 (m-80) REVERT: F 88 GLU cc_start: 0.8599 (mp0) cc_final: 0.8117 (mp0) REVERT: F 110 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8858 (tm-30) REVERT: F 226 MET cc_start: 0.7647 (mmt) cc_final: 0.7426 (mmm) REVERT: F 274 MET cc_start: 0.9303 (mmp) cc_final: 0.9044 (mmm) REVERT: F 551 PHE cc_start: 0.8612 (t80) cc_final: 0.8292 (t80) outliers start: 69 outliers final: 55 residues processed: 250 average time/residue: 0.0980 time to fit residues: 39.2862 Evaluate side-chains 254 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 190 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 146 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.074986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.061600 restraints weight = 60374.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.063483 restraints weight = 33088.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.064748 restraints weight = 21955.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065614 restraints weight = 16404.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066266 restraints weight = 13340.146| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15095 Z= 0.119 Angle : 0.764 10.554 20406 Z= 0.357 Chirality : 0.042 0.172 2424 Planarity : 0.003 0.035 2511 Dihedral : 5.817 87.529 2045 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.44 % Favored : 95.34 % Rotamer: Outliers : 3.67 % Allowed : 32.71 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1845 helix: 0.53 (0.16), residues: 1082 sheet: -0.58 (0.39), residues: 201 loop : -0.46 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.014 0.001 TYR C 144 PHE 0.029 0.001 PHE A 28 TRP 0.003 0.000 TRP F 138 HIS 0.007 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00257 (15095) covalent geometry : angle 0.76388 (20406) hydrogen bonds : bond 0.03276 ( 709) hydrogen bonds : angle 4.21377 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.8214 (tpp) cc_final: 0.7937 (tpp) REVERT: A 54 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9250 (mm) REVERT: B 67 MET cc_start: 0.8157 (tpp) cc_final: 0.7762 (tpp) REVERT: B 122 MET cc_start: 0.7727 (mpt) cc_final: 0.7368 (mpt) REVERT: B 185 MET cc_start: 0.9439 (mmt) cc_final: 0.9220 (mmp) REVERT: C 25 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8481 (tt) REVERT: C 134 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8598 (tp-100) REVERT: D 25 LEU cc_start: 0.9624 (tp) cc_final: 0.9325 (tp) REVERT: D 76 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8449 (mp) REVERT: D 77 LYS cc_start: 0.8903 (tptt) cc_final: 0.8621 (tptp) REVERT: D 101 THR cc_start: 0.9606 (OUTLIER) cc_final: 0.9344 (t) REVERT: E 50 TYR cc_start: 0.8311 (t80) cc_final: 0.7959 (t80) REVERT: E 162 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8844 (m-10) REVERT: E 181 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: E 226 MET cc_start: 0.7492 (mmp) cc_final: 0.7282 (mmm) REVERT: E 572 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8534 (ptmm) REVERT: F 69 PHE cc_start: 0.7965 (m-80) cc_final: 0.7735 (m-80) REVERT: F 88 GLU cc_start: 0.8527 (mp0) cc_final: 0.8054 (mp0) REVERT: F 110 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8871 (tm-30) REVERT: F 274 MET cc_start: 0.9276 (mmp) cc_final: 0.8979 (mmm) REVERT: F 551 PHE cc_start: 0.8560 (t80) cc_final: 0.8299 (t80) outliers start: 59 outliers final: 46 residues processed: 260 average time/residue: 0.0927 time to fit residues: 38.7902 Evaluate side-chains 259 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 LYS Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 570 THR Chi-restraints excluded: chain F residue 620 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 96 optimal weight: 6.9990 chunk 13 optimal weight: 0.0770 chunk 52 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060184 restraints weight = 61098.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.062003 restraints weight = 33624.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.063236 restraints weight = 22347.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064093 restraints weight = 16723.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.064617 restraints weight = 13573.297| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15095 Z= 0.179 Angle : 0.778 10.278 20406 Z= 0.370 Chirality : 0.043 0.167 2424 Planarity : 0.003 0.035 2511 Dihedral : 5.827 89.390 2045 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.88 % Favored : 94.91 % Rotamer: Outliers : 4.10 % Allowed : 32.40 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1845 helix: 0.52 (0.16), residues: 1091 sheet: -0.62 (0.38), residues: 201 loop : -0.59 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.014 0.001 TYR C 144 PHE 0.029 0.001 PHE A 28 TRP 0.004 0.001 TRP F 138 HIS 0.008 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00390 (15095) covalent geometry : angle 0.77842 (20406) hydrogen bonds : bond 0.03434 ( 709) hydrogen bonds : angle 4.29330 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.39 seconds wall clock time: 37 minutes 30.09 seconds (2250.09 seconds total)