Starting phenix.real_space_refine on Thu Sep 18 09:11:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yar_39105/09_2025/8yar_39105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yar_39105/09_2025/8yar_39105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yar_39105/09_2025/8yar_39105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yar_39105/09_2025/8yar_39105.map" model { file = "/net/cci-nas-00/data/ceres_data/8yar_39105/09_2025/8yar_39105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yar_39105/09_2025/8yar_39105.cif" } resolution = 3.6 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= -0.001 sd= 0.040 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 15 5.49 5 S 105 5.16 5 C 9730 2.51 5 N 2646 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15482 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3425 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 183} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3350 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3338 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3349 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 406} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 373 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.89, per 1000 atoms: 0.25 Number of scatterers: 15482 At special positions: 0 Unit cell: (115.54, 109.18, 124.02, 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 105 16.00 P 15 15.00 O 2986 8.00 N 2646 7.00 C 9730 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: 1.41 Conformation dependent library (CDL) restraints added in 739.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 12 sheets defined 52.9% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.064A pdb=" N GLY B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 4.210A pdb=" N PHE B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.816A pdb=" N ILE B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 85 removed outlier: 4.663A pdb=" N SER B 85 " --> pdb=" O THR B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 85' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 129 removed outlier: 4.103A pdb=" N ILE B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 4.100A pdb=" N GLU B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.820A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.829A pdb=" N LEU B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.665A pdb=" N TYR B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.843A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 338 removed outlier: 3.583A pdb=" N VAL B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 401 removed outlier: 4.023A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.814A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 437 removed outlier: 3.833A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 20 through 26 Processing helix chain 'C' and resid 31 through 50 removed outlier: 3.928A pdb=" N ALA C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.672A pdb=" N GLN C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 41 through 46 removed outlier: 4.491A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 78 removed outlier: 3.937A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 125 removed outlier: 4.230A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 4.117A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.641A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.625A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 4.023A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 260 through 263 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.632A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.626A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 removed outlier: 4.225A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 426 removed outlier: 3.597A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 48 through 51 removed outlier: 4.272A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.462A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 85 removed outlier: 4.649A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 85' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 111 through 129 removed outlier: 4.324A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.535A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.677A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 241 removed outlier: 3.529A pdb=" N LEU E 227 " --> pdb=" O SER E 223 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.579A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.991A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.852A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 384 through 400 removed outlier: 3.867A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.180A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 removed outlier: 4.063A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 436 " --> pdb=" O TYR E 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.729A pdb=" N ARG F 46 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE F 47 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASN F 48 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL F 49 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 79 removed outlier: 3.909A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.557A pdb=" N PHE F 85 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 107 through 126 removed outlier: 4.191A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.901A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 214 Processing helix chain 'F' and resid 221 through 237 Processing helix chain 'F' and resid 237 through 242 removed outlier: 3.970A pdb=" N ARG F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 removed outlier: 3.542A pdb=" N VAL F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 280 removed outlier: 4.497A pdb=" N GLN F 280 " --> pdb=" O ARG F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 322 through 337 Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 374 through 391 removed outlier: 3.705A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 removed outlier: 3.989A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 426 removed outlier: 3.656A pdb=" N THR F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 232 Processing helix chain 'I' and resid 247 through 256 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.793A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N MET B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 68 " --> pdb=" O HIS B 8 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER B 140 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN B 133 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N PHE B 135 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE B 171 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N HIS B 139 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 166 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE B 202 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU B 168 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL B 204 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER B 170 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'B' and resid 271 through 272 removed outlier: 3.625A pdb=" N CYS B 376 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LYS B 352 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU B 317 " --> pdb=" O GLY B 354 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASN B 356 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE B 319 " --> pdb=" O ASN B 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.605A pdb=" N LYS C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE C 83 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS C 76 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS C 85 " --> pdb=" O TRP C 74 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TRP C 74 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU C 87 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 72 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG C 89 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR C 70 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY C 91 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLN C 68 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 3 removed outlier: 8.162A pdb=" N LYS C 85 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL C 117 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU C 87 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE C 115 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG C 89 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 93 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 109 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 95 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 107 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA C 146 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N MET C 110 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP C 148 " --> pdb=" O MET C 110 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE C 112 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.256A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.647A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 14.005A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 315 " --> pdb=" O LYS D 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA8, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.929A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N MET E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER E 140 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN E 133 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'E' and resid 271 through 272 Processing sheet with id=AB2, first strand: chain 'F' and resid 90 through 92 removed outlier: 7.889A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS F 6 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU F 3 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLN F 134 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL F 5 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR F 136 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE F 7 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N SER F 138 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N ALA F 9 " --> pdb=" O SER F 138 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET F 164 " --> pdb=" O SER F 198 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR F 166 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE F 202 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER F 168 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 51 through 53 728 hydrogen bonds defined for protein. 2100 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: 2.84 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2999 1.33 - 1.45: 3996 1.45 - 1.57: 8650 1.57 - 1.69: 20 1.69 - 1.82: 175 Bond restraints: 15840 Sorted by residual: bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.593 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O5' G2P D 501 " pdb=" PA G2P D 501 " ideal model delta sigma weight residual 1.656 1.581 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O5' G2P F 501 " pdb=" PA G2P F 501 " ideal model delta sigma weight residual 1.656 1.581 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CA SER E 147 " pdb=" CB SER E 147 " ideal model delta sigma weight residual 1.537 1.474 0.063 1.76e-02 3.23e+03 1.30e+01 ... (remaining 15835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 21216 2.47 - 4.94: 257 4.94 - 7.41: 33 7.41 - 9.88: 19 9.88 - 12.35: 8 Bond angle restraints: 21533 Sorted by residual: angle pdb=" P1A ACO C 301 " pdb=" O3A ACO C 301 " pdb=" P2A ACO C 301 " ideal model delta sigma weight residual 136.83 128.07 8.76 1.00e+00 1.00e+00 7.68e+01 angle pdb=" C9P ACO C 301 " pdb=" CAP ACO C 301 " pdb=" CBP ACO C 301 " ideal model delta sigma weight residual 114.53 121.00 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" C3B ACO C 301 " pdb=" O3B ACO C 301 " pdb=" P3B ACO C 301 " ideal model delta sigma weight residual 121.12 115.38 5.74 1.00e+00 1.00e+00 3.29e+01 angle pdb=" C LYS C 160 " pdb=" CA LYS C 160 " pdb=" CB LYS C 160 " ideal model delta sigma weight residual 110.85 101.77 9.08 1.70e+00 3.46e-01 2.85e+01 angle pdb=" C PHE D 212 " pdb=" N ARG D 213 " pdb=" CA ARG D 213 " ideal model delta sigma weight residual 122.42 115.83 6.59 1.55e+00 4.16e-01 1.81e+01 ... (remaining 21528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.18: 9192 32.18 - 64.35: 225 64.35 - 96.53: 38 96.53 - 128.71: 1 128.71 - 160.88: 9 Dihedral angle restraints: 9465 sinusoidal: 3800 harmonic: 5665 Sorted by residual: dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -91.62 160.88 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O5' GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PA GTP B 501 " pdb=" PB GTP B 501 " ideal model delta sinusoidal sigma weight residual 274.12 113.84 160.28 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O3B GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PB GTP E 501 " pdb=" PA GTP E 501 " ideal model delta sinusoidal sigma weight residual -68.92 82.83 -151.75 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 9462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2133 0.074 - 0.147: 214 0.147 - 0.221: 8 0.221 - 0.295: 1 0.295 - 0.369: 2 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CAP ACO C 301 " pdb=" C9P ACO C 301 " pdb=" CBP ACO C 301 " pdb=" OAP ACO C 301 " both_signs ideal model delta sigma weight residual False -2.31 -1.94 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA LYS C 160 " pdb=" N LYS C 160 " pdb=" C LYS C 160 " pdb=" CB LYS C 160 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C3' GTP E 501 " pdb=" C2' GTP E 501 " pdb=" C4' GTP E 501 " pdb=" O3' GTP E 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2355 not shown) Planarity restraints: 2794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO C 301 " 0.239 2.00e-02 2.50e+03 2.00e-01 4.98e+02 pdb=" C5P ACO C 301 " -0.054 2.00e-02 2.50e+03 pdb=" C6P ACO C 301 " 0.160 2.00e-02 2.50e+03 pdb=" N4P ACO C 301 " -0.337 2.00e-02 2.50e+03 pdb=" O5P ACO C 301 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO C 301 " 0.209 2.00e-02 2.50e+03 1.73e-01 3.76e+02 pdb=" C9P ACO C 301 " -0.054 2.00e-02 2.50e+03 pdb=" CAP ACO C 301 " 0.148 2.00e-02 2.50e+03 pdb=" N8P ACO C 301 " -0.285 2.00e-02 2.50e+03 pdb=" O9P ACO C 301 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 107 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C HIS E 107 " 0.056 2.00e-02 2.50e+03 pdb=" O HIS E 107 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR E 108 " -0.019 2.00e-02 2.50e+03 ... (remaining 2791 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2752 2.77 - 3.30: 16019 3.30 - 3.83: 26983 3.83 - 4.37: 31476 4.37 - 4.90: 53656 Nonbonded interactions: 130886 Sorted by model distance: nonbonded pdb=" O THR B 334 " pdb=" OG1 THR B 337 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASN B 186 " pdb=" OH TYR B 408 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR E 399 " pdb=" OE2 GLU E 415 " model vdw 2.247 3.040 nonbonded pdb=" ND2 ASN B 226 " pdb=" OD2 ASP B 367 " model vdw 2.250 3.120 nonbonded pdb=" OG SER D 176 " pdb=" OE2 GLU D 181 " model vdw 2.258 3.040 ... (remaining 130881 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 'B' and (resid 1 through 36 or resid 48 through 112 or (resid 113 and (na \ me N or name CA or name C or name O or name CB )) or resid 114 through 366 or (r \ esid 367 and (name N or name CA or name C or name O or name CB )) or resid 368 t \ hrough 400 or (resid 401 through 403 and (name N or name CA or name C or name O \ or name CB )) or resid 404 through 501)) selection = (chain 'E' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name CB )) or resid 222 through 501)) } ncs_group { reference = (chain 'D' and (resid 1 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB )) or resid 158 through 358 or (resid 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 501)) selection = (chain 'F' and (resid 1 through 173 or (resid 174 and (name N or name CA or name \ C or name O or name CB )) or resid 175 through 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 501)) } 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: 6.430 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.200 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.004 0.125 15840 Z= 0.197 Angle : 0.687 12.351 21533 Z= 0.343 Chirality : 0.044 0.369 2358 Planarity : 0.006 0.200 2794 Dihedral : 15.786 160.885 5827 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.06 % Allowed : 0.06 % Favored : 99.88 % Cbeta Deviations : 0.05 % 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 aren not related in a simple way. whole: 1.04 (0.20), residues: 1946 helix: 1.96 (0.19), residues: 818 sheet: -0.51 (0.30), residues: 307 loop : -0.04 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 40 TYR 0.025 0.001 TYR E 172 PHE 0.023 0.001 PHE C 115 TRP 0.020 0.001 TRP I 263 HIS 0.005 0.001 HIS I 259 Details of bonding type rmsd covalent geometry : bond 0.00371 (15840) covalent geometry : angle 0.68745 (21533) hydrogen bonds : bond 0.16892 ( 726) hydrogen bonds : angle 5.92073 ( 2100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 LEU cc_start: 0.9232 (mp) cc_final: 0.8984 (tt) REVERT: C 44 MET cc_start: 0.9198 (ttm) cc_final: 0.8977 (mtm) REVERT: C 63 ASP cc_start: 0.9459 (t70) cc_final: 0.9205 (p0) REVERT: C 64 HIS cc_start: 0.8469 (t-90) cc_final: 0.8060 (t-90) REVERT: D 215 LEU cc_start: 0.8874 (tp) cc_final: 0.8659 (tp) REVERT: D 233 MET cc_start: 0.8562 (mmt) cc_final: 0.8232 (mmm) REVERT: D 267 MET cc_start: 0.7304 (ttt) cc_final: 0.6915 (ttp) REVERT: F 257 MET cc_start: 0.8687 (mmm) cc_final: 0.8341 (mmm) REVERT: F 406 MET cc_start: 0.8801 (tpt) cc_final: 0.8487 (tpp) REVERT: I 229 ASP cc_start: 0.9339 (m-30) cc_final: 0.9098 (p0) REVERT: I 230 LEU cc_start: 0.9218 (tp) cc_final: 0.8969 (tp) REVERT: I 231 MET cc_start: 0.8649 (ppp) cc_final: 0.8444 (ppp) REVERT: I 252 LYS cc_start: 0.9568 (tttm) cc_final: 0.8948 (ttmt) outliers start: 1 outliers final: 1 residues processed: 169 average time/residue: 0.1381 time to fit residues: 34.7977 Evaluate side-chains 126 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0070 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN F 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.040148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.032974 restraints weight = 113043.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.033957 restraints weight = 67916.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.034671 restraints weight = 47505.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.035164 restraints weight = 35950.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.035515 restraints weight = 29140.783| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15840 Z= 0.137 Angle : 0.591 9.849 21533 Z= 0.301 Chirality : 0.044 0.153 2358 Planarity : 0.004 0.042 2794 Dihedral : 12.951 166.823 2275 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.79 % Allowed : 6.00 % Favored : 93.21 % 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 aren not related in a simple way. whole: 1.02 (0.20), residues: 1946 helix: 1.79 (0.18), residues: 851 sheet: -0.40 (0.30), residues: 314 loop : -0.01 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 320 TYR 0.015 0.001 TYR B 357 PHE 0.016 0.001 PHE C 131 TRP 0.012 0.001 TRP I 263 HIS 0.005 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00282 (15840) covalent geometry : angle 0.59088 (21533) hydrogen bonds : bond 0.04112 ( 726) hydrogen bonds : angle 4.76897 ( 2100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 LEU cc_start: 0.9595 (mp) cc_final: 0.9116 (tt) REVERT: B 294 MET cc_start: 0.9329 (mtp) cc_final: 0.9060 (ptp) REVERT: C 39 ASP cc_start: 0.9210 (m-30) cc_final: 0.8856 (m-30) REVERT: C 61 ILE cc_start: 0.9159 (tp) cc_final: 0.8938 (pt) REVERT: C 66 GLU cc_start: 0.9018 (mp0) cc_final: 0.8767 (mp0) REVERT: D 233 MET cc_start: 0.9101 (mmt) cc_final: 0.8615 (mmm) REVERT: D 299 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8457 (tpp) REVERT: E 86 LEU cc_start: 0.9461 (mt) cc_final: 0.9119 (mt) REVERT: E 172 TYR cc_start: 0.7581 (t80) cc_final: 0.7337 (t80) REVERT: E 377 MET cc_start: 0.8718 (tmm) cc_final: 0.8380 (tmm) REVERT: E 398 MET cc_start: 0.9078 (ttm) cc_final: 0.8736 (tmm) REVERT: E 413 MET cc_start: 0.8290 (tmm) cc_final: 0.7817 (tmm) REVERT: F 299 MET cc_start: 0.8743 (tpt) cc_final: 0.7788 (tpt) REVERT: F 406 MET cc_start: 0.9214 (tpt) cc_final: 0.8715 (tpp) REVERT: I 229 ASP cc_start: 0.9392 (m-30) cc_final: 0.9056 (p0) outliers start: 13 outliers final: 6 residues processed: 142 average time/residue: 0.1349 time to fit residues: 28.7654 Evaluate side-chains 134 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 323 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 141 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 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 = 0.3225 r_free = 0.3225 target = 0.039958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.032656 restraints weight = 115037.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.033698 restraints weight = 68234.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.034432 restraints weight = 46811.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.034947 restraints weight = 35338.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.035308 restraints weight = 28561.346| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15840 Z= 0.129 Angle : 0.553 7.034 21533 Z= 0.279 Chirality : 0.042 0.156 2358 Planarity : 0.004 0.084 2794 Dihedral : 12.409 165.373 2275 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.79 % Allowed : 8.07 % Favored : 91.15 % 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 aren not related in a simple way. whole: 1.00 (0.20), residues: 1946 helix: 1.82 (0.18), residues: 853 sheet: -0.56 (0.31), residues: 291 loop : -0.03 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 156 TYR 0.014 0.001 TYR D 106 PHE 0.013 0.001 PHE C 131 TRP 0.015 0.001 TRP I 263 HIS 0.004 0.001 HIS F 227 Details of bonding type rmsd covalent geometry : bond 0.00275 (15840) covalent geometry : angle 0.55279 (21533) hydrogen bonds : bond 0.03743 ( 726) hydrogen bonds : angle 4.49482 ( 2100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 MET cc_start: 0.9364 (mmm) cc_final: 0.8931 (ttp) REVERT: B 286 LEU cc_start: 0.9651 (mp) cc_final: 0.9208 (tt) REVERT: B 294 MET cc_start: 0.9373 (mtp) cc_final: 0.9111 (ptp) REVERT: B 413 MET cc_start: 0.8650 (tpp) cc_final: 0.7986 (tpp) REVERT: C 39 ASP cc_start: 0.9168 (m-30) cc_final: 0.8826 (m-30) REVERT: C 44 MET cc_start: 0.9216 (ttm) cc_final: 0.9009 (mtm) REVERT: C 64 HIS cc_start: 0.8914 (t-90) cc_final: 0.8473 (t-90) REVERT: C 66 GLU cc_start: 0.9216 (mp0) cc_final: 0.8930 (mp0) REVERT: C 133 GLU cc_start: 0.8501 (pp20) cc_final: 0.8212 (pp20) REVERT: C 134 MET cc_start: 0.9515 (ptt) cc_final: 0.9136 (ptm) REVERT: D 233 MET cc_start: 0.9163 (mmt) cc_final: 0.8711 (mmm) REVERT: D 267 MET cc_start: 0.7950 (ttp) cc_final: 0.7722 (ttp) REVERT: D 299 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8502 (tpp) REVERT: D 363 MET cc_start: 0.8911 (ptt) cc_final: 0.8687 (pmm) REVERT: D 403 MET cc_start: 0.8142 (tpp) cc_final: 0.7911 (tpp) REVERT: E 86 LEU cc_start: 0.9541 (mt) cc_final: 0.9177 (mt) REVERT: E 377 MET cc_start: 0.8681 (tmm) cc_final: 0.8215 (tmm) REVERT: E 398 MET cc_start: 0.9104 (ttm) cc_final: 0.8684 (tmm) REVERT: E 413 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7554 (tmm) REVERT: F 257 MET cc_start: 0.9229 (mmm) cc_final: 0.8780 (mmm) REVERT: F 267 MET cc_start: 0.8076 (ptm) cc_final: 0.7859 (ttp) REVERT: F 299 MET cc_start: 0.8537 (tpt) cc_final: 0.8231 (mmm) REVERT: F 406 MET cc_start: 0.9236 (tpt) cc_final: 0.8731 (tpp) REVERT: I 219 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6143 (ptp90) REVERT: I 232 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8727 (mmp80) outliers start: 13 outliers final: 7 residues processed: 142 average time/residue: 0.1279 time to fit residues: 27.8831 Evaluate side-chains 137 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain I residue 219 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN F 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.039500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032225 restraints weight = 115771.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.033291 restraints weight = 69414.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.034017 restraints weight = 47341.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.034515 restraints weight = 35820.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.034856 restraints weight = 29008.341| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15840 Z= 0.147 Angle : 0.548 7.133 21533 Z= 0.277 Chirality : 0.042 0.144 2358 Planarity : 0.004 0.049 2794 Dihedral : 11.991 166.464 2275 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.39 % Allowed : 9.28 % Favored : 89.33 % 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 aren not related in a simple way. whole: 1.00 (0.20), residues: 1946 helix: 1.82 (0.18), residues: 860 sheet: -0.61 (0.30), residues: 295 loop : -0.01 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 17 TYR 0.011 0.001 TYR B 432 PHE 0.010 0.001 PHE F 200 TRP 0.021 0.001 TRP I 263 HIS 0.006 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00307 (15840) covalent geometry : angle 0.54780 (21533) hydrogen bonds : bond 0.03524 ( 726) hydrogen bonds : angle 4.31004 ( 2100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.9415 (tp30) cc_final: 0.9061 (tm-30) REVERT: B 286 LEU cc_start: 0.9630 (mp) cc_final: 0.9359 (tt) REVERT: B 290 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8750 (pt0) REVERT: B 294 MET cc_start: 0.9354 (mtp) cc_final: 0.9123 (ptp) REVERT: C 39 ASP cc_start: 0.9115 (m-30) cc_final: 0.8755 (m-30) REVERT: C 44 MET cc_start: 0.9231 (ttm) cc_final: 0.9030 (mtm) REVERT: C 66 GLU cc_start: 0.9232 (mp0) cc_final: 0.8981 (mp0) REVERT: D 147 MET cc_start: 0.9459 (ttm) cc_final: 0.9087 (tpt) REVERT: D 267 MET cc_start: 0.8230 (ttp) cc_final: 0.8021 (ttp) REVERT: D 363 MET cc_start: 0.8916 (ptt) cc_final: 0.8706 (pmm) REVERT: E 86 LEU cc_start: 0.9483 (mt) cc_final: 0.9174 (mt) REVERT: E 377 MET cc_start: 0.8703 (tmm) cc_final: 0.8198 (tmm) REVERT: F 147 MET cc_start: 0.9375 (mmm) cc_final: 0.8970 (mmm) REVERT: F 406 MET cc_start: 0.9268 (tpt) cc_final: 0.8838 (tpp) REVERT: I 229 ASP cc_start: 0.9469 (m-30) cc_final: 0.9001 (p0) REVERT: I 230 LEU cc_start: 0.9355 (tp) cc_final: 0.9136 (tp) REVERT: I 232 ARG cc_start: 0.9099 (mmp80) cc_final: 0.8839 (mmp80) outliers start: 23 outliers final: 12 residues processed: 143 average time/residue: 0.1164 time to fit residues: 26.0787 Evaluate side-chains 139 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 323 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 129 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 93 optimal weight: 0.0770 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 0.0670 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.040422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.032992 restraints weight = 115573.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.034082 restraints weight = 68764.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.034834 restraints weight = 47045.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.035360 restraints weight = 35368.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.035737 restraints weight = 28469.435| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15840 Z= 0.096 Angle : 0.549 10.530 21533 Z= 0.271 Chirality : 0.042 0.145 2358 Planarity : 0.004 0.046 2794 Dihedral : 11.741 170.728 2275 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.85 % Allowed : 10.13 % Favored : 89.02 % 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 aren not related in a simple way. whole: 1.06 (0.20), residues: 1946 helix: 1.83 (0.18), residues: 859 sheet: -0.55 (0.31), residues: 291 loop : 0.05 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 261 TYR 0.010 0.001 TYR B 357 PHE 0.016 0.001 PHE C 181 TRP 0.022 0.001 TRP I 263 HIS 0.006 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00207 (15840) covalent geometry : angle 0.54894 (21533) hydrogen bonds : bond 0.03354 ( 726) hydrogen bonds : angle 4.17237 ( 2100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.9413 (tp30) cc_final: 0.9059 (tm-30) REVERT: B 286 LEU cc_start: 0.9628 (mp) cc_final: 0.9326 (tt) REVERT: B 294 MET cc_start: 0.9360 (mtp) cc_final: 0.9098 (ptp) REVERT: B 357 TYR cc_start: 0.8304 (m-80) cc_final: 0.7890 (m-80) REVERT: B 377 MET cc_start: 0.8499 (ttt) cc_final: 0.7859 (tmm) REVERT: B 413 MET cc_start: 0.8528 (tpp) cc_final: 0.7852 (tpp) REVERT: C 39 ASP cc_start: 0.9078 (m-30) cc_final: 0.8673 (m-30) REVERT: C 64 HIS cc_start: 0.9074 (t-90) cc_final: 0.8725 (t-90) REVERT: C 66 GLU cc_start: 0.9275 (mp0) cc_final: 0.8936 (mp0) REVERT: C 106 MET cc_start: 0.8920 (tmm) cc_final: 0.8652 (tpt) REVERT: C 134 MET cc_start: 0.9539 (ptt) cc_final: 0.9323 (ptt) REVERT: D 147 MET cc_start: 0.9433 (ttm) cc_final: 0.9168 (tpt) REVERT: D 233 MET cc_start: 0.9092 (mmp) cc_final: 0.8440 (mmm) REVERT: D 363 MET cc_start: 0.8953 (ptt) cc_final: 0.8695 (pmm) REVERT: E 86 LEU cc_start: 0.9568 (mt) cc_final: 0.9255 (mt) REVERT: E 377 MET cc_start: 0.8697 (tmm) cc_final: 0.8100 (tmm) REVERT: F 147 MET cc_start: 0.9457 (mmm) cc_final: 0.9057 (mmm) REVERT: F 257 MET cc_start: 0.9407 (mmm) cc_final: 0.9138 (mmm) REVERT: F 299 MET cc_start: 0.8203 (mmm) cc_final: 0.7679 (mmm) REVERT: F 406 MET cc_start: 0.9280 (tpt) cc_final: 0.8730 (tpp) REVERT: I 229 ASP cc_start: 0.9352 (m-30) cc_final: 0.8904 (p0) REVERT: I 232 ARG cc_start: 0.9067 (mmp80) cc_final: 0.8780 (mmp80) outliers start: 14 outliers final: 8 residues processed: 142 average time/residue: 0.1222 time to fit residues: 27.1724 Evaluate side-chains 138 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 323 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN F 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.039056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.031840 restraints weight = 116764.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.032884 restraints weight = 69413.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.033588 restraints weight = 47810.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.034074 restraints weight = 36185.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.034414 restraints weight = 29313.390| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15840 Z= 0.188 Angle : 0.577 8.870 21533 Z= 0.289 Chirality : 0.042 0.155 2358 Planarity : 0.004 0.039 2794 Dihedral : 11.716 165.803 2275 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.15 % Allowed : 10.67 % Favored : 88.17 % 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 aren not related in a simple way. whole: 1.04 (0.20), residues: 1946 helix: 1.83 (0.18), residues: 861 sheet: -0.54 (0.31), residues: 279 loop : -0.00 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 17 TYR 0.022 0.001 TYR D 183 PHE 0.011 0.001 PHE F 260 TRP 0.025 0.001 TRP I 263 HIS 0.006 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00391 (15840) covalent geometry : angle 0.57740 (21533) hydrogen bonds : bond 0.03506 ( 726) hydrogen bonds : angle 4.25344 ( 2100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.9478 (tp30) cc_final: 0.9111 (tm-30) REVERT: B 286 LEU cc_start: 0.9725 (mp) cc_final: 0.9322 (tt) REVERT: B 294 MET cc_start: 0.9355 (mtp) cc_final: 0.9136 (ptp) REVERT: B 357 TYR cc_start: 0.8461 (m-80) cc_final: 0.8056 (m-80) REVERT: B 377 MET cc_start: 0.8499 (ttt) cc_final: 0.7915 (tmm) REVERT: C 39 ASP cc_start: 0.9047 (m-30) cc_final: 0.8690 (m-30) REVERT: C 64 HIS cc_start: 0.9168 (t-90) cc_final: 0.8747 (t-90) REVERT: C 66 GLU cc_start: 0.9324 (mp0) cc_final: 0.8966 (mp0) REVERT: D 147 MET cc_start: 0.9496 (ttm) cc_final: 0.9035 (tpt) REVERT: D 299 MET cc_start: 0.8601 (tpp) cc_final: 0.8146 (tpp) REVERT: D 403 MET cc_start: 0.8076 (tpp) cc_final: 0.7848 (tpp) REVERT: E 86 LEU cc_start: 0.9512 (mt) cc_final: 0.9204 (mt) REVERT: E 377 MET cc_start: 0.8708 (tmm) cc_final: 0.8458 (tmm) REVERT: E 398 MET cc_start: 0.9098 (ttm) cc_final: 0.8767 (ttm) REVERT: F 299 MET cc_start: 0.8121 (mmm) cc_final: 0.6645 (mmm) REVERT: F 406 MET cc_start: 0.9283 (tpt) cc_final: 0.8874 (tpp) REVERT: I 232 ARG cc_start: 0.9074 (mmp80) cc_final: 0.8753 (mmp80) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.1199 time to fit residues: 26.6541 Evaluate side-chains 141 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS E 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.039184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.031992 restraints weight = 116054.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.033026 restraints weight = 68515.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.033725 restraints weight = 47132.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.034212 restraints weight = 35714.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.034547 restraints weight = 29004.193| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15840 Z= 0.155 Angle : 0.578 9.750 21533 Z= 0.286 Chirality : 0.042 0.143 2358 Planarity : 0.004 0.045 2794 Dihedral : 11.650 167.277 2275 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.03 % Allowed : 11.70 % Favored : 87.27 % 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 aren not related in a simple way. whole: 1.01 (0.20), residues: 1946 helix: 1.81 (0.18), residues: 860 sheet: -0.53 (0.31), residues: 280 loop : -0.03 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 261 TYR 0.018 0.001 TYR D 183 PHE 0.010 0.001 PHE F 260 TRP 0.025 0.001 TRP I 263 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00328 (15840) covalent geometry : angle 0.57775 (21533) hydrogen bonds : bond 0.03494 ( 726) hydrogen bonds : angle 4.25686 ( 2100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.9428 (tp30) cc_final: 0.9136 (tp30) REVERT: B 286 LEU cc_start: 0.9705 (mp) cc_final: 0.9326 (tt) REVERT: B 357 TYR cc_start: 0.8394 (m-80) cc_final: 0.8008 (m-80) REVERT: B 377 MET cc_start: 0.8423 (ttt) cc_final: 0.7860 (tmm) REVERT: B 413 MET cc_start: 0.8446 (tpp) cc_final: 0.7778 (tpp) REVERT: C 39 ASP cc_start: 0.9057 (m-30) cc_final: 0.8734 (m-30) REVERT: C 44 MET cc_start: 0.9225 (ttm) cc_final: 0.8985 (mtm) REVERT: C 64 HIS cc_start: 0.9188 (t-90) cc_final: 0.8753 (t-90) REVERT: C 66 GLU cc_start: 0.9342 (mp0) cc_final: 0.8956 (mp0) REVERT: D 147 MET cc_start: 0.9500 (ttm) cc_final: 0.8997 (tpt) REVERT: D 233 MET cc_start: 0.9089 (mmt) cc_final: 0.8615 (mmm) REVERT: D 403 MET cc_start: 0.7955 (tpp) cc_final: 0.7705 (tpp) REVERT: E 86 LEU cc_start: 0.9535 (mt) cc_final: 0.9221 (mt) REVERT: E 377 MET cc_start: 0.8718 (tmm) cc_final: 0.8480 (tmm) REVERT: F 147 MET cc_start: 0.9298 (mmm) cc_final: 0.8552 (ptm) REVERT: F 406 MET cc_start: 0.9273 (tpt) cc_final: 0.8862 (tpp) REVERT: I 229 ASP cc_start: 0.9336 (m-30) cc_final: 0.8891 (p0) REVERT: I 232 ARG cc_start: 0.9070 (mmp80) cc_final: 0.8821 (mmp80) REVERT: I 263 TRP cc_start: 0.8654 (p-90) cc_final: 0.8327 (p-90) outliers start: 17 outliers final: 13 residues processed: 140 average time/residue: 0.1247 time to fit residues: 27.0872 Evaluate side-chains 140 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 323 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 33 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.039825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.032553 restraints weight = 115420.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.033626 restraints weight = 67662.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.034377 restraints weight = 45979.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.034880 restraints weight = 34480.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.035223 restraints weight = 27724.585| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15840 Z= 0.108 Angle : 0.592 9.962 21533 Z= 0.287 Chirality : 0.042 0.200 2358 Planarity : 0.004 0.040 2794 Dihedral : 11.463 170.649 2275 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.67 % Allowed : 12.49 % Favored : 86.84 % 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 aren not related in a simple way. whole: 1.06 (0.20), residues: 1946 helix: 1.79 (0.18), residues: 863 sheet: -0.45 (0.31), residues: 279 loop : 0.03 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 261 TYR 0.015 0.001 TYR D 183 PHE 0.017 0.001 PHE B 255 TRP 0.025 0.001 TRP I 263 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00241 (15840) covalent geometry : angle 0.59217 (21533) hydrogen bonds : bond 0.03371 ( 726) hydrogen bonds : angle 4.15777 ( 2100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.9431 (tp30) cc_final: 0.9108 (tp30) REVERT: B 286 LEU cc_start: 0.9705 (mp) cc_final: 0.9329 (tt) REVERT: B 294 MET cc_start: 0.9232 (ptp) cc_final: 0.8898 (ptm) REVERT: B 357 TYR cc_start: 0.8316 (m-80) cc_final: 0.7964 (m-80) REVERT: C 39 ASP cc_start: 0.9023 (m-30) cc_final: 0.8709 (m-30) REVERT: C 64 HIS cc_start: 0.9170 (t-90) cc_final: 0.8655 (t-90) REVERT: C 66 GLU cc_start: 0.9367 (mp0) cc_final: 0.8974 (mp0) REVERT: C 134 MET cc_start: 0.9535 (ptt) cc_final: 0.9180 (ptm) REVERT: D 147 MET cc_start: 0.9487 (ttm) cc_final: 0.9081 (tpt) REVERT: D 233 MET cc_start: 0.9063 (mmt) cc_final: 0.8683 (mmm) REVERT: D 299 MET cc_start: 0.8595 (tpp) cc_final: 0.8303 (tpp) REVERT: D 403 MET cc_start: 0.7917 (tpp) cc_final: 0.7645 (tpp) REVERT: D 406 MET cc_start: 0.9253 (ppp) cc_final: 0.8769 (ppp) REVERT: E 86 LEU cc_start: 0.9543 (mt) cc_final: 0.9242 (mt) REVERT: E 377 MET cc_start: 0.8687 (tmm) cc_final: 0.8450 (tmm) REVERT: F 147 MET cc_start: 0.9357 (mmm) cc_final: 0.8640 (ptm) REVERT: F 257 MET cc_start: 0.9436 (mmm) cc_final: 0.9020 (mmm) REVERT: F 406 MET cc_start: 0.9278 (tpt) cc_final: 0.8866 (tpp) REVERT: I 229 ASP cc_start: 0.9281 (m-30) cc_final: 0.8860 (p0) REVERT: I 232 ARG cc_start: 0.9096 (mmp80) cc_final: 0.8841 (mmp80) outliers start: 11 outliers final: 9 residues processed: 138 average time/residue: 0.1234 time to fit residues: 26.6190 Evaluate side-chains 137 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 323 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 0.0040 chunk 165 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 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 = 0.3230 r_free = 0.3230 target = 0.040129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.032741 restraints weight = 113879.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.033811 restraints weight = 68014.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.034530 restraints weight = 46859.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.035042 restraints weight = 35490.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.035399 restraints weight = 28627.949| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15840 Z= 0.104 Angle : 0.591 10.563 21533 Z= 0.286 Chirality : 0.042 0.172 2358 Planarity : 0.004 0.058 2794 Dihedral : 11.314 173.338 2275 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.79 % Allowed : 12.67 % Favored : 86.54 % 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 aren not related in a simple way. whole: 1.04 (0.20), residues: 1946 helix: 1.77 (0.18), residues: 867 sheet: -0.39 (0.32), residues: 269 loop : -0.01 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 260 TYR 0.018 0.001 TYR F 281 PHE 0.010 0.001 PHE C 157 TRP 0.029 0.001 TRP I 263 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00233 (15840) covalent geometry : angle 0.59072 (21533) hydrogen bonds : bond 0.03295 ( 726) hydrogen bonds : angle 4.12118 ( 2100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.9078 (m-80) cc_final: 0.8786 (m-80) REVERT: B 77 GLU cc_start: 0.9443 (tp30) cc_final: 0.9102 (tp30) REVERT: B 286 LEU cc_start: 0.9668 (mp) cc_final: 0.9320 (tt) REVERT: B 294 MET cc_start: 0.9248 (ptp) cc_final: 0.8963 (ptm) REVERT: B 357 TYR cc_start: 0.8377 (m-80) cc_final: 0.8002 (m-80) REVERT: B 413 MET cc_start: 0.8342 (tpp) cc_final: 0.7591 (tpp) REVERT: C 38 ILE cc_start: 0.9443 (tp) cc_final: 0.9223 (pt) REVERT: C 39 ASP cc_start: 0.9096 (m-30) cc_final: 0.8714 (m-30) REVERT: C 44 MET cc_start: 0.9227 (ttm) cc_final: 0.8983 (mtm) REVERT: C 64 HIS cc_start: 0.9201 (t-90) cc_final: 0.8673 (t-90) REVERT: C 66 GLU cc_start: 0.9399 (mp0) cc_final: 0.9001 (mp0) REVERT: C 134 MET cc_start: 0.9563 (ptt) cc_final: 0.9236 (ptm) REVERT: D 147 MET cc_start: 0.9451 (ttm) cc_final: 0.9086 (tpp) REVERT: D 233 MET cc_start: 0.9070 (mmt) cc_final: 0.8705 (mmm) REVERT: D 299 MET cc_start: 0.8578 (tpp) cc_final: 0.8312 (tpp) REVERT: D 403 MET cc_start: 0.7961 (tpp) cc_final: 0.7681 (tpp) REVERT: D 406 MET cc_start: 0.9270 (ppp) cc_final: 0.8800 (ppp) REVERT: E 86 LEU cc_start: 0.9587 (mt) cc_final: 0.9272 (mt) REVERT: E 377 MET cc_start: 0.8681 (tmm) cc_final: 0.8394 (tmm) REVERT: F 147 MET cc_start: 0.9346 (mmm) cc_final: 0.8515 (ptm) REVERT: F 257 MET cc_start: 0.9399 (mmm) cc_final: 0.8946 (mmm) REVERT: F 299 MET cc_start: 0.7427 (mmm) cc_final: 0.6783 (tpt) REVERT: F 406 MET cc_start: 0.9283 (tpt) cc_final: 0.8873 (tpp) REVERT: I 229 ASP cc_start: 0.9262 (m-30) cc_final: 0.8831 (p0) REVERT: I 232 ARG cc_start: 0.9161 (mmp80) cc_final: 0.8834 (mmp80) outliers start: 13 outliers final: 9 residues processed: 139 average time/residue: 0.1252 time to fit residues: 27.1547 Evaluate side-chains 137 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 7.9990 chunk 148 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 153 optimal weight: 0.0570 chunk 151 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 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 = 0.3243 r_free = 0.3243 target = 0.040486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.033136 restraints weight = 114061.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.034204 restraints weight = 67773.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.034952 restraints weight = 46616.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.035471 restraints weight = 35011.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.035830 restraints weight = 28159.071| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15840 Z= 0.101 Angle : 0.599 11.617 21533 Z= 0.290 Chirality : 0.042 0.170 2358 Planarity : 0.004 0.041 2794 Dihedral : 11.158 177.068 2275 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.67 % Allowed : 12.67 % Favored : 86.66 % 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 aren not related in a simple way. whole: 1.02 (0.20), residues: 1946 helix: 1.74 (0.18), residues: 868 sheet: -0.39 (0.32), residues: 269 loop : -0.01 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 261 TYR 0.021 0.001 TYR F 281 PHE 0.012 0.001 PHE B 255 TRP 0.033 0.001 TRP I 263 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00224 (15840) covalent geometry : angle 0.59936 (21533) hydrogen bonds : bond 0.03263 ( 726) hydrogen bonds : angle 4.11197 ( 2100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.9121 (m-80) cc_final: 0.8845 (m-80) REVERT: B 77 GLU cc_start: 0.9432 (tp30) cc_final: 0.9075 (tp30) REVERT: B 286 LEU cc_start: 0.9645 (mp) cc_final: 0.9297 (tt) REVERT: B 294 MET cc_start: 0.9267 (ptp) cc_final: 0.8878 (ptm) REVERT: B 357 TYR cc_start: 0.8385 (m-80) cc_final: 0.8006 (m-80) REVERT: B 413 MET cc_start: 0.8190 (tpp) cc_final: 0.7457 (tpp) REVERT: C 36 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8960 (pm20) REVERT: C 38 ILE cc_start: 0.9473 (tp) cc_final: 0.9154 (pt) REVERT: C 39 ASP cc_start: 0.9106 (m-30) cc_final: 0.8731 (m-30) REVERT: C 44 MET cc_start: 0.9235 (ttm) cc_final: 0.8986 (mtm) REVERT: C 64 HIS cc_start: 0.9222 (t-90) cc_final: 0.8587 (t-90) REVERT: C 66 GLU cc_start: 0.9415 (mp0) cc_final: 0.8995 (mp0) REVERT: C 110 MET cc_start: 0.8370 (mmm) cc_final: 0.7890 (mmm) REVERT: C 134 MET cc_start: 0.9564 (ptt) cc_final: 0.9257 (ptm) REVERT: D 147 MET cc_start: 0.9369 (ttm) cc_final: 0.9068 (tpp) REVERT: D 233 MET cc_start: 0.9050 (mmt) cc_final: 0.8740 (mmm) REVERT: D 299 MET cc_start: 0.8579 (tpp) cc_final: 0.8305 (tpp) REVERT: D 403 MET cc_start: 0.7915 (tpp) cc_final: 0.7641 (tpp) REVERT: D 406 MET cc_start: 0.9242 (ppp) cc_final: 0.8888 (ppp) REVERT: E 86 LEU cc_start: 0.9565 (mt) cc_final: 0.9301 (mt) REVERT: E 377 MET cc_start: 0.8691 (tmm) cc_final: 0.8400 (tmm) REVERT: F 147 MET cc_start: 0.9290 (mmm) cc_final: 0.8810 (mmm) REVERT: F 257 MET cc_start: 0.9349 (mmm) cc_final: 0.8875 (mmm) REVERT: F 406 MET cc_start: 0.9266 (tpt) cc_final: 0.8857 (tpp) REVERT: I 229 ASP cc_start: 0.9238 (m-30) cc_final: 0.8790 (p0) REVERT: I 232 ARG cc_start: 0.9164 (mmp80) cc_final: 0.8812 (mmp80) outliers start: 11 outliers final: 10 residues processed: 137 average time/residue: 0.1233 time to fit residues: 26.5881 Evaluate side-chains 139 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.0050 chunk 91 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.040006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.032709 restraints weight = 114914.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.033753 restraints weight = 68787.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.034474 restraints weight = 47541.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.034976 restraints weight = 35936.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.035339 restraints weight = 29088.169| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15840 Z= 0.120 Angle : 0.602 11.037 21533 Z= 0.291 Chirality : 0.042 0.140 2358 Planarity : 0.004 0.040 2794 Dihedral : 11.079 176.949 2275 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.79 % Allowed : 12.80 % Favored : 86.42 % 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 aren not related in a simple way. whole: 1.00 (0.20), residues: 1946 helix: 1.68 (0.18), residues: 881 sheet: -0.42 (0.32), residues: 269 loop : 0.02 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 261 TYR 0.020 0.001 TYR F 281 PHE 0.009 0.001 PHE D 167 TRP 0.035 0.001 TRP I 263 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00265 (15840) covalent geometry : angle 0.60166 (21533) hydrogen bonds : bond 0.03218 ( 726) hydrogen bonds : angle 4.11551 ( 2100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2451.85 seconds wall clock time: 43 minutes 35.58 seconds (2615.58 seconds total)