Starting phenix.real_space_refine on Sat Mar 16 04:05:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2i_42915/03_2024/8v2i_42915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2i_42915/03_2024/8v2i_42915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2i_42915/03_2024/8v2i_42915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2i_42915/03_2024/8v2i_42915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2i_42915/03_2024/8v2i_42915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2i_42915/03_2024/8v2i_42915_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 93 5.16 5 C 8556 2.51 5 N 2318 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "I PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 279": "OE1" <-> "OE2" Residue "I GLU 290": "OE1" <-> "OE2" Residue "Q ASP 209": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13623 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3401 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3348 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3385 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3357 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.46, per 1000 atoms: 0.55 Number of scatterers: 13623 At special positions: 0 Unit cell: (73.14, 74.2, 195.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 93 16.00 P 12 15.00 Mg 4 11.99 O 2640 8.00 N 2318 7.00 C 8556 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 - 3.50 Amino acid : False - 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: 5.38 Conformation dependent library (CDL) restraints added in 2.5 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 10 sheets defined 49.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.702A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.628A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.476A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.110A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.127A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.475A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.818A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.904A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.579A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.596A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 434 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.976A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 Processing helix chain 'B' and resid 179 through 194 Proline residue: B 182 - end of helix removed outlier: 4.086A pdb=" N HIS B 190 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 194 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 236 removed outlier: 3.565A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 278 through 281 Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.505A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 372 through 389 Processing helix chain 'B' and resid 392 through 399 removed outlier: 4.065A pdb=" N HIS B 396 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP B 397 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 427 Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 44 through 52 removed outlier: 3.878A pdb=" N SER I 48 " --> pdb=" O GLY I 45 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE I 49 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 80 Processing helix chain 'I' and resid 82 through 84 No H-bonds generated for 'chain 'I' and resid 82 through 84' Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 111 through 128 removed outlier: 4.274A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 4.232A pdb=" N HIS I 192 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 217 Processing helix chain 'I' and resid 224 through 243 removed outlier: 4.420A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 278 through 283 removed outlier: 4.456A pdb=" N TYR I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N HIS I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 278 through 283' Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.753A pdb=" N PHE I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 325 through 337 Processing helix chain 'I' and resid 382 through 401 removed outlier: 4.065A pdb=" N LEU I 397 " --> pdb=" O LYS I 394 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA I 400 " --> pdb=" O LEU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 410 Processing helix chain 'I' and resid 415 through 435 removed outlier: 3.852A pdb=" N VAL I 435 " --> pdb=" O TYR I 432 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 28 Processing helix chain 'Q' and resid 41 through 45 Processing helix chain 'Q' and resid 47 through 49 No H-bonds generated for 'chain 'Q' and resid 47 through 49' Processing helix chain 'Q' and resid 70 through 77 Processing helix chain 'Q' and resid 82 through 84 No H-bonds generated for 'chain 'Q' and resid 82 through 84' Processing helix chain 'Q' and resid 87 through 89 No H-bonds generated for 'chain 'Q' and resid 87 through 89' Processing helix chain 'Q' and resid 101 through 125 removed outlier: 5.015A pdb=" N GLU Q 108 " --> pdb=" O GLY Q 104 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY Q 109 " --> pdb=" O HIS Q 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA Q 110 " --> pdb=" O TYR Q 106 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU Q 111 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 158 Processing helix chain 'Q' and resid 181 through 194 removed outlier: 3.867A pdb=" N HIS Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU Q 194 " --> pdb=" O HIS Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 213 Processing helix chain 'Q' and resid 222 through 236 Processing helix chain 'Q' and resid 250 through 257 Processing helix chain 'Q' and resid 276 through 281 removed outlier: 4.092A pdb=" N GLN Q 280 " --> pdb=" O ARG Q 276 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR Q 281 " --> pdb=" O GLY Q 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 276 through 281' Processing helix chain 'Q' and resid 286 through 294 Processing helix chain 'Q' and resid 296 through 298 No H-bonds generated for 'chain 'Q' and resid 296 through 298' Processing helix chain 'Q' and resid 323 through 336 Processing helix chain 'Q' and resid 338 through 340 No H-bonds generated for 'chain 'Q' and resid 338 through 340' Processing helix chain 'Q' and resid 372 through 390 removed outlier: 3.524A pdb=" N GLN Q 375 " --> pdb=" O THR Q 372 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG Q 390 " --> pdb=" O ALA Q 387 " (cutoff:3.500A) Processing helix chain 'Q' and resid 395 through 401 removed outlier: 3.736A pdb=" N GLU Q 401 " --> pdb=" O TRP Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 427 Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.069A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.578A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.222A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA B 9 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS B 137 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 202 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 12.138A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'I' and resid 92 through 94 removed outlier: 8.173A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER I 140 " --> pdb=" O VAL I 9 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU I 167 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N HIS I 139 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS I 200 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER I 170 " --> pdb=" O CYS I 200 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR I 172 " --> pdb=" O PHE I 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL I 204 " --> pdb=" O TYR I 172 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'I' and resid 269 through 273 removed outlier: 3.564A pdb=" N ALA I 314 " --> pdb=" O ASN I 380 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Q' and resid 90 through 92 removed outlier: 8.455A pdb=" N VAL Q 91 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU Q 65 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ILE Q 64 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS Q 6 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL Q 66 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN Q 8 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 131 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE Q 133 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE Q 7 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU Q 135 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA Q 9 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N HIS Q 137 " --> pdb=" O ALA Q 9 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE Q 163 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N LEU Q 135 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN Q 165 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N HIS Q 137 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N PHE Q 167 " --> pdb=" O HIS Q 137 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU Q 198 " --> pdb=" O THR Q 166 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N SER Q 168 " --> pdb=" O GLU Q 198 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR Q 200 " --> pdb=" O SER Q 168 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL Q 170 " --> pdb=" O TYR Q 200 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE Q 202 " --> pdb=" O VAL Q 170 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASP Q 203 " --> pdb=" O PRO Q 268 " (cutoff:3.500A) removed outlier: 11.906A pdb=" N PHE Q 270 " --> pdb=" O ASP Q 203 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE Q 265 " --> pdb=" O SER Q 371 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER Q 371 " --> pdb=" O PHE Q 265 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Q' and resid 51 through 53 603 hydrogen bonds defined for protein. 1524 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: 4.23 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4501 1.34 - 1.47: 3372 1.47 - 1.59: 5892 1.59 - 1.72: 16 1.72 - 1.84: 150 Bond restraints: 13931 Sorted by residual: bond pdb=" N PHE I 87 " pdb=" CA PHE I 87 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.33e-02 5.65e+03 6.15e+00 bond pdb=" N LYS I 280 " pdb=" CA LYS I 280 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.33e-02 5.65e+03 5.77e+00 bond pdb=" C LEU I 70 " pdb=" N GLU I 71 " ideal model delta sigma weight residual 1.333 1.394 -0.061 2.74e-02 1.33e+03 5.02e+00 bond pdb=" N GLU I 279 " pdb=" CA GLU I 279 " ideal model delta sigma weight residual 1.458 1.486 -0.027 1.26e-02 6.30e+03 4.63e+00 bond pdb=" N MET Q 1 " pdb=" CA MET Q 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 ... (remaining 13926 not shown) Histogram of bond angle deviations from ideal: 96.61 - 104.10: 217 104.10 - 111.58: 6011 111.58 - 119.07: 5354 119.07 - 126.56: 7156 126.56 - 134.04: 202 Bond angle restraints: 18940 Sorted by residual: angle pdb=" CB MET B 406 " pdb=" CG MET B 406 " pdb=" SD MET B 406 " ideal model delta sigma weight residual 112.70 125.84 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CB MET Q 406 " pdb=" CG MET Q 406 " pdb=" SD MET Q 406 " ideal model delta sigma weight residual 112.70 125.31 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" CB GLU B 157 " pdb=" CG GLU B 157 " pdb=" CD GLU B 157 " ideal model delta sigma weight residual 112.60 118.88 -6.28 1.70e+00 3.46e-01 1.36e+01 angle pdb=" CA ALA I 281 " pdb=" C ALA I 281 " pdb=" O ALA I 281 " ideal model delta sigma weight residual 120.90 117.02 3.88 1.07e+00 8.73e-01 1.32e+01 angle pdb=" CA ARG B 320 " pdb=" CB ARG B 320 " pdb=" CG ARG B 320 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.23e+01 ... (remaining 18935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 8052 33.65 - 67.30: 217 67.30 - 100.95: 17 100.95 - 134.61: 4 134.61 - 168.26: 4 Dihedral angle restraints: 8294 sinusoidal: 3304 harmonic: 4990 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -98.99 168.26 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP I 501 " pdb=" O5' GTP I 501 " pdb=" PA GTP I 501 " pdb=" O3A GTP I 501 " ideal model delta sinusoidal sigma weight residual 69.27 -133.71 -157.03 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -41.26 145.85 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 8291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1327 0.038 - 0.076: 522 0.076 - 0.114: 156 0.114 - 0.152: 65 0.152 - 0.190: 8 Chirality restraints: 2078 Sorted by residual: chirality pdb=" CB ILE B 155 " pdb=" CA ILE B 155 " pdb=" CG1 ILE B 155 " pdb=" CG2 ILE B 155 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA VAL I 204 " pdb=" N VAL I 204 " pdb=" C VAL I 204 " pdb=" CB VAL I 204 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.51e-01 ... (remaining 2075 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 278 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C ALA I 278 " -0.068 2.00e-02 2.50e+03 pdb=" O ALA I 278 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU I 279 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 141 " 0.024 2.00e-02 2.50e+03 2.12e-02 7.87e+00 pdb=" CG PHE I 141 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE I 141 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE I 141 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE I 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 141 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE I 141 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 320 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C ARG B 320 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG B 320 " -0.018 2.00e-02 2.50e+03 pdb=" N MET B 321 " -0.016 2.00e-02 2.50e+03 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 49 2.54 - 3.13: 10486 3.13 - 3.72: 21280 3.72 - 4.31: 29980 4.31 - 4.90: 51668 Nonbonded interactions: 113463 Sorted by model distance: nonbonded pdb=" O3G G2P Q 501 " pdb="MG MG Q 502 " model vdw 1.947 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.951 2.170 nonbonded pdb=" O3G G2P B 501 " pdb="MG MG B 502 " model vdw 1.953 2.170 nonbonded pdb=" O2B GTP I 501 " pdb="MG MG I 502 " model vdw 1.957 2.170 nonbonded pdb=" O1G GTP I 501 " pdb="MG MG I 502 " model vdw 1.970 2.170 ... (remaining 113458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB )) or resid 164 through 220 or (resid 22 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 441 or resid 501 through 502)) selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 281 or (resid 282 through 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 429 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.770 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: 39.180 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 39.080 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13931 Z= 0.351 Angle : 0.869 13.143 18940 Z= 0.443 Chirality : 0.048 0.190 2078 Planarity : 0.005 0.047 2467 Dihedral : 15.722 168.257 5098 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.41 % Allowed : 9.77 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.31 (0.19), residues: 1720 helix: 1.22 (0.18), residues: 766 sheet: 0.77 (0.34), residues: 232 loop : -1.09 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.007 0.001 HIS B 307 PHE 0.049 0.002 PHE I 141 TYR 0.035 0.002 TYR B 281 ARG 0.008 0.001 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 304 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6621 (tpp) cc_final: 0.6411 (tpt) REVERT: A 97 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7531 (mm-30) REVERT: A 116 ASP cc_start: 0.7686 (m-30) cc_final: 0.7409 (m-30) REVERT: A 120 ASP cc_start: 0.7042 (m-30) cc_final: 0.6563 (m-30) REVERT: A 163 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8057 (pmtt) REVERT: A 196 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 200 CYS cc_start: 0.8080 (m) cc_final: 0.7715 (m) REVERT: A 290 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7554 (mp0) REVERT: A 309 HIS cc_start: 0.7935 (m-70) cc_final: 0.7669 (m-70) REVERT: A 338 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6777 (mtpt) REVERT: A 432 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.5441 (t80) REVERT: B 118 ASP cc_start: 0.8845 (m-30) cc_final: 0.8536 (m-30) REVERT: B 284 LEU cc_start: 0.7205 (mt) cc_final: 0.6970 (mt) REVERT: B 332 ASN cc_start: 0.7237 (t0) cc_final: 0.6687 (m110) REVERT: B 379 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8774 (mtmm) REVERT: I 20 CYS cc_start: 0.6394 (t) cc_final: 0.5689 (m) REVERT: I 102 ASN cc_start: 0.8521 (t0) cc_final: 0.8295 (t0) REVERT: I 200 CYS cc_start: 0.8136 (t) cc_final: 0.7848 (t) REVERT: I 279 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: I 284 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6703 (tt0) REVERT: I 300 ASN cc_start: 0.7279 (t0) cc_final: 0.6780 (t160) REVERT: I 370 LYS cc_start: 0.7236 (tttt) cc_final: 0.6621 (tptt) REVERT: I 414 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7484 (mm-30) REVERT: Q 31 ASP cc_start: 0.7904 (m-30) cc_final: 0.7688 (m-30) REVERT: Q 69 GLU cc_start: 0.6299 (pt0) cc_final: 0.5654 (pt0) REVERT: Q 108 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6796 (mm-30) REVERT: Q 118 ASP cc_start: 0.7105 (t0) cc_final: 0.6402 (m-30) REVERT: Q 176 SER cc_start: 0.8316 (p) cc_final: 0.7971 (t) REVERT: Q 190 HIS cc_start: 0.8190 (t70) cc_final: 0.7848 (t-170) REVERT: Q 275 SER cc_start: 0.7085 (t) cc_final: 0.6823 (p) REVERT: Q 276 ARG cc_start: 0.6351 (mmm160) cc_final: 0.6014 (mmt180) REVERT: Q 291 GLN cc_start: 0.7497 (tt0) cc_final: 0.7076 (mp10) REVERT: Q 298 ASN cc_start: 0.8772 (t0) cc_final: 0.8436 (t160) REVERT: Q 332 ASN cc_start: 0.7123 (m-40) cc_final: 0.6782 (t0) outliers start: 6 outliers final: 1 residues processed: 307 average time/residue: 1.3923 time to fit residues: 463.3318 Evaluate side-chains 169 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.3980 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 133 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 139 HIS A 285 GLN A 309 HIS A 358 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN Q 100 ASN Q 137 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13931 Z= 0.293 Angle : 0.589 9.623 18940 Z= 0.310 Chirality : 0.045 0.196 2078 Planarity : 0.005 0.041 2467 Dihedral : 11.332 176.859 1976 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.72 % Allowed : 12.94 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.53 (0.20), residues: 1720 helix: 1.20 (0.18), residues: 768 sheet: 1.02 (0.34), residues: 248 loop : -0.81 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.007 0.001 HIS A 266 PHE 0.020 0.002 PHE I 87 TYR 0.016 0.002 TYR I 224 ARG 0.008 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7369 (mm-30) REVERT: A 116 ASP cc_start: 0.7780 (m-30) cc_final: 0.7384 (m-30) REVERT: A 120 ASP cc_start: 0.7184 (m-30) cc_final: 0.6574 (m-30) REVERT: A 163 LYS cc_start: 0.8377 (tmtt) cc_final: 0.7945 (pmtt) REVERT: A 284 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: A 290 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7424 (mp0) REVERT: A 309 HIS cc_start: 0.7886 (m170) cc_final: 0.7623 (m-70) REVERT: A 338 LYS cc_start: 0.7334 (mtpp) cc_final: 0.7039 (mtpp) REVERT: A 384 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6866 (tt) REVERT: A 432 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.5481 (t80) REVERT: B 118 ASP cc_start: 0.8765 (m-30) cc_final: 0.8402 (m-30) REVERT: B 328 GLU cc_start: 0.6724 (tp30) cc_final: 0.6308 (tp30) REVERT: B 394 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6709 (t80) REVERT: B 406 MET cc_start: 0.8342 (tpp) cc_final: 0.8124 (tpp) REVERT: I 96 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8678 (mtpp) REVERT: I 102 ASN cc_start: 0.8490 (t0) cc_final: 0.8095 (t0) REVERT: I 120 ASP cc_start: 0.6092 (m-30) cc_final: 0.5856 (m-30) REVERT: I 154 MET cc_start: 0.7848 (mmm) cc_final: 0.7006 (mtp) REVERT: I 168 GLU cc_start: 0.7422 (tt0) cc_final: 0.6723 (mt-10) REVERT: I 279 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: I 300 ASN cc_start: 0.7124 (t0) cc_final: 0.6490 (t160) REVERT: I 308 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7141 (mtt90) REVERT: I 370 LYS cc_start: 0.7718 (tttt) cc_final: 0.7001 (tptt) REVERT: I 414 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7417 (mm-30) REVERT: Q 118 ASP cc_start: 0.7269 (t0) cc_final: 0.6558 (m-30) REVERT: Q 158 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: Q 176 SER cc_start: 0.8389 (p) cc_final: 0.8024 (t) REVERT: Q 267 MET cc_start: 0.7922 (ttm) cc_final: 0.7560 (ttm) REVERT: Q 275 SER cc_start: 0.7507 (t) cc_final: 0.6919 (p) REVERT: Q 276 ARG cc_start: 0.6963 (mmm160) cc_final: 0.6528 (tpm170) REVERT: Q 291 GLN cc_start: 0.7602 (tt0) cc_final: 0.7102 (mp10) REVERT: Q 298 ASN cc_start: 0.8550 (t0) cc_final: 0.8043 (t160) REVERT: Q 300 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7589 (mtt) REVERT: Q 306 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7506 (mpp80) REVERT: Q 332 ASN cc_start: 0.7038 (m-40) cc_final: 0.6795 (t0) REVERT: Q 336 LYS cc_start: 0.7967 (mptt) cc_final: 0.7691 (mptt) REVERT: Q 343 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7471 (pm20) outliers start: 54 outliers final: 18 residues processed: 220 average time/residue: 1.3387 time to fit residues: 320.5921 Evaluate side-chains 173 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 308 ARG Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 237 THR Chi-restraints excluded: chain Q residue 300 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 153 optimal weight: 0.4980 chunk 52 optimal weight: 0.0270 chunk 124 optimal weight: 0.2980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS Q 6 HIS Q 8 GLN ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13931 Z= 0.210 Angle : 0.521 9.180 18940 Z= 0.272 Chirality : 0.042 0.152 2078 Planarity : 0.005 0.039 2467 Dihedral : 11.126 179.309 1976 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.30 % Allowed : 14.45 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.58 (0.20), residues: 1720 helix: 1.20 (0.19), residues: 768 sheet: 1.19 (0.34), residues: 248 loop : -0.81 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.004 0.001 HIS I 266 PHE 0.026 0.001 PHE B 20 TYR 0.017 0.001 TYR B 159 ARG 0.008 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7373 (mm-30) REVERT: A 116 ASP cc_start: 0.7780 (m-30) cc_final: 0.7350 (m-30) REVERT: A 120 ASP cc_start: 0.7055 (m-30) cc_final: 0.6435 (m-30) REVERT: A 163 LYS cc_start: 0.8360 (tmtt) cc_final: 0.7882 (pmtt) REVERT: A 168 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 284 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 290 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7421 (mp0) REVERT: A 309 HIS cc_start: 0.7836 (m170) cc_final: 0.7582 (m-70) REVERT: A 432 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.5255 (t80) REVERT: B 118 ASP cc_start: 0.8721 (m-30) cc_final: 0.8419 (m-30) REVERT: B 328 GLU cc_start: 0.6540 (tp30) cc_final: 0.6162 (tp30) REVERT: B 394 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6479 (t80) REVERT: I 50 ASN cc_start: 0.7198 (t0) cc_final: 0.6758 (t0) REVERT: I 64 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5913 (mtt90) REVERT: I 96 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8639 (mtpp) REVERT: I 102 ASN cc_start: 0.8467 (t0) cc_final: 0.8089 (t0) REVERT: I 211 ASP cc_start: 0.6601 (t70) cc_final: 0.6295 (t70) REVERT: I 215 ARG cc_start: 0.6664 (ttp-110) cc_final: 0.5875 (mtm110) REVERT: I 279 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: I 300 ASN cc_start: 0.7002 (t0) cc_final: 0.6515 (t160) REVERT: I 370 LYS cc_start: 0.7834 (tttt) cc_final: 0.6970 (tptt) REVERT: I 414 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7378 (mm-30) REVERT: Q 108 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7256 (mm-30) REVERT: Q 118 ASP cc_start: 0.7219 (t0) cc_final: 0.6513 (m-30) REVERT: Q 158 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: Q 176 SER cc_start: 0.8362 (p) cc_final: 0.7971 (t) REVERT: Q 275 SER cc_start: 0.7503 (t) cc_final: 0.6604 (p) REVERT: Q 276 ARG cc_start: 0.6696 (mmm160) cc_final: 0.6375 (tpm170) REVERT: Q 279 GLN cc_start: 0.7229 (tp40) cc_final: 0.6661 (mt0) REVERT: Q 291 GLN cc_start: 0.7674 (tt0) cc_final: 0.7158 (mp10) REVERT: Q 298 ASN cc_start: 0.8642 (t0) cc_final: 0.8073 (t160) REVERT: Q 306 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7502 (mpp80) REVERT: Q 343 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7578 (pm20) outliers start: 48 outliers final: 15 residues processed: 199 average time/residue: 1.3756 time to fit residues: 297.4952 Evaluate side-chains 167 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 237 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 358 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 309 HIS Q 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13931 Z= 0.405 Angle : 0.607 12.087 18940 Z= 0.318 Chirality : 0.046 0.163 2078 Planarity : 0.005 0.042 2467 Dihedral : 11.610 179.355 1976 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.85 % Allowed : 14.25 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.24 (0.20), residues: 1720 helix: 0.88 (0.19), residues: 764 sheet: 0.86 (0.32), residues: 268 loop : -0.90 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 21 HIS 0.007 0.002 HIS A 266 PHE 0.023 0.002 PHE B 20 TYR 0.019 0.002 TYR Q 425 ARG 0.009 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 154 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7477 (mm-30) REVERT: A 116 ASP cc_start: 0.7811 (m-30) cc_final: 0.7396 (m-30) REVERT: A 120 ASP cc_start: 0.7304 (m-30) cc_final: 0.6703 (m-30) REVERT: A 163 LYS cc_start: 0.8223 (tmtt) cc_final: 0.7674 (pmtt) REVERT: A 168 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 215 ARG cc_start: 0.7527 (ttm110) cc_final: 0.7297 (ttp-110) REVERT: A 284 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: A 290 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7293 (mp0) REVERT: A 432 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.4574 (t80) REVERT: B 118 ASP cc_start: 0.8711 (m-30) cc_final: 0.8391 (m-30) REVERT: B 328 GLU cc_start: 0.6516 (tp30) cc_final: 0.6310 (tm-30) REVERT: B 394 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6585 (t80) REVERT: B 406 MET cc_start: 0.8802 (mpm) cc_final: 0.8394 (tpp) REVERT: I 64 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.5947 (mtt90) REVERT: I 279 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7569 (mm-30) REVERT: I 300 ASN cc_start: 0.7180 (t0) cc_final: 0.6622 (t160) REVERT: I 370 LYS cc_start: 0.8021 (tttt) cc_final: 0.7151 (tptt) REVERT: I 414 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7528 (mm-30) REVERT: Q 118 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6602 (m-30) REVERT: Q 158 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: Q 176 SER cc_start: 0.8295 (p) cc_final: 0.7862 (t) REVERT: Q 212 PHE cc_start: 0.7580 (m-80) cc_final: 0.7356 (m-10) REVERT: Q 275 SER cc_start: 0.7660 (t) cc_final: 0.7029 (p) REVERT: Q 279 GLN cc_start: 0.7235 (tp40) cc_final: 0.6989 (mt0) REVERT: Q 291 GLN cc_start: 0.7818 (tt0) cc_final: 0.7208 (mp-120) REVERT: Q 298 ASN cc_start: 0.8620 (t0) cc_final: 0.8043 (t160) REVERT: Q 300 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7661 (mtt) REVERT: Q 306 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7581 (mpp80) REVERT: Q 343 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7340 (pm20) outliers start: 56 outliers final: 26 residues processed: 197 average time/residue: 1.3491 time to fit residues: 289.5998 Evaluate side-chains 176 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 237 THR Chi-restraints excluded: chain Q residue 300 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 113 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 309 HIS Q 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13931 Z= 0.278 Angle : 0.544 12.085 18940 Z= 0.282 Chirality : 0.044 0.148 2078 Planarity : 0.005 0.045 2467 Dihedral : 11.311 178.634 1973 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.30 % Allowed : 15.42 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.22 (0.20), residues: 1720 helix: 0.92 (0.19), residues: 764 sheet: 0.62 (0.31), residues: 278 loop : -0.90 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.004 0.001 HIS I 266 PHE 0.024 0.001 PHE B 20 TYR 0.014 0.001 TYR B 159 ARG 0.010 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 153 time to evaluate : 1.582 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 116 ASP cc_start: 0.7809 (m-30) cc_final: 0.7376 (m-30) REVERT: A 120 ASP cc_start: 0.7210 (m-30) cc_final: 0.6626 (m-30) REVERT: A 154 MET cc_start: 0.7890 (mmp) cc_final: 0.7562 (mmm) REVERT: A 163 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7702 (pmtt) REVERT: A 168 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 215 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7293 (ttp-110) REVERT: A 284 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 290 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7347 (mp0) REVERT: A 432 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.4566 (t80) REVERT: B 118 ASP cc_start: 0.8712 (m-30) cc_final: 0.8396 (m-30) REVERT: B 394 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6507 (t80) REVERT: I 20 CYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6796 (m) REVERT: I 64 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.5945 (mtt90) REVERT: I 211 ASP cc_start: 0.6436 (t70) cc_final: 0.6208 (t70) REVERT: I 279 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7559 (mm-30) REVERT: I 300 ASN cc_start: 0.7172 (t0) cc_final: 0.6592 (t160) REVERT: I 370 LYS cc_start: 0.8009 (tttt) cc_final: 0.7174 (tptt) REVERT: I 414 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7521 (mm-30) REVERT: Q 118 ASP cc_start: 0.7299 (t0) cc_final: 0.6554 (m-30) REVERT: Q 158 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: Q 176 SER cc_start: 0.8280 (p) cc_final: 0.7887 (t) REVERT: Q 212 PHE cc_start: 0.7625 (m-80) cc_final: 0.7415 (m-10) REVERT: Q 274 THR cc_start: 0.8484 (p) cc_final: 0.8079 (p) REVERT: Q 275 SER cc_start: 0.7690 (t) cc_final: 0.7253 (p) REVERT: Q 291 GLN cc_start: 0.7795 (tt0) cc_final: 0.7171 (mp-120) REVERT: Q 298 ASN cc_start: 0.8741 (t0) cc_final: 0.8079 (t160) REVERT: Q 300 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7655 (mtt) REVERT: Q 306 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7486 (mpp80) REVERT: Q 343 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7469 (pm20) outliers start: 48 outliers final: 26 residues processed: 190 average time/residue: 1.2735 time to fit residues: 264.3002 Evaluate side-chains 172 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 194 GLU Chi-restraints excluded: chain Q residue 237 THR Chi-restraints excluded: chain Q residue 300 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13931 Z= 0.334 Angle : 0.576 12.365 18940 Z= 0.298 Chirality : 0.044 0.154 2078 Planarity : 0.005 0.047 2467 Dihedral : 11.408 177.580 1973 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.37 % Allowed : 16.66 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.12 (0.20), residues: 1720 helix: 0.82 (0.19), residues: 764 sheet: 0.54 (0.31), residues: 278 loop : -0.91 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.005 0.001 HIS A 266 PHE 0.022 0.001 PHE B 20 TYR 0.016 0.001 TYR Q 425 ARG 0.011 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 147 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 116 ASP cc_start: 0.7825 (m-30) cc_final: 0.7412 (m-30) REVERT: A 120 ASP cc_start: 0.7205 (m-30) cc_final: 0.6620 (m-30) REVERT: A 154 MET cc_start: 0.7913 (mmp) cc_final: 0.7608 (mmm) REVERT: A 163 LYS cc_start: 0.8178 (tmtt) cc_final: 0.7686 (pmtt) REVERT: A 168 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 284 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: A 290 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7294 (mp0) REVERT: A 338 LYS cc_start: 0.7366 (mtpp) cc_final: 0.7093 (mtpp) REVERT: A 432 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.4603 (t80) REVERT: B 118 ASP cc_start: 0.8711 (m-30) cc_final: 0.8392 (m-30) REVERT: B 406 MET cc_start: 0.8690 (mpm) cc_final: 0.8456 (tpp) REVERT: I 20 CYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6782 (m) REVERT: I 64 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.5974 (mtt90) REVERT: I 205 ASP cc_start: 0.7414 (t0) cc_final: 0.6816 (t0) REVERT: I 215 ARG cc_start: 0.6743 (ttp-110) cc_final: 0.6533 (ttp-110) REVERT: I 279 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7513 (mm-30) REVERT: I 300 ASN cc_start: 0.7285 (t0) cc_final: 0.6650 (t160) REVERT: I 370 LYS cc_start: 0.8087 (tttt) cc_final: 0.7245 (tptt) REVERT: I 414 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7538 (mm-30) REVERT: Q 69 GLU cc_start: 0.6387 (pt0) cc_final: 0.6170 (pt0) REVERT: Q 118 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6586 (m-30) REVERT: Q 158 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: Q 176 SER cc_start: 0.8177 (p) cc_final: 0.7772 (t) REVERT: Q 274 THR cc_start: 0.8397 (p) cc_final: 0.8136 (p) REVERT: Q 275 SER cc_start: 0.7601 (t) cc_final: 0.7186 (p) REVERT: Q 291 GLN cc_start: 0.7826 (tt0) cc_final: 0.7153 (mp-120) REVERT: Q 298 ASN cc_start: 0.8587 (t0) cc_final: 0.7861 (t160) REVERT: Q 300 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7698 (mtt) REVERT: Q 306 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7508 (mpp80) REVERT: Q 343 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7484 (pm20) outliers start: 49 outliers final: 28 residues processed: 186 average time/residue: 1.3272 time to fit residues: 269.2603 Evaluate side-chains 177 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 194 GLU Chi-restraints excluded: chain Q residue 237 THR Chi-restraints excluded: chain Q residue 300 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 0.4980 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 163 optimal weight: 0.0670 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN I 31 GLN I 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13931 Z= 0.229 Angle : 0.523 10.954 18940 Z= 0.270 Chirality : 0.042 0.134 2078 Planarity : 0.005 0.052 2467 Dihedral : 11.189 176.414 1973 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.62 % Allowed : 17.83 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.27 (0.20), residues: 1720 helix: 0.97 (0.19), residues: 764 sheet: 0.58 (0.31), residues: 278 loop : -0.85 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 21 HIS 0.004 0.001 HIS Q 396 PHE 0.029 0.001 PHE B 20 TYR 0.012 0.001 TYR B 340 ARG 0.010 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 116 ASP cc_start: 0.7801 (m-30) cc_final: 0.7303 (m-30) REVERT: A 120 ASP cc_start: 0.7214 (m-30) cc_final: 0.6598 (m-30) REVERT: A 154 MET cc_start: 0.7864 (mmp) cc_final: 0.7547 (mmm) REVERT: A 163 LYS cc_start: 0.8145 (tmtt) cc_final: 0.7677 (pmtt) REVERT: A 215 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7390 (ttp-110) REVERT: A 284 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: A 290 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7344 (mp0) REVERT: A 432 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.4484 (t80) REVERT: B 118 ASP cc_start: 0.8705 (m-30) cc_final: 0.8380 (m-30) REVERT: B 406 MET cc_start: 0.8816 (mpm) cc_final: 0.8530 (tpp) REVERT: I 20 CYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6479 (m) REVERT: I 64 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.5961 (mtt90) REVERT: I 102 ASN cc_start: 0.8572 (t0) cc_final: 0.8211 (t0) REVERT: I 205 ASP cc_start: 0.7382 (t0) cc_final: 0.6812 (t0) REVERT: I 215 ARG cc_start: 0.6764 (ttp-110) cc_final: 0.6538 (mtm-85) REVERT: I 279 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7523 (mm-30) REVERT: I 300 ASN cc_start: 0.7206 (t0) cc_final: 0.6560 (t160) REVERT: I 370 LYS cc_start: 0.8081 (tttt) cc_final: 0.7236 (tptt) REVERT: I 414 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7491 (mm-30) REVERT: Q 69 GLU cc_start: 0.6515 (pt0) cc_final: 0.6282 (pt0) REVERT: Q 118 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: Q 158 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: Q 176 SER cc_start: 0.8163 (p) cc_final: 0.7771 (t) REVERT: Q 212 PHE cc_start: 0.7595 (m-80) cc_final: 0.7370 (m-10) REVERT: Q 274 THR cc_start: 0.8393 (p) cc_final: 0.8172 (p) REVERT: Q 275 SER cc_start: 0.7561 (t) cc_final: 0.7154 (p) REVERT: Q 278 SER cc_start: 0.8300 (m) cc_final: 0.8047 (t) REVERT: Q 291 GLN cc_start: 0.7694 (tt0) cc_final: 0.7068 (mp-120) REVERT: Q 298 ASN cc_start: 0.8736 (t0) cc_final: 0.7997 (t160) REVERT: Q 300 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7676 (mtt) REVERT: Q 306 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7480 (mpp80) REVERT: Q 336 LYS cc_start: 0.7025 (mptt) cc_final: 0.6815 (mppt) REVERT: Q 343 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7484 (pm20) outliers start: 38 outliers final: 22 residues processed: 185 average time/residue: 1.3539 time to fit residues: 273.1799 Evaluate side-chains 175 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 194 GLU Chi-restraints excluded: chain Q residue 237 THR Chi-restraints excluded: chain Q residue 300 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 149 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13931 Z= 0.256 Angle : 0.541 10.850 18940 Z= 0.279 Chirality : 0.043 0.134 2078 Planarity : 0.005 0.054 2467 Dihedral : 11.157 176.695 1971 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.96 % Allowed : 17.55 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.26 (0.20), residues: 1720 helix: 0.96 (0.19), residues: 766 sheet: 0.60 (0.31), residues: 278 loop : -0.86 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.004 0.001 HIS A 266 PHE 0.028 0.001 PHE B 20 TYR 0.015 0.001 TYR B 159 ARG 0.012 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 116 ASP cc_start: 0.7809 (m-30) cc_final: 0.7306 (m-30) REVERT: A 120 ASP cc_start: 0.7142 (m-30) cc_final: 0.6520 (m-30) REVERT: A 154 MET cc_start: 0.7857 (mmp) cc_final: 0.7542 (mmm) REVERT: A 163 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7702 (pmtt) REVERT: A 284 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: A 290 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7357 (mp0) REVERT: A 313 MET cc_start: 0.8777 (mtm) cc_final: 0.8496 (mtm) REVERT: A 432 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.4500 (t80) REVERT: B 118 ASP cc_start: 0.8680 (m-30) cc_final: 0.8351 (m-30) REVERT: B 406 MET cc_start: 0.8824 (mpm) cc_final: 0.8518 (tpp) REVERT: B 416 ASN cc_start: 0.8805 (m-40) cc_final: 0.8523 (m-40) REVERT: I 20 CYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6632 (m) REVERT: I 64 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.5966 (mtt90) REVERT: I 205 ASP cc_start: 0.7403 (t0) cc_final: 0.6907 (t0) REVERT: I 279 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7507 (mm-30) REVERT: I 300 ASN cc_start: 0.7192 (t0) cc_final: 0.6530 (t160) REVERT: I 370 LYS cc_start: 0.8108 (tttt) cc_final: 0.7255 (tptt) REVERT: I 414 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7500 (mm-30) REVERT: Q 69 GLU cc_start: 0.6636 (pt0) cc_final: 0.6407 (pt0) REVERT: Q 118 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: Q 158 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: Q 176 SER cc_start: 0.8213 (p) cc_final: 0.7825 (t) REVERT: Q 212 PHE cc_start: 0.7601 (m-80) cc_final: 0.7359 (m-10) REVERT: Q 274 THR cc_start: 0.8476 (p) cc_final: 0.8259 (p) REVERT: Q 275 SER cc_start: 0.7669 (t) cc_final: 0.7278 (p) REVERT: Q 278 SER cc_start: 0.8271 (m) cc_final: 0.8017 (t) REVERT: Q 291 GLN cc_start: 0.7705 (tt0) cc_final: 0.7073 (mp-120) REVERT: Q 298 ASN cc_start: 0.8603 (t0) cc_final: 0.7811 (t160) REVERT: Q 300 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7684 (mtt) REVERT: Q 306 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7486 (mpp80) REVERT: Q 343 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7485 (pm20) outliers start: 43 outliers final: 24 residues processed: 186 average time/residue: 1.2986 time to fit residues: 263.8416 Evaluate side-chains 177 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 194 GLU Chi-restraints excluded: chain Q residue 237 THR Chi-restraints excluded: chain Q residue 300 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 chunk 66 optimal weight: 0.0050 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 101 ASN I 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13931 Z= 0.247 Angle : 0.550 10.298 18940 Z= 0.281 Chirality : 0.043 0.137 2078 Planarity : 0.005 0.058 2467 Dihedral : 11.099 176.518 1971 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.75 % Allowed : 18.10 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.26 (0.20), residues: 1720 helix: 0.98 (0.19), residues: 764 sheet: 0.59 (0.31), residues: 278 loop : -0.89 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 21 HIS 0.004 0.001 HIS I 266 PHE 0.027 0.001 PHE B 20 TYR 0.015 0.001 TYR B 281 ARG 0.013 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7810 (m-30) cc_final: 0.7304 (m-30) REVERT: A 120 ASP cc_start: 0.7143 (m-30) cc_final: 0.6518 (m-30) REVERT: A 154 MET cc_start: 0.7852 (mmp) cc_final: 0.7537 (mmm) REVERT: A 163 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7693 (pmtt) REVERT: A 284 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: A 290 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7358 (mp0) REVERT: A 313 MET cc_start: 0.8769 (mtm) cc_final: 0.8396 (mtm) REVERT: A 432 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.4533 (t80) REVERT: B 118 ASP cc_start: 0.8673 (m-30) cc_final: 0.8343 (m-30) REVERT: B 125 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 406 MET cc_start: 0.8834 (mpm) cc_final: 0.8523 (tpp) REVERT: B 416 ASN cc_start: 0.8813 (m-40) cc_final: 0.8524 (m-40) REVERT: I 20 CYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6657 (m) REVERT: I 64 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5951 (mtt90) REVERT: I 205 ASP cc_start: 0.7394 (t0) cc_final: 0.6903 (t0) REVERT: I 215 ARG cc_start: 0.7002 (ttp-110) cc_final: 0.6779 (mtm-85) REVERT: I 279 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7477 (mm-30) REVERT: I 300 ASN cc_start: 0.7183 (t0) cc_final: 0.6532 (t160) REVERT: I 370 LYS cc_start: 0.8108 (tttt) cc_final: 0.7255 (tptt) REVERT: I 414 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7501 (mm-30) REVERT: Q 69 GLU cc_start: 0.7001 (pt0) cc_final: 0.6739 (pt0) REVERT: Q 118 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: Q 158 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: Q 176 SER cc_start: 0.8159 (p) cc_final: 0.7768 (t) REVERT: Q 212 PHE cc_start: 0.7611 (m-80) cc_final: 0.7368 (m-10) REVERT: Q 274 THR cc_start: 0.8481 (p) cc_final: 0.8265 (p) REVERT: Q 275 SER cc_start: 0.7678 (t) cc_final: 0.7293 (p) REVERT: Q 278 SER cc_start: 0.8268 (m) cc_final: 0.8018 (t) REVERT: Q 291 GLN cc_start: 0.7703 (tt0) cc_final: 0.7063 (mp-120) REVERT: Q 298 ASN cc_start: 0.8554 (t0) cc_final: 0.7832 (t160) REVERT: Q 300 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7668 (mtt) REVERT: Q 306 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7483 (mpp80) REVERT: Q 343 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7485 (pm20) outliers start: 40 outliers final: 27 residues processed: 185 average time/residue: 1.2814 time to fit residues: 259.4600 Evaluate side-chains 181 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 194 GLU Chi-restraints excluded: chain Q residue 237 THR Chi-restraints excluded: chain Q residue 300 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 134 optimal weight: 0.0170 chunk 14 optimal weight: 0.5980 chunk 104 optimal weight: 0.0870 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 101 ASN I 309 HIS ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13931 Z= 0.196 Angle : 0.534 11.225 18940 Z= 0.271 Chirality : 0.042 0.135 2078 Planarity : 0.005 0.059 2467 Dihedral : 10.883 175.265 1971 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.00 % Allowed : 19.06 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.34 (0.20), residues: 1720 helix: 1.08 (0.19), residues: 764 sheet: 0.67 (0.32), residues: 266 loop : -0.88 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 21 HIS 0.004 0.001 HIS Q 396 PHE 0.027 0.001 PHE B 20 TYR 0.015 0.001 TYR B 281 ARG 0.015 0.000 ARG A 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7805 (m-30) cc_final: 0.7284 (m-30) REVERT: A 120 ASP cc_start: 0.7138 (m-30) cc_final: 0.6486 (m-30) REVERT: A 154 MET cc_start: 0.7829 (mmp) cc_final: 0.7535 (mmm) REVERT: A 163 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7597 (pmtt) REVERT: A 284 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: A 290 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7353 (mp0) REVERT: A 313 MET cc_start: 0.8766 (mtm) cc_final: 0.8452 (mtm) REVERT: A 432 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.4480 (t80) REVERT: B 118 ASP cc_start: 0.8672 (m-30) cc_final: 0.8335 (m-30) REVERT: B 125 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8012 (mm-30) REVERT: B 406 MET cc_start: 0.8828 (mpm) cc_final: 0.8515 (tpp) REVERT: B 416 ASN cc_start: 0.8787 (m-40) cc_final: 0.8491 (m-40) REVERT: I 20 CYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6427 (m) REVERT: I 64 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5907 (mtt90) REVERT: I 91 GLN cc_start: 0.6252 (mt0) cc_final: 0.5564 (mm-40) REVERT: I 102 ASN cc_start: 0.8536 (t0) cc_final: 0.8199 (t0) REVERT: I 205 ASP cc_start: 0.7350 (t0) cc_final: 0.6796 (t0) REVERT: I 215 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.6800 (mtm-85) REVERT: I 279 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7426 (mm-30) REVERT: I 300 ASN cc_start: 0.7205 (t0) cc_final: 0.6577 (t160) REVERT: I 370 LYS cc_start: 0.8100 (tttt) cc_final: 0.7249 (tptt) REVERT: I 414 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7496 (mm-30) REVERT: Q 118 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: Q 176 SER cc_start: 0.8199 (p) cc_final: 0.7817 (t) REVERT: Q 212 PHE cc_start: 0.7606 (m-80) cc_final: 0.7370 (m-10) REVERT: Q 274 THR cc_start: 0.8472 (p) cc_final: 0.8257 (p) REVERT: Q 275 SER cc_start: 0.7670 (t) cc_final: 0.7305 (p) REVERT: Q 278 SER cc_start: 0.8289 (m) cc_final: 0.8014 (t) REVERT: Q 291 GLN cc_start: 0.7685 (tt0) cc_final: 0.7064 (mp-120) REVERT: Q 298 ASN cc_start: 0.8529 (t0) cc_final: 0.7791 (t160) REVERT: Q 306 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7457 (mpp80) REVERT: Q 343 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7772 (pm20) outliers start: 29 outliers final: 23 residues processed: 186 average time/residue: 1.2170 time to fit residues: 248.3823 Evaluate side-chains 174 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 237 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 17 optimal weight: 0.0270 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.121138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092433 restraints weight = 17255.885| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.76 r_work: 0.3329 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13931 Z= 0.253 Angle : 0.552 10.412 18940 Z= 0.282 Chirality : 0.043 0.141 2078 Planarity : 0.005 0.066 2467 Dihedral : 10.953 176.579 1971 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.34 % Allowed : 19.00 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.33 (0.20), residues: 1720 helix: 1.05 (0.19), residues: 752 sheet: 0.61 (0.31), residues: 278 loop : -0.82 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.004 0.001 HIS I 266 PHE 0.026 0.001 PHE B 20 TYR 0.015 0.001 TYR B 281 ARG 0.015 0.000 ARG B 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5536.63 seconds wall clock time: 99 minutes 28.51 seconds (5968.51 seconds total)