Starting phenix.real_space_refine on Mon Nov 18 05:58:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yar_39105/11_2024/8yar_39105.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yar_39105/11_2024/8yar_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yar_39105/11_2024/8yar_39105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yar_39105/11_2024/8yar_39105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yar_39105/11_2024/8yar_39105.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yar_39105/11_2024/8yar_39105.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} 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, 'ARG:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG: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: 10.78, per 1000 atoms: 0.70 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: 4.20 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.96 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: 5.55 Time building geometry restraints manager: 4.81 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 439 or resid 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 439 or resid 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 \ 427 or resid 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 427 or resid 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: 7.230 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.620 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.470 ------------------------------------------------------------------------------- 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= 0.239 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (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 TRP 0.020 0.001 TRP I 263 HIS 0.005 0.001 HIS I 259 PHE 0.023 0.001 PHE C 115 TYR 0.025 0.001 TYR E 172 ARG 0.003 0.000 ARG B 40 *********************** 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 : 1.926 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: C 131 PHE cc_start: 0.9005 (m-80) cc_final: 0.8714 (m-80) 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: 0.8233 (mmm) REVERT: D 267 MET cc_start: 0.7304 (ttt) cc_final: 0.6914 (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: 0.2954 time to fit residues: 74.8631 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 : 2.077 ------------------------------------------------------------------------------- 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 162 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15840 Z= 0.357 Angle : 0.668 10.375 21533 Z= 0.344 Chirality : 0.045 0.151 2358 Planarity : 0.004 0.042 2794 Dihedral : 13.052 161.219 2275 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.97 % Allowed : 6.97 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1946 helix: 1.59 (0.18), residues: 853 sheet: -0.60 (0.31), residues: 284 loop : -0.10 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 407 HIS 0.006 0.002 HIS F 28 PHE 0.015 0.002 PHE F 200 TYR 0.016 0.002 TYR B 432 ARG 0.005 0.001 ARG C 89 *********************** 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 148 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ASP cc_start: 0.9205 (m-30) cc_final: 0.8700 (m-30) REVERT: C 64 HIS cc_start: 0.8615 (t-90) cc_final: 0.8332 (t-90) REVERT: C 66 GLU cc_start: 0.8913 (mp0) cc_final: 0.8641 (mp0) REVERT: C 181 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: D 164 MET cc_start: 0.9069 (tpp) cc_final: 0.8512 (tpt) REVERT: D 233 MET cc_start: 0.8771 (mmt) cc_final: 0.8450 (mmm) REVERT: E 86 LEU cc_start: 0.9158 (mt) cc_final: 0.8935 (mt) REVERT: E 398 MET cc_start: 0.8894 (ttm) cc_final: 0.8675 (ttm) REVERT: F 299 MET cc_start: 0.8544 (tpt) cc_final: 0.7680 (tpt) REVERT: F 406 MET cc_start: 0.8851 (tpt) cc_final: 0.8522 (tpp) REVERT: I 252 LYS cc_start: 0.9534 (tttm) cc_final: 0.8961 (ttmm) outliers start: 16 outliers final: 9 residues processed: 140 average time/residue: 0.2913 time to fit residues: 61.3972 Evaluate side-chains 135 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 C residue 179 ASN Chi-restraints excluded: chain C residue 181 PHE 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 96 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15840 Z= 0.363 Angle : 0.647 8.143 21533 Z= 0.333 Chirality : 0.044 0.165 2358 Planarity : 0.004 0.055 2794 Dihedral : 12.533 161.936 2275 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.33 % Allowed : 9.82 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1946 helix: 1.36 (0.18), residues: 848 sheet: -0.85 (0.30), residues: 300 loop : -0.18 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 263 HIS 0.007 0.002 HIS E 28 PHE 0.016 0.002 PHE F 200 TYR 0.020 0.002 TYR E 172 ARG 0.006 0.000 ARG I 261 *********************** 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: 22 poor density : 126 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8838 (ptm) REVERT: B 413 MET cc_start: 0.8114 (tpp) cc_final: 0.7649 (tpp) REVERT: C 39 ASP cc_start: 0.9157 (m-30) cc_final: 0.8696 (m-30) REVERT: C 44 MET cc_start: 0.9250 (mtm) cc_final: 0.8714 (mtm) REVERT: C 64 HIS cc_start: 0.8758 (t-90) cc_final: 0.7830 (t-90) REVERT: C 181 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: D 267 MET cc_start: 0.7965 (ttm) cc_final: 0.7736 (ttm) REVERT: E 86 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8982 (mt) REVERT: F 267 MET cc_start: 0.8323 (ptm) cc_final: 0.8120 (ttp) REVERT: F 406 MET cc_start: 0.8855 (tpt) cc_final: 0.8486 (tpp) REVERT: I 252 LYS cc_start: 0.9524 (tttm) cc_final: 0.8999 (ttmm) outliers start: 22 outliers final: 12 residues processed: 137 average time/residue: 0.2870 time to fit residues: 59.9511 Evaluate side-chains 132 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 86 LEU 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 I residue 224 HIS Chi-restraints excluded: chain I residue 229 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15840 Z= 0.183 Angle : 0.576 11.589 21533 Z= 0.288 Chirality : 0.043 0.146 2358 Planarity : 0.004 0.041 2794 Dihedral : 12.134 163.195 2275 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.27 % Allowed : 10.67 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1946 helix: 1.58 (0.18), residues: 851 sheet: -0.60 (0.30), residues: 286 loop : -0.13 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 263 HIS 0.004 0.001 HIS B 8 PHE 0.010 0.001 PHE F 260 TYR 0.015 0.001 TYR E 172 ARG 0.003 0.000 ARG I 261 *********************** 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 153 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: B 294 MET cc_start: 0.9000 (ptp) cc_final: 0.8761 (ptm) REVERT: C 39 ASP cc_start: 0.9116 (m-30) cc_final: 0.8652 (m-30) REVERT: C 44 MET cc_start: 0.9178 (mtm) cc_final: 0.8673 (mtm) REVERT: C 106 MET cc_start: 0.8519 (tpp) cc_final: 0.8217 (tpp) REVERT: C 134 MET cc_start: 0.9455 (mtm) cc_final: 0.9164 (mtp) REVERT: C 181 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: D 164 MET cc_start: 0.9214 (tpp) cc_final: 0.8809 (tpt) REVERT: D 267 MET cc_start: 0.7759 (ttm) cc_final: 0.7432 (ttm) REVERT: E 86 LEU cc_start: 0.9167 (mt) cc_final: 0.8955 (mt) REVERT: F 406 MET cc_start: 0.8833 (tpt) cc_final: 0.8443 (tpp) REVERT: I 252 LYS cc_start: 0.9486 (tttm) cc_final: 0.9184 (tttp) outliers start: 21 outliers final: 11 residues processed: 146 average time/residue: 0.2639 time to fit residues: 60.3063 Evaluate side-chains 137 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 181 PHE 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 284 ILE Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain I residue 229 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 166 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15840 Z= 0.312 Angle : 0.618 9.687 21533 Z= 0.312 Chirality : 0.043 0.148 2358 Planarity : 0.004 0.041 2794 Dihedral : 12.068 164.053 2275 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.24 % Allowed : 11.40 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1946 helix: 1.48 (0.18), residues: 854 sheet: -0.59 (0.32), residues: 262 loop : -0.23 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 263 HIS 0.007 0.001 HIS F 6 PHE 0.013 0.001 PHE F 200 TYR 0.017 0.001 TYR E 172 ARG 0.004 0.000 ARG I 232 *********************** 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 155 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8174 (pm20) REVERT: B 294 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8805 (ptm) REVERT: B 413 MET cc_start: 0.7978 (tpp) cc_final: 0.7496 (tpp) REVERT: C 39 ASP cc_start: 0.9112 (m-30) cc_final: 0.8656 (m-30) REVERT: C 44 MET cc_start: 0.9211 (mtm) cc_final: 0.8691 (mtm) REVERT: C 106 MET cc_start: 0.8499 (tpp) cc_final: 0.8145 (tpp) REVERT: C 134 MET cc_start: 0.9526 (mtm) cc_final: 0.9266 (mtm) REVERT: C 181 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: D 267 MET cc_start: 0.7720 (ttm) cc_final: 0.7460 (ttm) REVERT: E 86 LEU cc_start: 0.9244 (mt) cc_final: 0.9007 (mt) REVERT: F 267 MET cc_start: 0.8848 (ptp) cc_final: 0.8407 (ptp) REVERT: F 299 MET cc_start: 0.8321 (mmm) cc_final: 0.7790 (tpt) REVERT: F 406 MET cc_start: 0.8853 (tpt) cc_final: 0.8510 (tpp) REVERT: I 252 LYS cc_start: 0.9437 (tttm) cc_final: 0.9074 (ttmt) REVERT: I 257 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7839 (m-10) outliers start: 37 outliers final: 17 residues processed: 145 average time/residue: 0.2670 time to fit residues: 60.8171 Evaluate side-chains 139 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 135 LEU 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 E residue 437 VAL 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 I residue 229 ASP Chi-restraints excluded: chain I residue 257 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15840 Z= 0.190 Angle : 0.579 8.774 21533 Z= 0.285 Chirality : 0.043 0.144 2358 Planarity : 0.004 0.039 2794 Dihedral : 11.913 163.036 2275 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.82 % Allowed : 12.55 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1946 helix: 1.63 (0.18), residues: 854 sheet: -0.51 (0.32), residues: 255 loop : -0.20 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 263 HIS 0.004 0.001 HIS B 8 PHE 0.010 0.001 PHE F 260 TYR 0.016 0.001 TYR E 172 ARG 0.003 0.000 ARG I 261 *********************** 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 156 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.9146 (tp30) cc_final: 0.8678 (tp30) REVERT: B 290 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: B 294 MET cc_start: 0.9003 (ptp) cc_final: 0.8732 (ptm) REVERT: B 413 MET cc_start: 0.7990 (tpp) cc_final: 0.7598 (tpp) REVERT: C 39 ASP cc_start: 0.9113 (m-30) cc_final: 0.8657 (m-30) REVERT: C 44 MET cc_start: 0.9214 (mtm) cc_final: 0.8669 (mtm) REVERT: C 64 HIS cc_start: 0.9193 (t-90) cc_final: 0.8963 (t-90) REVERT: C 106 MET cc_start: 0.8457 (tpp) cc_final: 0.8117 (tpp) REVERT: C 154 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9468 (mt) REVERT: C 181 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: D 406 MET cc_start: 0.9033 (ppp) cc_final: 0.8493 (ppp) REVERT: E 86 LEU cc_start: 0.9220 (mt) cc_final: 0.9013 (mt) REVERT: F 257 MET cc_start: 0.8885 (mmm) cc_final: 0.8629 (mmm) REVERT: F 267 MET cc_start: 0.8902 (ptp) cc_final: 0.7641 (ptm) REVERT: F 299 MET cc_start: 0.8338 (mmm) cc_final: 0.7990 (mmm) REVERT: F 406 MET cc_start: 0.8814 (tpt) cc_final: 0.8465 (tpp) REVERT: I 252 LYS cc_start: 0.9383 (tttm) cc_final: 0.9019 (ttmt) REVERT: I 257 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7776 (m-10) outliers start: 30 outliers final: 20 residues processed: 148 average time/residue: 0.2552 time to fit residues: 59.3192 Evaluate side-chains 146 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 437 VAL 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 Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 257 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 185 optimal weight: 0.0070 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN D 137 HIS ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15840 Z= 0.156 Angle : 0.571 9.307 21533 Z= 0.280 Chirality : 0.043 0.143 2358 Planarity : 0.004 0.044 2794 Dihedral : 11.723 165.649 2275 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.21 % Allowed : 13.64 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1946 helix: 1.70 (0.18), residues: 854 sheet: -0.46 (0.33), residues: 255 loop : -0.20 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 263 HIS 0.004 0.001 HIS B 8 PHE 0.010 0.001 PHE B 149 TYR 0.015 0.001 TYR E 172 ARG 0.009 0.000 ARG I 261 *********************** 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: 20 poor density : 126 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.9133 (tp30) cc_final: 0.8672 (tp30) REVERT: B 294 MET cc_start: 0.9012 (ptp) cc_final: 0.8758 (ptm) REVERT: C 17 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8581 (ttp80) REVERT: C 38 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9441 (pt) REVERT: C 39 ASP cc_start: 0.9105 (m-30) cc_final: 0.8656 (m-30) REVERT: C 44 MET cc_start: 0.9160 (mtm) cc_final: 0.8627 (mtm) REVERT: C 64 HIS cc_start: 0.9179 (t-90) cc_final: 0.8882 (t-90) REVERT: C 106 MET cc_start: 0.8426 (tpp) cc_final: 0.8145 (tpp) REVERT: C 181 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: D 406 MET cc_start: 0.8997 (ppp) cc_final: 0.8515 (ppp) REVERT: F 257 MET cc_start: 0.8871 (mmm) cc_final: 0.8598 (mmm) REVERT: F 267 MET cc_start: 0.8828 (ptp) cc_final: 0.8496 (ptm) REVERT: F 406 MET cc_start: 0.8810 (tpt) cc_final: 0.8488 (tpp) REVERT: I 229 ASP cc_start: 0.9456 (OUTLIER) cc_final: 0.8993 (p0) REVERT: I 252 LYS cc_start: 0.9367 (tttm) cc_final: 0.9005 (ttmt) REVERT: I 257 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7776 (m-10) outliers start: 20 outliers final: 11 residues processed: 139 average time/residue: 0.2820 time to fit residues: 60.6614 Evaluate side-chains 139 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 192 HIS 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 Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 257 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15840 Z= 0.224 Angle : 0.596 9.719 21533 Z= 0.292 Chirality : 0.043 0.161 2358 Planarity : 0.004 0.040 2794 Dihedral : 11.725 164.008 2275 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.64 % Allowed : 13.52 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1946 helix: 1.65 (0.18), residues: 861 sheet: -0.43 (0.33), residues: 253 loop : -0.22 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 263 HIS 0.004 0.001 HIS B 8 PHE 0.034 0.001 PHE D 167 TYR 0.017 0.001 TYR E 172 ARG 0.007 0.000 ARG I 261 *********************** 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 149 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8870 (m-80) cc_final: 0.8653 (m-80) REVERT: B 294 MET cc_start: 0.9015 (ptp) cc_final: 0.8750 (ptm) REVERT: B 413 MET cc_start: 0.7899 (tpp) cc_final: 0.7404 (tpp) REVERT: C 17 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8562 (tpp80) REVERT: C 38 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9367 (pt) REVERT: C 39 ASP cc_start: 0.9141 (m-30) cc_final: 0.8705 (m-30) REVERT: C 44 MET cc_start: 0.9182 (mtm) cc_final: 0.8669 (mtm) REVERT: C 64 HIS cc_start: 0.9199 (t-90) cc_final: 0.8827 (t-90) REVERT: C 106 MET cc_start: 0.8460 (tpp) cc_final: 0.8138 (tpp) REVERT: C 154 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9434 (mt) REVERT: C 181 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: D 406 MET cc_start: 0.9059 (ppp) cc_final: 0.8590 (ppp) REVERT: F 406 MET cc_start: 0.8827 (tpt) cc_final: 0.8496 (tpp) REVERT: I 229 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.8977 (p0) REVERT: I 252 LYS cc_start: 0.9420 (tttm) cc_final: 0.9049 (ttmt) REVERT: I 257 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7793 (m-10) outliers start: 27 outliers final: 17 residues processed: 142 average time/residue: 0.2758 time to fit residues: 60.2041 Evaluate side-chains 144 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain E residue 226 ASN 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 Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 257 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 163 optimal weight: 0.0980 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2772 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= 0.161 Angle : 0.590 10.116 21533 Z= 0.287 Chirality : 0.043 0.145 2358 Planarity : 0.004 0.040 2794 Dihedral : 11.588 167.739 2275 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.58 % Allowed : 13.58 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1946 helix: 1.69 (0.18), residues: 861 sheet: -0.27 (0.33), residues: 253 loop : -0.25 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 263 HIS 0.006 0.001 HIS B 61 PHE 0.028 0.001 PHE D 167 TYR 0.016 0.001 TYR E 172 ARG 0.009 0.000 ARG I 261 *********************** 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 152 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 MET cc_start: 0.7541 (tmm) cc_final: 0.7261 (tmm) REVERT: B 294 MET cc_start: 0.8991 (ptp) cc_final: 0.8691 (ptm) REVERT: B 413 MET cc_start: 0.7940 (tpp) cc_final: 0.7448 (tpp) REVERT: C 17 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8671 (tpp80) REVERT: C 38 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9374 (pt) REVERT: C 39 ASP cc_start: 0.9116 (m-30) cc_final: 0.8665 (m-30) REVERT: C 44 MET cc_start: 0.9172 (mtm) cc_final: 0.8667 (mtm) REVERT: C 64 HIS cc_start: 0.9167 (t-90) cc_final: 0.8667 (t-90) REVERT: C 106 MET cc_start: 0.8423 (tpp) cc_final: 0.8115 (tpp) REVERT: C 130 MET cc_start: 0.8978 (mtt) cc_final: 0.8764 (mtt) REVERT: C 134 MET cc_start: 0.9454 (mtp) cc_final: 0.9097 (mmm) REVERT: C 154 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9455 (mt) REVERT: C 181 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: D 164 MET cc_start: 0.9074 (tpt) cc_final: 0.8840 (tpt) REVERT: D 233 MET cc_start: 0.8460 (mmm) cc_final: 0.7910 (mmm) REVERT: D 406 MET cc_start: 0.9040 (ppp) cc_final: 0.8578 (ppp) REVERT: F 267 MET cc_start: 0.8847 (ptm) cc_final: 0.8569 (ptm) REVERT: F 406 MET cc_start: 0.8836 (tpt) cc_final: 0.8516 (tpp) REVERT: I 229 ASP cc_start: 0.9422 (OUTLIER) cc_final: 0.8959 (p0) REVERT: I 252 LYS cc_start: 0.9386 (tttm) cc_final: 0.9029 (ttmt) outliers start: 26 outliers final: 16 residues processed: 144 average time/residue: 0.2756 time to fit residues: 61.2254 Evaluate side-chains 142 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 257 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 126 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15840 Z= 0.172 Angle : 0.622 11.677 21533 Z= 0.298 Chirality : 0.042 0.180 2358 Planarity : 0.004 0.040 2794 Dihedral : 11.500 168.717 2275 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.33 % Allowed : 14.01 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1946 helix: 1.62 (0.18), residues: 874 sheet: -0.44 (0.32), residues: 266 loop : -0.14 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP I 263 HIS 0.005 0.001 HIS B 8 PHE 0.029 0.001 PHE D 167 TYR 0.017 0.001 TYR C 162 ARG 0.006 0.000 ARG I 261 ********************** 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 143 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 MET cc_start: 0.7500 (tmm) cc_final: 0.7227 (tmm) REVERT: B 294 MET cc_start: 0.9010 (ptp) cc_final: 0.8697 (ptm) REVERT: B 413 MET cc_start: 0.7931 (tpp) cc_final: 0.7438 (tpp) REVERT: C 17 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8645 (tpp80) REVERT: C 38 ILE cc_start: 0.9670 (OUTLIER) cc_final: 0.9382 (pt) REVERT: C 39 ASP cc_start: 0.9098 (m-30) cc_final: 0.8648 (m-30) REVERT: C 44 MET cc_start: 0.9182 (mtm) cc_final: 0.8729 (mtm) REVERT: C 64 HIS cc_start: 0.9227 (t-90) cc_final: 0.8801 (t-90) REVERT: C 106 MET cc_start: 0.8416 (tpp) cc_final: 0.8101 (tpp) REVERT: C 130 MET cc_start: 0.8901 (mtt) cc_final: 0.8668 (mtt) REVERT: C 134 MET cc_start: 0.9495 (mtp) cc_final: 0.9133 (mmm) REVERT: C 154 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9450 (mt) REVERT: D 164 MET cc_start: 0.9083 (tpt) cc_final: 0.8859 (tpt) REVERT: D 233 MET cc_start: 0.8524 (mmm) cc_final: 0.8065 (mmm) REVERT: D 299 MET cc_start: 0.7862 (tpp) cc_final: 0.7642 (tpp) REVERT: D 406 MET cc_start: 0.9029 (ppp) cc_final: 0.8531 (ppp) REVERT: F 267 MET cc_start: 0.8872 (ptm) cc_final: 0.8611 (ptm) REVERT: F 406 MET cc_start: 0.8833 (tpt) cc_final: 0.8526 (tpp) REVERT: I 229 ASP cc_start: 0.9396 (OUTLIER) cc_final: 0.8940 (p0) REVERT: I 252 LYS cc_start: 0.9397 (tttm) cc_final: 0.9045 (ttmt) outliers start: 22 outliers final: 17 residues processed: 138 average time/residue: 0.2675 time to fit residues: 56.6936 Evaluate side-chains 141 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 154 LEU 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 E residue 62 VAL Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain I residue 229 ASP Chi-restraints excluded: chain I residue 257 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 0.0050 chunk 133 optimal weight: 0.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- 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 = 0.3210 r_free = 0.3210 target = 0.039460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.032187 restraints weight = 114209.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.033228 restraints weight = 67581.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.033934 restraints weight = 46540.382| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15840 Z= 0.164 Angle : 0.608 10.855 21533 Z= 0.291 Chirality : 0.042 0.180 2358 Planarity : 0.004 0.039 2794 Dihedral : 11.421 170.843 2275 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.21 % Allowed : 13.95 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1946 helix: 1.66 (0.18), residues: 874 sheet: -0.27 (0.32), residues: 262 loop : -0.20 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 263 HIS 0.006 0.001 HIS B 61 PHE 0.025 0.001 PHE D 167 TYR 0.017 0.001 TYR C 162 ARG 0.009 0.000 ARG I 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.65 seconds wall clock time: 51 minutes 16.84 seconds (3076.84 seconds total)