Starting phenix.real_space_refine on Sun Jul 21 09:11:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t42_41018/07_2024/8t42_41018_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t42_41018/07_2024/8t42_41018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t42_41018/07_2024/8t42_41018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t42_41018/07_2024/8t42_41018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t42_41018/07_2024/8t42_41018_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t42_41018/07_2024/8t42_41018_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 94 5.16 5 C 8703 2.51 5 N 2363 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 90": "OE1" <-> "OE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 160": "OD1" <-> "OD2" Residue "F ASP 211": "OD1" <-> "OD2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 423": "OE1" <-> "OE2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F GLU 433": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13854 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3348 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3371 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain: "F" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3401 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Chain: "N" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 208 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "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: "E" 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: "F" 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} Time building chain proxies: 12.07, per 1000 atoms: 0.87 Number of scatterers: 13854 At special positions: 0 Unit cell: (74.75, 85.1, 196.65, 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 94 16.00 P 12 15.00 Mg 4 11.99 O 2678 8.00 N 2363 7.00 C 8703 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: 5.40 Conformation dependent library (CDL) restraints added in 2.5 seconds 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 12 sheets defined 52.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.579A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 removed outlier: 4.341A pdb=" N PHE A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.794A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.523A pdb=" N GLY A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.017A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.787A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.632A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 Processing helix chain 'A' and resid 241 through 244 removed outlier: 3.975A pdb=" N PHE A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.053A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.511A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.942A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.484A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.881A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.359A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) 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 69 through 79 removed outlier: 4.370A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 106 removed outlier: 3.518A pdb=" N GLY B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 127 removed outlier: 4.442A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.557A pdb=" N GLY B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 4.254A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.693A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.650A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.587A pdb=" N ASP B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.637A pdb=" N HIS B 307 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.371A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 removed outlier: 4.196A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.625A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 46 through 49 removed outlier: 3.581A pdb=" N VAL E 49 " --> pdb=" O ARG E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 69 through 78 removed outlier: 4.668A pdb=" N MET E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 108 through 127 removed outlier: 4.042A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 159 removed outlier: 4.553A pdb=" N MET E 147 " --> pdb=" O THR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 removed outlier: 3.515A pdb=" N ASN E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 214 Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.974A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR E 237 " --> pdb=" O MET E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.898A pdb=" N ARG E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.804A pdb=" N PHE E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 299 removed outlier: 4.033A pdb=" N MET E 299 " --> pdb=" O ALA E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 299' Processing helix chain 'E' and resid 304 through 308 Processing helix chain 'E' and resid 323 through 337 Processing helix chain 'E' and resid 338 through 341 Processing helix chain 'E' and resid 374 through 388 removed outlier: 3.616A pdb=" N ILE E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 400 removed outlier: 3.905A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY E 400 " --> pdb=" O HIS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 426 removed outlier: 4.029A pdb=" N PHE E 408 " --> pdb=" O ASP E 404 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 45 through 51 removed outlier: 4.417A pdb=" N PHE F 49 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR F 51 " --> pdb=" O SER F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.353A pdb=" N ILE F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.582A pdb=" N ASP F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 removed outlier: 4.410A pdb=" N THR F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 190 through 197 removed outlier: 3.709A pdb=" N HIS F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 239 Processing helix chain 'F' and resid 239 through 244 removed outlier: 3.838A pdb=" N ARG F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.595A pdb=" N PHE F 296 " --> pdb=" O THR F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 337 removed outlier: 3.515A pdb=" N VAL F 328 " --> pdb=" O VAL F 324 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 400 removed outlier: 4.109A pdb=" N ALA F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 412 removed outlier: 3.611A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 436 removed outlier: 4.353A pdb=" N SER F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 436 " --> pdb=" O TYR F 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 480 through 499 removed outlier: 3.748A pdb=" N GLN N 489 " --> pdb=" O GLN N 485 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.871A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.697A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.084A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 198 " --> pdb=" O MET B 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'B' and resid 270 through 271 removed outlier: 4.078A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 92 removed outlier: 8.013A pdb=" N VAL E 91 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 65 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU E 3 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE E 133 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL E 5 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU E 135 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE E 7 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU E 198 " --> pdb=" O MET E 164 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR E 199 " --> pdb=" O PHE E 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'E' and resid 270 through 271 Processing sheet with id=AB1, first strand: chain 'F' and resid 65 through 68 removed outlier: 8.662A pdb=" N VAL F 66 " --> pdb=" O CYS F 4 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER F 6 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL F 68 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER F 140 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE F 135 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE F 171 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N HIS F 139 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS F 200 " --> pdb=" O LYS F 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'F' and resid 269 through 273 658 hydrogen bonds defined for protein. 1911 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: 4.52 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2642 1.33 - 1.46: 4025 1.46 - 1.59: 7326 1.59 - 1.71: 18 1.71 - 1.84: 152 Bond restraints: 14163 Sorted by residual: bond pdb=" C ILE F 171 " pdb=" N TYR F 172 " ideal model delta sigma weight residual 1.331 1.275 0.056 2.07e-02 2.33e+03 7.42e+00 bond pdb=" CB ILE A 7 " pdb=" CG2 ILE A 7 " ideal model delta sigma weight residual 1.521 1.608 -0.087 3.30e-02 9.18e+02 7.00e+00 bond pdb=" CG LYS B 324 " pdb=" CD LYS B 324 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.64e+00 bond pdb=" C ARG A 221 " pdb=" N PRO A 222 " ideal model delta sigma weight residual 1.334 1.393 -0.060 2.34e-02 1.83e+03 6.48e+00 bond pdb=" C ARG F 221 " pdb=" N PRO F 222 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.99e+00 ... (remaining 14158 not shown) Histogram of bond angle deviations from ideal: 93.04 - 101.23: 28 101.23 - 109.42: 1578 109.42 - 117.61: 8500 117.61 - 125.80: 8868 125.80 - 133.99: 263 Bond angle restraints: 19237 Sorted by residual: angle pdb=" CA PRO A 298 " pdb=" N PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 112.00 104.43 7.57 1.40e+00 5.10e-01 2.92e+01 angle pdb=" CB ARG F 221 " pdb=" CG ARG F 221 " pdb=" CD ARG F 221 " ideal model delta sigma weight residual 111.30 122.78 -11.48 2.30e+00 1.89e-01 2.49e+01 angle pdb=" CB GLU B 108 " pdb=" CG GLU B 108 " pdb=" CD GLU B 108 " ideal model delta sigma weight residual 112.60 121.00 -8.40 1.70e+00 3.46e-01 2.44e+01 angle pdb=" CA GLN E 291 " pdb=" CB GLN E 291 " pdb=" CG GLN E 291 " ideal model delta sigma weight residual 114.10 123.33 -9.23 2.00e+00 2.50e-01 2.13e+01 angle pdb=" CB MET F 36 " pdb=" CG MET F 36 " pdb=" SD MET F 36 " ideal model delta sigma weight residual 112.70 126.38 -13.68 3.00e+00 1.11e-01 2.08e+01 ... (remaining 19232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 8179 32.81 - 65.62: 259 65.62 - 98.43: 14 98.43 - 131.23: 0 131.23 - 164.04: 4 Dihedral angle restraints: 8456 sinusoidal: 3404 harmonic: 5052 Sorted by residual: dihedral pdb=" C8 GTP F 501 " pdb=" C1' GTP F 501 " pdb=" N9 GTP F 501 " pdb=" O4' GTP F 501 " ideal model delta sinusoidal sigma weight residual 104.59 -59.45 164.04 1 2.00e+01 2.50e-03 4.71e+01 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 -137.13 -153.60 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" CA SER B 322 " pdb=" C SER B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual -180.00 -147.63 -32.37 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 8453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1690 0.064 - 0.128: 360 0.128 - 0.192: 50 0.192 - 0.256: 5 0.256 - 0.320: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" CB ILE A 7 " pdb=" CA ILE A 7 " pdb=" CG1 ILE A 7 " pdb=" CG2 ILE A 7 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB THR A 239 " pdb=" CA THR A 239 " pdb=" OG1 THR A 239 " pdb=" CG2 THR A 239 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLN B 329 " pdb=" N GLN B 329 " pdb=" C GLN B 329 " pdb=" CB GLN B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2103 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 297 " -0.093 5.00e-02 4.00e+02 1.37e-01 3.00e+01 pdb=" N PRO A 298 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 121 " 0.339 9.50e-02 1.11e+02 1.52e-01 1.55e+01 pdb=" NE ARG B 121 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 121 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 121 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 121 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 221 " -0.326 9.50e-02 1.11e+02 1.46e-01 1.33e+01 pdb=" NE ARG A 221 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 221 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 221 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 221 " -0.009 2.00e-02 2.50e+03 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 145 2.58 - 3.16: 11652 3.16 - 3.74: 22616 3.74 - 4.32: 30765 4.32 - 4.90: 51225 Nonbonded interactions: 116403 Sorted by model distance: nonbonded pdb=" O3G G2P E 501 " pdb="MG MG E 502 " model vdw 1.998 2.170 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 1.999 2.170 nonbonded pdb=" O1G GTP F 501 " pdb="MG MG F 502 " model vdw 2.006 2.170 nonbonded pdb=" O3G G2P B 501 " pdb="MG MG B 502 " model vdw 2.015 2.170 nonbonded pdb=" OE1 GLU F 71 " pdb="MG MG F 502 " model vdw 2.024 2.170 ... (remaining 116398 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 44 or resid 46 through 439 or resid 501 through \ 502)) selection = (chain 'F' and (resid 1 through 325 or (resid 326 and (name N or name CA or name \ C or name O or name CB )) or resid 327 through 439 or resid 501 through 502)) } ncs_group { reference = chain 'B' selection = (chain 'E' and (resid 1 through 389 or (resid 390 and (name N or name CA or name \ C or name O or name CB )) or resid 391 through 427 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.770 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 44.190 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 : 0.007 0.087 14163 Z= 0.449 Angle : 1.110 13.675 19237 Z= 0.581 Chirality : 0.054 0.320 2106 Planarity : 0.009 0.152 2502 Dihedral : 16.003 164.042 5218 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.13 % Allowed : 14.40 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1738 helix: 0.12 (0.17), residues: 750 sheet: -2.25 (0.27), residues: 277 loop : -1.29 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 407 HIS 0.039 0.003 HIS E 190 PHE 0.020 0.002 PHE F 149 TYR 0.044 0.002 TYR B 159 ARG 0.034 0.001 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 565 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.6888 (mp0) cc_final: 0.6550 (mp0) REVERT: A 8 HIS cc_start: 0.7666 (m-70) cc_final: 0.7381 (m170) REVERT: A 26 LEU cc_start: 0.8267 (mp) cc_final: 0.8049 (mt) REVERT: A 47 ASP cc_start: 0.7806 (p0) cc_final: 0.7425 (p0) REVERT: A 91 GLN cc_start: 0.7981 (pt0) cc_final: 0.7693 (pt0) REVERT: A 154 MET cc_start: 0.7926 (mmm) cc_final: 0.7575 (mmm) REVERT: A 166 LYS cc_start: 0.7372 (mtmm) cc_final: 0.7122 (mttp) REVERT: A 181 VAL cc_start: 0.8509 (m) cc_final: 0.8308 (p) REVERT: A 187 SER cc_start: 0.8149 (m) cc_final: 0.7797 (p) REVERT: A 203 MET cc_start: 0.7412 (mmp) cc_final: 0.7068 (mmp) REVERT: A 215 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6899 (mtt180) REVERT: A 237 SER cc_start: 0.8445 (m) cc_final: 0.8068 (p) REVERT: A 243 ARG cc_start: 0.8281 (ptt90) cc_final: 0.8040 (ptt180) REVERT: A 254 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6767 (mt-10) REVERT: A 259 LEU cc_start: 0.7732 (tp) cc_final: 0.7514 (mp) REVERT: A 276 ILE cc_start: 0.8579 (tp) cc_final: 0.8179 (tp) REVERT: A 284 GLU cc_start: 0.7794 (tt0) cc_final: 0.7299 (tt0) REVERT: A 290 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6739 (mt-10) REVERT: A 304 LYS cc_start: 0.8316 (tppt) cc_final: 0.8095 (tppt) REVERT: A 309 HIS cc_start: 0.6596 (m-70) cc_final: 0.6187 (m-70) REVERT: A 311 LYS cc_start: 0.8277 (mttp) cc_final: 0.7794 (mtpp) REVERT: A 312 TYR cc_start: 0.7479 (m-80) cc_final: 0.7183 (m-80) REVERT: A 376 CYS cc_start: 0.8033 (t) cc_final: 0.7493 (t) REVERT: A 391 LEU cc_start: 0.7596 (mm) cc_final: 0.7384 (mt) REVERT: A 405 VAL cc_start: 0.7851 (m) cc_final: 0.7622 (t) REVERT: A 433 GLU cc_start: 0.7315 (tp30) cc_final: 0.7039 (pt0) REVERT: B 35 THR cc_start: 0.8342 (p) cc_final: 0.8114 (p) REVERT: B 44 LEU cc_start: 0.8499 (mt) cc_final: 0.8269 (mt) REVERT: B 53 GLU cc_start: 0.6489 (tp30) cc_final: 0.6180 (tp30) REVERT: B 74 ASP cc_start: 0.7173 (m-30) cc_final: 0.6970 (m-30) REVERT: B 86 ARG cc_start: 0.7622 (mtt180) cc_final: 0.6276 (mmp80) REVERT: B 99 ASN cc_start: 0.7631 (m-40) cc_final: 0.7173 (m-40) REVERT: B 122 LYS cc_start: 0.7538 (tttt) cc_final: 0.7249 (tmtt) REVERT: B 209 ASP cc_start: 0.7650 (t70) cc_final: 0.7074 (t0) REVERT: B 221 THR cc_start: 0.8287 (t) cc_final: 0.8074 (p) REVERT: B 247 ASN cc_start: 0.7947 (m110) cc_final: 0.7706 (m-40) REVERT: B 280 GLN cc_start: 0.7487 (mt0) cc_final: 0.6996 (mt0) REVERT: B 298 ASN cc_start: 0.6609 (t0) cc_final: 0.6339 (t0) REVERT: B 318 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7422 (mtp-110) REVERT: B 362 LYS cc_start: 0.8378 (tttt) cc_final: 0.8150 (tttt) REVERT: B 381 ILE cc_start: 0.7763 (mm) cc_final: 0.7535 (tt) REVERT: B 415 MET cc_start: 0.7867 (mmm) cc_final: 0.7286 (tpt) REVERT: E 1 MET cc_start: 0.6013 (ptm) cc_final: 0.5676 (ptm) REVERT: E 3 GLU cc_start: 0.6937 (mp0) cc_final: 0.6098 (mp0) REVERT: E 35 THR cc_start: 0.8128 (p) cc_final: 0.7829 (p) REVERT: E 51 TYR cc_start: 0.8076 (m-80) cc_final: 0.7804 (m-80) REVERT: E 59 TYR cc_start: 0.8187 (m-80) cc_final: 0.7561 (m-80) REVERT: E 65 LEU cc_start: 0.8376 (mp) cc_final: 0.8114 (mt) REVERT: E 69 GLU cc_start: 0.6656 (tt0) cc_final: 0.6312 (tt0) REVERT: E 86 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6062 (tpm170) REVERT: E 137 HIS cc_start: 0.7533 (p90) cc_final: 0.7314 (p90) REVERT: E 154 LYS cc_start: 0.7577 (mmtm) cc_final: 0.7364 (mmtm) REVERT: E 164 MET cc_start: 0.5874 (mpp) cc_final: 0.5525 (mpp) REVERT: E 174 LYS cc_start: 0.8049 (mptt) cc_final: 0.7694 (mptt) REVERT: E 175 VAL cc_start: 0.7853 (m) cc_final: 0.7266 (t) REVERT: E 203 ASP cc_start: 0.7432 (t0) cc_final: 0.7161 (t0) REVERT: E 209 ASP cc_start: 0.7414 (t0) cc_final: 0.5367 (t0) REVERT: E 213 ARG cc_start: 0.6519 (mtm180) cc_final: 0.6007 (mtm180) REVERT: E 216 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7863 (mmtt) REVERT: E 265 PHE cc_start: 0.8046 (m-80) cc_final: 0.7839 (m-80) REVERT: E 279 GLN cc_start: 0.7891 (pt0) cc_final: 0.7503 (pt0) REVERT: E 280 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7714 (mm-40) REVERT: E 288 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6325 (tm-30) REVERT: E 299 MET cc_start: 0.6110 (mmm) cc_final: 0.5656 (mmm) REVERT: E 338 SER cc_start: 0.8195 (t) cc_final: 0.7821 (p) REVERT: E 385 PHE cc_start: 0.7761 (t80) cc_final: 0.7547 (t80) REVERT: E 394 PHE cc_start: 0.8003 (m-80) cc_final: 0.7573 (m-80) REVERT: E 405 GLU cc_start: 0.7140 (tt0) cc_final: 0.6479 (mt-10) REVERT: E 413 SER cc_start: 0.8074 (m) cc_final: 0.7507 (p) REVERT: F 3 GLU cc_start: 0.6198 (mp0) cc_final: 0.5983 (mp0) REVERT: F 18 ASN cc_start: 0.7413 (m-40) cc_final: 0.7187 (m-40) REVERT: F 24 TYR cc_start: 0.7817 (m-10) cc_final: 0.7583 (m-10) REVERT: F 49 PHE cc_start: 0.7365 (p90) cc_final: 0.7105 (p90) REVERT: F 67 PHE cc_start: 0.7778 (m-80) cc_final: 0.7554 (m-10) REVERT: F 70 LEU cc_start: 0.7252 (mm) cc_final: 0.7041 (mt) REVERT: F 129 CYS cc_start: 0.7556 (m) cc_final: 0.7124 (m) REVERT: F 160 ASP cc_start: 0.7310 (t0) cc_final: 0.6526 (t0) REVERT: F 166 LYS cc_start: 0.7257 (mtmm) cc_final: 0.6785 (mtmm) REVERT: F 179 THR cc_start: 0.7729 (m) cc_final: 0.7509 (m) REVERT: F 248 LEU cc_start: 0.7730 (mp) cc_final: 0.7523 (mt) REVERT: F 264 ARG cc_start: 0.7638 (mtp85) cc_final: 0.6777 (mpt180) REVERT: F 276 ILE cc_start: 0.8299 (tp) cc_final: 0.7725 (tp) REVERT: F 280 LYS cc_start: 0.5034 (tptt) cc_final: 0.4603 (ttpp) REVERT: F 285 GLN cc_start: 0.7804 (mt0) cc_final: 0.7520 (mt0) REVERT: F 295 CYS cc_start: 0.7089 (m) cc_final: 0.6872 (m) REVERT: F 320 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7635 (mtt-85) REVERT: F 342 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7685 (mm110) REVERT: F 376 CYS cc_start: 0.7759 (t) cc_final: 0.7545 (t) REVERT: F 380 ASN cc_start: 0.7470 (t0) cc_final: 0.7000 (t0) REVERT: F 392 ASP cc_start: 0.6809 (m-30) cc_final: 0.6478 (m-30) REVERT: F 425 MET cc_start: 0.7510 (tpp) cc_final: 0.7231 (tpt) outliers start: 2 outliers final: 1 residues processed: 566 average time/residue: 0.3202 time to fit residues: 245.5063 Evaluate side-chains 517 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 516 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 0.0020 chunk 72 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 82 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN B 43 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 424 GLN E 14 ASN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 245 GLN E 292 GLN E 298 ASN E 307 HIS F 31 GLN F 91 GLN F 233 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14163 Z= 0.279 Angle : 0.646 8.769 19237 Z= 0.332 Chirality : 0.047 0.156 2106 Planarity : 0.005 0.089 2502 Dihedral : 9.964 161.396 1994 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.70 % Allowed : 16.49 % Favored : 79.81 % 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: -0.68 (0.20), residues: 1738 helix: 0.74 (0.18), residues: 781 sheet: -1.81 (0.28), residues: 286 loop : -1.15 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 407 HIS 0.008 0.001 HIS E 190 PHE 0.014 0.002 PHE F 202 TYR 0.024 0.002 TYR E 36 ARG 0.006 0.001 ARG F 422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 532 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8271 (m-80) cc_final: 0.7968 (m-80) REVERT: A 71 GLU cc_start: 0.6747 (tt0) cc_final: 0.6433 (tt0) REVERT: A 91 GLN cc_start: 0.8144 (pt0) cc_final: 0.7832 (pt0) REVERT: A 154 MET cc_start: 0.7908 (mmm) cc_final: 0.7173 (mmm) REVERT: A 187 SER cc_start: 0.8163 (m) cc_final: 0.7789 (p) REVERT: A 215 ARG cc_start: 0.7451 (mtt180) cc_final: 0.7098 (mtt180) REVERT: A 226 ASN cc_start: 0.7431 (m110) cc_final: 0.7062 (m110) REVERT: A 237 SER cc_start: 0.8426 (m) cc_final: 0.8003 (p) REVERT: A 239 THR cc_start: 0.7853 (p) cc_final: 0.7543 (t) REVERT: A 254 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6721 (mt-10) REVERT: A 259 LEU cc_start: 0.7920 (tp) cc_final: 0.7689 (tt) REVERT: A 280 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8036 (mtmm) REVERT: A 284 GLU cc_start: 0.7784 (tt0) cc_final: 0.7040 (tm-30) REVERT: A 286 LEU cc_start: 0.8535 (mm) cc_final: 0.8143 (mm) REVERT: A 290 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6859 (mt-10) REVERT: A 302 MET cc_start: 0.8083 (mmm) cc_final: 0.7502 (mmm) REVERT: A 304 LYS cc_start: 0.8250 (tppt) cc_final: 0.7924 (tppt) REVERT: A 309 HIS cc_start: 0.6734 (m-70) cc_final: 0.6320 (m-70) REVERT: A 311 LYS cc_start: 0.8094 (mttp) cc_final: 0.7839 (mttt) REVERT: A 370 LYS cc_start: 0.8315 (tptp) cc_final: 0.8085 (tptp) REVERT: A 376 CYS cc_start: 0.8339 (t) cc_final: 0.7922 (t) REVERT: A 402 ARG cc_start: 0.7324 (mpt180) cc_final: 0.7048 (mmt-90) REVERT: A 405 VAL cc_start: 0.8009 (m) cc_final: 0.7758 (t) REVERT: A 424 ASP cc_start: 0.6556 (m-30) cc_final: 0.6305 (m-30) REVERT: A 433 GLU cc_start: 0.7390 (tp30) cc_final: 0.6976 (pt0) REVERT: A 435 VAL cc_start: 0.8410 (p) cc_final: 0.8194 (m) REVERT: B 53 GLU cc_start: 0.6609 (tp30) cc_final: 0.6237 (tp30) REVERT: B 73 MET cc_start: 0.7514 (mmm) cc_final: 0.7058 (mmm) REVERT: B 86 ARG cc_start: 0.7663 (mtt180) cc_final: 0.6673 (tpm170) REVERT: B 99 ASN cc_start: 0.7996 (m-40) cc_final: 0.7381 (m-40) REVERT: B 122 LYS cc_start: 0.7706 (tttt) cc_final: 0.7291 (tmtt) REVERT: B 195 ASN cc_start: 0.7552 (m110) cc_final: 0.6978 (m-40) REVERT: B 209 ASP cc_start: 0.7685 (t70) cc_final: 0.7338 (t0) REVERT: B 213 ARG cc_start: 0.7429 (ptm160) cc_final: 0.7127 (ptm160) REVERT: B 241 ARG cc_start: 0.8453 (mtp180) cc_final: 0.8184 (mtm110) REVERT: B 247 ASN cc_start: 0.8006 (m110) cc_final: 0.7632 (m-40) REVERT: B 265 PHE cc_start: 0.8491 (m-80) cc_final: 0.8257 (m-80) REVERT: B 266 PHE cc_start: 0.7572 (m-10) cc_final: 0.7361 (m-80) REVERT: B 279 GLN cc_start: 0.8041 (pm20) cc_final: 0.7599 (pp30) REVERT: B 298 ASN cc_start: 0.7173 (t0) cc_final: 0.6868 (t0) REVERT: B 309 ARG cc_start: 0.6999 (mtt-85) cc_final: 0.6142 (mtt-85) REVERT: E 3 GLU cc_start: 0.6743 (mp0) cc_final: 0.5947 (mp0) REVERT: E 19 LYS cc_start: 0.7855 (tptm) cc_final: 0.7626 (tptm) REVERT: E 41 ASP cc_start: 0.7438 (t0) cc_final: 0.7115 (t0) REVERT: E 53 GLU cc_start: 0.6826 (tp30) cc_final: 0.6486 (tp30) REVERT: E 65 LEU cc_start: 0.8376 (mp) cc_final: 0.8139 (mt) REVERT: E 69 GLU cc_start: 0.6712 (tt0) cc_final: 0.6452 (tt0) REVERT: E 108 GLU cc_start: 0.7624 (tm-30) cc_final: 0.6816 (tm-30) REVERT: E 123 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7294 (mm-30) REVERT: E 137 HIS cc_start: 0.7741 (p90) cc_final: 0.7503 (p90) REVERT: E 154 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7459 (mmtm) REVERT: E 164 MET cc_start: 0.5958 (mpp) cc_final: 0.5303 (mpp) REVERT: E 174 LYS cc_start: 0.8135 (mptt) cc_final: 0.7761 (mptt) REVERT: E 175 VAL cc_start: 0.7826 (m) cc_final: 0.7586 (t) REVERT: E 192 LEU cc_start: 0.7738 (tp) cc_final: 0.7452 (tp) REVERT: E 216 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8057 (mmtt) REVERT: E 225 LEU cc_start: 0.8241 (mp) cc_final: 0.7917 (mp) REVERT: E 279 GLN cc_start: 0.7875 (pt0) cc_final: 0.7481 (pt0) REVERT: E 280 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7542 (mm-40) REVERT: E 281 TYR cc_start: 0.8243 (m-80) cc_final: 0.8010 (m-10) REVERT: E 300 MET cc_start: 0.8555 (mtp) cc_final: 0.8250 (mtm) REVERT: E 366 THR cc_start: 0.8314 (m) cc_final: 0.7950 (t) REVERT: E 380 ARG cc_start: 0.7583 (ptm160) cc_final: 0.6799 (ptm160) REVERT: E 392 LYS cc_start: 0.6942 (mmtp) cc_final: 0.6398 (mmtt) REVERT: E 405 GLU cc_start: 0.7087 (tt0) cc_final: 0.6565 (mt-10) REVERT: E 413 SER cc_start: 0.8096 (m) cc_final: 0.7831 (p) REVERT: F 3 GLU cc_start: 0.6457 (mp0) cc_final: 0.5833 (mp0) REVERT: F 24 TYR cc_start: 0.7934 (m-10) cc_final: 0.7451 (m-10) REVERT: F 51 THR cc_start: 0.8417 (p) cc_final: 0.8211 (t) REVERT: F 70 LEU cc_start: 0.7676 (mm) cc_final: 0.7376 (mt) REVERT: F 77 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6929 (tm-30) REVERT: F 123 ARG cc_start: 0.6737 (tpp-160) cc_final: 0.6214 (tpp-160) REVERT: F 127 ASP cc_start: 0.7616 (m-30) cc_final: 0.7167 (m-30) REVERT: F 154 MET cc_start: 0.7431 (mmm) cc_final: 0.7066 (mmm) REVERT: F 215 ARG cc_start: 0.7017 (mtm110) cc_final: 0.6711 (mtm110) REVERT: F 217 LEU cc_start: 0.7926 (mt) cc_final: 0.7647 (mm) REVERT: F 233 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7800 (mm110) REVERT: F 234 ILE cc_start: 0.8079 (mm) cc_final: 0.7866 (tp) REVERT: F 280 LYS cc_start: 0.5469 (tptt) cc_final: 0.3917 (tptt) REVERT: F 295 CYS cc_start: 0.7718 (m) cc_final: 0.7255 (m) REVERT: F 306 ASP cc_start: 0.7646 (t0) cc_final: 0.7058 (t0) REVERT: F 342 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7886 (mm-40) REVERT: F 376 CYS cc_start: 0.7915 (t) cc_final: 0.7504 (t) REVERT: F 379 SER cc_start: 0.7838 (p) cc_final: 0.7622 (p) REVERT: F 380 ASN cc_start: 0.7886 (t0) cc_final: 0.7596 (t0) REVERT: F 390 ARG cc_start: 0.6857 (ptp-110) cc_final: 0.6607 (ptp-110) REVERT: F 391 LEU cc_start: 0.7828 (mm) cc_final: 0.7569 (tt) REVERT: F 395 PHE cc_start: 0.7737 (t80) cc_final: 0.7521 (t80) REVERT: F 425 MET cc_start: 0.7512 (tpp) cc_final: 0.7222 (tpt) outliers start: 55 outliers final: 38 residues processed: 549 average time/residue: 0.3081 time to fit residues: 230.7296 Evaluate side-chains 531 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 493 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 170 optimal weight: 0.5980 chunk 140 optimal weight: 0.4980 chunk 156 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 102 ASN A 300 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 HIS F 393 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14163 Z= 0.233 Angle : 0.593 8.979 19237 Z= 0.303 Chirality : 0.045 0.169 2106 Planarity : 0.005 0.070 2502 Dihedral : 9.864 162.261 1994 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.16 % Allowed : 19.04 % Favored : 77.79 % 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: -0.35 (0.20), residues: 1738 helix: 1.01 (0.18), residues: 775 sheet: -1.44 (0.28), residues: 281 loop : -1.06 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 407 HIS 0.004 0.001 HIS F 406 PHE 0.017 0.002 PHE A 267 TYR 0.013 0.001 TYR E 36 ARG 0.005 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 519 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8300 (m-80) cc_final: 0.8055 (m-80) REVERT: A 71 GLU cc_start: 0.6570 (tt0) cc_final: 0.6197 (tt0) REVERT: A 105 ARG cc_start: 0.6929 (ttm-80) cc_final: 0.6585 (ttm-80) REVERT: A 120 ASP cc_start: 0.7178 (m-30) cc_final: 0.6800 (t0) REVERT: A 154 MET cc_start: 0.7911 (mmm) cc_final: 0.7039 (mmm) REVERT: A 166 LYS cc_start: 0.7678 (mttp) cc_final: 0.7192 (mttp) REVERT: A 168 GLU cc_start: 0.6665 (mp0) cc_final: 0.6032 (mp0) REVERT: A 187 SER cc_start: 0.8234 (m) cc_final: 0.7809 (p) REVERT: A 209 ILE cc_start: 0.8194 (mm) cc_final: 0.7743 (mt) REVERT: A 215 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7073 (mtt180) REVERT: A 226 ASN cc_start: 0.7416 (m110) cc_final: 0.7067 (m110) REVERT: A 254 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 259 LEU cc_start: 0.7984 (tp) cc_final: 0.7769 (tt) REVERT: A 265 ILE cc_start: 0.7620 (mm) cc_final: 0.7375 (mm) REVERT: A 280 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8244 (mtmm) REVERT: A 284 GLU cc_start: 0.7747 (tt0) cc_final: 0.6961 (tm-30) REVERT: A 286 LEU cc_start: 0.8568 (mm) cc_final: 0.7881 (mt) REVERT: A 290 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6789 (mt-10) REVERT: A 302 MET cc_start: 0.8086 (mmm) cc_final: 0.7586 (mmm) REVERT: A 304 LYS cc_start: 0.8307 (tppt) cc_final: 0.7988 (tppt) REVERT: A 309 HIS cc_start: 0.6777 (m-70) cc_final: 0.6341 (m-70) REVERT: A 370 LYS cc_start: 0.8348 (tptp) cc_final: 0.8102 (tptp) REVERT: A 376 CYS cc_start: 0.8353 (t) cc_final: 0.8020 (t) REVERT: A 402 ARG cc_start: 0.7287 (mpt180) cc_final: 0.6889 (mmt-90) REVERT: A 420 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6386 (tm-30) REVERT: A 424 ASP cc_start: 0.7315 (m-30) cc_final: 0.7071 (m-30) REVERT: A 433 GLU cc_start: 0.7416 (tp30) cc_final: 0.7039 (pt0) REVERT: A 435 VAL cc_start: 0.8463 (p) cc_final: 0.8227 (m) REVERT: B 73 MET cc_start: 0.7495 (mmm) cc_final: 0.7136 (mmt) REVERT: B 86 ARG cc_start: 0.7790 (mtt180) cc_final: 0.6582 (tpm170) REVERT: B 99 ASN cc_start: 0.8062 (m-40) cc_final: 0.7769 (m-40) REVERT: B 122 LYS cc_start: 0.7707 (tttt) cc_final: 0.7325 (tmtt) REVERT: B 209 ASP cc_start: 0.7656 (t70) cc_final: 0.7285 (t0) REVERT: B 213 ARG cc_start: 0.7446 (ptm160) cc_final: 0.7163 (ptm160) REVERT: B 237 THR cc_start: 0.8053 (p) cc_final: 0.7750 (t) REVERT: B 241 ARG cc_start: 0.8605 (mtp180) cc_final: 0.8270 (mtm180) REVERT: B 247 ASN cc_start: 0.8019 (m110) cc_final: 0.7545 (m-40) REVERT: B 265 PHE cc_start: 0.8494 (m-80) cc_final: 0.8234 (m-80) REVERT: B 266 PHE cc_start: 0.7612 (m-10) cc_final: 0.7360 (m-80) REVERT: B 279 GLN cc_start: 0.7972 (pm20) cc_final: 0.7387 (pp30) REVERT: B 280 GLN cc_start: 0.7576 (mt0) cc_final: 0.7115 (mt0) REVERT: B 282 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7703 (ptm-80) REVERT: B 298 ASN cc_start: 0.7205 (t0) cc_final: 0.6692 (t0) REVERT: B 309 ARG cc_start: 0.6969 (mtt-85) cc_final: 0.6093 (mtt-85) REVERT: B 406 MET cc_start: 0.6576 (ptt) cc_final: 0.6368 (ptt) REVERT: B 412 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7783 (tm-30) REVERT: E 3 GLU cc_start: 0.6724 (mp0) cc_final: 0.5776 (mp0) REVERT: E 41 ASP cc_start: 0.7555 (t0) cc_final: 0.7189 (t0) REVERT: E 65 LEU cc_start: 0.8332 (mp) cc_final: 0.8111 (mt) REVERT: E 117 LEU cc_start: 0.7967 (mm) cc_final: 0.7700 (mt) REVERT: E 123 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7293 (mm-30) REVERT: E 131 GLN cc_start: 0.7405 (tm-30) cc_final: 0.6591 (tm-30) REVERT: E 137 HIS cc_start: 0.7766 (p90) cc_final: 0.7550 (p90) REVERT: E 174 LYS cc_start: 0.8228 (mptt) cc_final: 0.7951 (mptt) REVERT: E 175 VAL cc_start: 0.7761 (m) cc_final: 0.7459 (t) REVERT: E 197 ASP cc_start: 0.7690 (m-30) cc_final: 0.6719 (t0) REVERT: E 257 MET cc_start: 0.7103 (mpp) cc_final: 0.6453 (mpp) REVERT: E 279 GLN cc_start: 0.7856 (pt0) cc_final: 0.7112 (pt0) REVERT: E 280 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7440 (mm-40) REVERT: E 299 MET cc_start: 0.6216 (mmm) cc_final: 0.5935 (mmm) REVERT: E 300 MET cc_start: 0.8484 (mtp) cc_final: 0.8169 (mtm) REVERT: E 366 THR cc_start: 0.8339 (m) cc_final: 0.7982 (t) REVERT: E 391 ARG cc_start: 0.4738 (ptt180) cc_final: 0.3382 (ptt90) REVERT: E 392 LYS cc_start: 0.7029 (mmtp) cc_final: 0.6317 (mptt) REVERT: E 413 SER cc_start: 0.8055 (m) cc_final: 0.7780 (p) REVERT: F 3 GLU cc_start: 0.6235 (mp0) cc_final: 0.5978 (mp0) REVERT: F 24 TYR cc_start: 0.7981 (m-10) cc_final: 0.7613 (m-10) REVERT: F 51 THR cc_start: 0.8433 (p) cc_final: 0.8221 (t) REVERT: F 69 ASP cc_start: 0.7736 (t0) cc_final: 0.7266 (t0) REVERT: F 70 LEU cc_start: 0.7673 (mm) cc_final: 0.7280 (mt) REVERT: F 77 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6877 (tm-30) REVERT: F 91 GLN cc_start: 0.8247 (mt0) cc_final: 0.8031 (mt0) REVERT: F 97 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6533 (tm-30) REVERT: F 123 ARG cc_start: 0.6769 (tpp-160) cc_final: 0.6329 (tpp-160) REVERT: F 154 MET cc_start: 0.7444 (mmm) cc_final: 0.7211 (mmm) REVERT: F 155 GLU cc_start: 0.6800 (tp30) cc_final: 0.6167 (tp30) REVERT: F 215 ARG cc_start: 0.6954 (mtm110) cc_final: 0.6637 (mtm110) REVERT: F 248 LEU cc_start: 0.7769 (mp) cc_final: 0.7564 (mt) REVERT: F 280 LYS cc_start: 0.5425 (tptt) cc_final: 0.3931 (tptt) REVERT: F 285 GLN cc_start: 0.8020 (mt0) cc_final: 0.7759 (mt0) REVERT: F 295 CYS cc_start: 0.7697 (m) cc_final: 0.7255 (m) REVERT: F 306 ASP cc_start: 0.7628 (t0) cc_final: 0.6985 (t0) REVERT: F 342 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7908 (mm110) REVERT: F 352 LYS cc_start: 0.7784 (tptt) cc_final: 0.6784 (tppt) REVERT: F 372 GLN cc_start: 0.7641 (pm20) cc_final: 0.7437 (pt0) REVERT: F 390 ARG cc_start: 0.6905 (ptp-110) cc_final: 0.6603 (ptp-110) REVERT: F 398 MET cc_start: 0.7007 (mpp) cc_final: 0.6786 (mpp) REVERT: F 413 MET cc_start: 0.6932 (mmm) cc_final: 0.6688 (tpp) outliers start: 47 outliers final: 28 residues processed: 538 average time/residue: 0.3112 time to fit residues: 228.4618 Evaluate side-chains 544 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 515 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 chunk 17 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 157 optimal weight: 0.0970 chunk 167 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 149 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN E 245 GLN E 298 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14163 Z= 0.195 Angle : 0.560 8.702 19237 Z= 0.284 Chirality : 0.043 0.171 2106 Planarity : 0.004 0.063 2502 Dihedral : 9.764 164.102 1994 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.83 % Allowed : 21.74 % Favored : 75.44 % 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: -0.07 (0.20), residues: 1738 helix: 1.18 (0.19), residues: 778 sheet: -1.19 (0.28), residues: 289 loop : -0.89 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 101 HIS 0.006 0.001 HIS F 88 PHE 0.015 0.001 PHE E 167 TYR 0.011 0.001 TYR E 36 ARG 0.008 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 527 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7755 (m-80) cc_final: 0.7240 (m-80) REVERT: A 67 PHE cc_start: 0.8269 (m-80) cc_final: 0.7747 (m-80) REVERT: A 120 ASP cc_start: 0.7137 (m-30) cc_final: 0.6731 (t0) REVERT: A 154 MET cc_start: 0.7857 (mmm) cc_final: 0.7101 (mmm) REVERT: A 166 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7174 (mttp) REVERT: A 168 GLU cc_start: 0.6551 (mp0) cc_final: 0.5957 (mp0) REVERT: A 175 PRO cc_start: 0.8503 (Cg_endo) cc_final: 0.8277 (Cg_endo) REVERT: A 187 SER cc_start: 0.8237 (m) cc_final: 0.7821 (p) REVERT: A 209 ILE cc_start: 0.8189 (mm) cc_final: 0.7885 (mt) REVERT: A 215 ARG cc_start: 0.7455 (mtt180) cc_final: 0.7091 (mtt180) REVERT: A 226 ASN cc_start: 0.7398 (m110) cc_final: 0.7033 (m110) REVERT: A 254 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6847 (mt-10) REVERT: A 265 ILE cc_start: 0.7599 (mm) cc_final: 0.7333 (mm) REVERT: A 280 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8285 (mtmm) REVERT: A 290 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6980 (mt-10) REVERT: A 302 MET cc_start: 0.7994 (mmm) cc_final: 0.7598 (mmm) REVERT: A 304 LYS cc_start: 0.8165 (tppt) cc_final: 0.7852 (tppt) REVERT: A 309 HIS cc_start: 0.6766 (m-70) cc_final: 0.6309 (m-70) REVERT: A 376 CYS cc_start: 0.8333 (t) cc_final: 0.7984 (t) REVERT: A 402 ARG cc_start: 0.7261 (mpt180) cc_final: 0.6927 (mmt-90) REVERT: A 435 VAL cc_start: 0.8538 (p) cc_final: 0.8294 (m) REVERT: B 53 GLU cc_start: 0.6812 (tp30) cc_final: 0.6343 (tp30) REVERT: B 73 MET cc_start: 0.7549 (mmm) cc_final: 0.7216 (mmt) REVERT: B 86 ARG cc_start: 0.7771 (mtt180) cc_final: 0.6623 (tpm170) REVERT: B 99 ASN cc_start: 0.8065 (m-40) cc_final: 0.7721 (m-40) REVERT: B 164 MET cc_start: 0.6285 (tpp) cc_final: 0.6081 (tpp) REVERT: B 197 ASP cc_start: 0.7580 (m-30) cc_final: 0.7157 (m-30) REVERT: B 209 ASP cc_start: 0.7689 (t70) cc_final: 0.7310 (t0) REVERT: B 213 ARG cc_start: 0.7448 (ptm160) cc_final: 0.7220 (ptm160) REVERT: B 233 MET cc_start: 0.7213 (mmt) cc_final: 0.6917 (mmt) REVERT: B 237 THR cc_start: 0.7932 (p) cc_final: 0.7688 (t) REVERT: B 247 ASN cc_start: 0.8006 (m110) cc_final: 0.7688 (m-40) REVERT: B 265 PHE cc_start: 0.8498 (m-80) cc_final: 0.8237 (m-80) REVERT: B 280 GLN cc_start: 0.7561 (mt0) cc_final: 0.7208 (mt0) REVERT: B 282 ARG cc_start: 0.8249 (ptm160) cc_final: 0.7660 (ptm-80) REVERT: B 284 LEU cc_start: 0.8281 (pt) cc_final: 0.8074 (pt) REVERT: B 292 GLN cc_start: 0.7307 (tt0) cc_final: 0.7105 (tt0) REVERT: B 309 ARG cc_start: 0.7019 (mtt-85) cc_final: 0.6114 (mtt-85) REVERT: B 380 ARG cc_start: 0.7230 (ptp-170) cc_final: 0.6986 (ptp-170) REVERT: B 412 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 418 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7851 (tp) REVERT: E 41 ASP cc_start: 0.7562 (t0) cc_final: 0.7108 (t0) REVERT: E 53 GLU cc_start: 0.7122 (tp30) cc_final: 0.6738 (tp30) REVERT: E 62 ARG cc_start: 0.7318 (ttm170) cc_final: 0.7083 (mtt90) REVERT: E 65 LEU cc_start: 0.8299 (mp) cc_final: 0.8089 (mt) REVERT: E 86 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7576 (ttp-110) REVERT: E 108 GLU cc_start: 0.7635 (tm-30) cc_final: 0.6924 (tm-30) REVERT: E 123 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7337 (mm-30) REVERT: E 174 LYS cc_start: 0.8204 (mptt) cc_final: 0.7927 (mptt) REVERT: E 175 VAL cc_start: 0.7864 (m) cc_final: 0.7587 (t) REVERT: E 197 ASP cc_start: 0.7692 (m-30) cc_final: 0.6749 (t0) REVERT: E 199 THR cc_start: 0.7844 (m) cc_final: 0.7547 (p) REVERT: E 225 LEU cc_start: 0.8266 (mp) cc_final: 0.7965 (mp) REVERT: E 251 ARG cc_start: 0.7542 (tpp80) cc_final: 0.6862 (tpp80) REVERT: E 257 MET cc_start: 0.7065 (mpp) cc_final: 0.6319 (mpp) REVERT: E 279 GLN cc_start: 0.7827 (pt0) cc_final: 0.7401 (pt0) REVERT: E 280 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7534 (mm-40) REVERT: E 299 MET cc_start: 0.6121 (mmm) cc_final: 0.5918 (mmm) REVERT: E 300 MET cc_start: 0.8320 (mtp) cc_final: 0.8016 (mtm) REVERT: E 366 THR cc_start: 0.8312 (m) cc_final: 0.7917 (t) REVERT: E 391 ARG cc_start: 0.4927 (ptt180) cc_final: 0.3409 (ptt90) REVERT: E 405 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6852 (mt-10) REVERT: E 413 SER cc_start: 0.8074 (m) cc_final: 0.7837 (p) REVERT: F 3 GLU cc_start: 0.6249 (mp0) cc_final: 0.5949 (mp0) REVERT: F 24 TYR cc_start: 0.7933 (m-10) cc_final: 0.7626 (m-10) REVERT: F 51 THR cc_start: 0.8433 (p) cc_final: 0.8165 (t) REVERT: F 69 ASP cc_start: 0.7807 (t0) cc_final: 0.7335 (t0) REVERT: F 70 LEU cc_start: 0.7659 (mm) cc_final: 0.7274 (mt) REVERT: F 77 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6882 (tm-30) REVERT: F 78 VAL cc_start: 0.7741 (t) cc_final: 0.7503 (t) REVERT: F 97 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6651 (tm-30) REVERT: F 123 ARG cc_start: 0.6957 (tpp-160) cc_final: 0.6350 (tpp-160) REVERT: F 154 MET cc_start: 0.7478 (mmm) cc_final: 0.7232 (mmm) REVERT: F 155 GLU cc_start: 0.6773 (tp30) cc_final: 0.6168 (tp30) REVERT: F 215 ARG cc_start: 0.6882 (mtm110) cc_final: 0.6537 (mtm110) REVERT: F 301 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6467 (mp10) REVERT: F 306 ASP cc_start: 0.7701 (t0) cc_final: 0.7088 (t0) REVERT: F 352 LYS cc_start: 0.7789 (tptt) cc_final: 0.6805 (tppt) REVERT: F 390 ARG cc_start: 0.6913 (ptp-110) cc_final: 0.6622 (ptp-110) REVERT: F 398 MET cc_start: 0.6987 (tpp) cc_final: 0.6717 (tpp) REVERT: F 413 MET cc_start: 0.6988 (mmm) cc_final: 0.6762 (tpp) REVERT: F 432 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.5711 (t80) outliers start: 42 outliers final: 29 residues processed: 544 average time/residue: 0.3182 time to fit residues: 236.6316 Evaluate side-chains 546 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 514 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 150 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 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 102 ASN B 43 GLN B 137 HIS B 298 ASN B 424 GLN E 14 ASN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 298 ASN F 31 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 301 GLN F 342 GLN N 489 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14163 Z= 0.268 Angle : 0.587 8.453 19237 Z= 0.303 Chirality : 0.045 0.177 2106 Planarity : 0.004 0.060 2502 Dihedral : 9.815 164.631 1994 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.64 % Allowed : 22.48 % Favored : 72.88 % 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: -0.13 (0.20), residues: 1738 helix: 1.07 (0.19), residues: 785 sheet: -1.06 (0.29), residues: 279 loop : -0.95 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 21 HIS 0.006 0.001 HIS F 88 PHE 0.021 0.002 PHE E 167 TYR 0.014 0.001 TYR F 312 ARG 0.006 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 536 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7742 (m-80) cc_final: 0.7199 (m-80) REVERT: A 120 ASP cc_start: 0.7202 (m-30) cc_final: 0.6769 (t0) REVERT: A 154 MET cc_start: 0.7897 (mmm) cc_final: 0.7093 (mmm) REVERT: A 166 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7118 (mttp) REVERT: A 168 GLU cc_start: 0.6653 (mp0) cc_final: 0.5979 (mp0) REVERT: A 175 PRO cc_start: 0.8480 (Cg_endo) cc_final: 0.8278 (Cg_endo) REVERT: A 187 SER cc_start: 0.8288 (m) cc_final: 0.7895 (p) REVERT: A 209 ILE cc_start: 0.8235 (mm) cc_final: 0.7852 (mt) REVERT: A 215 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7116 (mtt180) REVERT: A 226 ASN cc_start: 0.7469 (m110) cc_final: 0.7160 (m110) REVERT: A 254 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6843 (mt-10) REVERT: A 265 ILE cc_start: 0.7629 (mm) cc_final: 0.7392 (mm) REVERT: A 280 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8181 (mtmm) REVERT: A 290 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 297 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 302 MET cc_start: 0.8038 (mmm) cc_final: 0.7639 (mmm) REVERT: A 304 LYS cc_start: 0.8125 (tppt) cc_final: 0.7863 (tppt) REVERT: A 309 HIS cc_start: 0.6778 (m-70) cc_final: 0.6347 (m-70) REVERT: A 356 ASN cc_start: 0.8057 (t0) cc_final: 0.7604 (t0) REVERT: A 376 CYS cc_start: 0.8360 (t) cc_final: 0.8085 (t) REVERT: A 402 ARG cc_start: 0.7319 (mpt180) cc_final: 0.6972 (mmt-90) REVERT: A 424 ASP cc_start: 0.7573 (m-30) cc_final: 0.7260 (m-30) REVERT: A 433 GLU cc_start: 0.7411 (tp30) cc_final: 0.7036 (pt0) REVERT: A 435 VAL cc_start: 0.8532 (p) cc_final: 0.8312 (m) REVERT: B 53 GLU cc_start: 0.6825 (tp30) cc_final: 0.6326 (tp30) REVERT: B 86 ARG cc_start: 0.7731 (mtt180) cc_final: 0.6626 (tpm170) REVERT: B 99 ASN cc_start: 0.8208 (m-40) cc_final: 0.7955 (m-40) REVERT: B 122 LYS cc_start: 0.7762 (tmtt) cc_final: 0.7420 (tmtt) REVERT: B 197 ASP cc_start: 0.7628 (m-30) cc_final: 0.7120 (m-30) REVERT: B 209 ASP cc_start: 0.7710 (t70) cc_final: 0.7357 (t0) REVERT: B 213 ARG cc_start: 0.7433 (ptm160) cc_final: 0.7007 (ptm160) REVERT: B 237 THR cc_start: 0.8005 (p) cc_final: 0.7699 (t) REVERT: B 241 ARG cc_start: 0.8632 (mtp180) cc_final: 0.8332 (mtp180) REVERT: B 247 ASN cc_start: 0.8056 (m110) cc_final: 0.7624 (m-40) REVERT: B 279 GLN cc_start: 0.7859 (pm20) cc_final: 0.7392 (pp30) REVERT: B 280 GLN cc_start: 0.7605 (mt0) cc_final: 0.7098 (mt0) REVERT: B 318 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7603 (mtm-85) REVERT: B 380 ARG cc_start: 0.7261 (ptp-170) cc_final: 0.7014 (ptp-170) REVERT: B 412 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 415 MET cc_start: 0.7806 (tpt) cc_final: 0.7504 (tpt) REVERT: B 418 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7898 (tp) REVERT: E 53 GLU cc_start: 0.7148 (tp30) cc_final: 0.6649 (tp30) REVERT: E 86 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7657 (ttp-170) REVERT: E 108 GLU cc_start: 0.7699 (tm-30) cc_final: 0.6913 (tm-30) REVERT: E 123 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7423 (mm-30) REVERT: E 131 GLN cc_start: 0.7533 (tm-30) cc_final: 0.6548 (tm-30) REVERT: E 174 LYS cc_start: 0.8231 (mptt) cc_final: 0.7906 (mptt) REVERT: E 175 VAL cc_start: 0.7813 (m) cc_final: 0.7490 (t) REVERT: E 197 ASP cc_start: 0.7698 (m-30) cc_final: 0.7102 (t0) REVERT: E 199 THR cc_start: 0.7918 (m) cc_final: 0.7697 (p) REVERT: E 205 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6796 (tm-30) REVERT: E 225 LEU cc_start: 0.8248 (mp) cc_final: 0.7967 (mp) REVERT: E 251 ARG cc_start: 0.7519 (tpp80) cc_final: 0.7283 (tpp80) REVERT: E 257 MET cc_start: 0.6982 (mpp) cc_final: 0.6068 (mpp) REVERT: E 262 ARG cc_start: 0.7117 (mtp180) cc_final: 0.6869 (ttm-80) REVERT: E 279 GLN cc_start: 0.7806 (pt0) cc_final: 0.7037 (pt0) REVERT: E 280 GLN cc_start: 0.7872 (mm110) cc_final: 0.7395 (mm-40) REVERT: E 299 MET cc_start: 0.6249 (mmm) cc_final: 0.5844 (mmm) REVERT: E 366 THR cc_start: 0.8323 (m) cc_final: 0.7935 (t) REVERT: E 391 ARG cc_start: 0.4733 (ptt180) cc_final: 0.3331 (ptt90) REVERT: E 405 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6599 (mt-10) REVERT: E 413 SER cc_start: 0.8053 (m) cc_final: 0.7848 (p) REVERT: E 421 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6629 (mm-30) REVERT: F 24 TYR cc_start: 0.7975 (m-10) cc_final: 0.7672 (m-10) REVERT: F 51 THR cc_start: 0.8420 (p) cc_final: 0.8129 (t) REVERT: F 69 ASP cc_start: 0.7846 (t0) cc_final: 0.7384 (t0) REVERT: F 70 LEU cc_start: 0.7664 (mm) cc_final: 0.7269 (mt) REVERT: F 77 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6883 (tm-30) REVERT: F 78 VAL cc_start: 0.7734 (t) cc_final: 0.7441 (t) REVERT: F 97 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6638 (tm-30) REVERT: F 102 ASN cc_start: 0.6944 (t0) cc_final: 0.6404 (t0) REVERT: F 123 ARG cc_start: 0.6985 (tpp-160) cc_final: 0.6409 (tpp-160) REVERT: F 154 MET cc_start: 0.7487 (mmm) cc_final: 0.7236 (mmm) REVERT: F 155 GLU cc_start: 0.6858 (tp30) cc_final: 0.6306 (tp30) REVERT: F 215 ARG cc_start: 0.6865 (mtm110) cc_final: 0.6443 (mtm110) REVERT: F 216 ASN cc_start: 0.8324 (m-40) cc_final: 0.8083 (m110) REVERT: F 295 CYS cc_start: 0.7711 (m) cc_final: 0.7097 (m) REVERT: F 301 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6711 (mt0) REVERT: F 306 ASP cc_start: 0.7707 (t0) cc_final: 0.7088 (t0) REVERT: F 352 LYS cc_start: 0.7790 (tptt) cc_final: 0.6843 (tppt) REVERT: F 367 ASP cc_start: 0.7514 (t0) cc_final: 0.6830 (t0) REVERT: F 398 MET cc_start: 0.7178 (tpp) cc_final: 0.6809 (tpp) REVERT: F 413 MET cc_start: 0.7128 (mmm) cc_final: 0.6884 (tpp) REVERT: F 432 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.5696 (t80) outliers start: 69 outliers final: 44 residues processed: 560 average time/residue: 0.3272 time to fit residues: 251.3612 Evaluate side-chains 575 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 527 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 87 optimal weight: 0.0060 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 298 ASN E 100 ASN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 280 GLN E 298 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 342 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14163 Z= 0.216 Angle : 0.575 9.887 19237 Z= 0.294 Chirality : 0.044 0.178 2106 Planarity : 0.004 0.058 2502 Dihedral : 9.619 166.488 1994 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.64 % Allowed : 23.76 % Favored : 71.60 % 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: -0.02 (0.20), residues: 1738 helix: 1.17 (0.19), residues: 779 sheet: -0.97 (0.29), residues: 279 loop : -0.91 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 101 HIS 0.006 0.001 HIS F 88 PHE 0.029 0.001 PHE E 167 TYR 0.021 0.001 TYR A 103 ARG 0.006 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 519 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8250 (m-80) cc_final: 0.7814 (m-80) REVERT: A 71 GLU cc_start: 0.6472 (tt0) cc_final: 0.6142 (tt0) REVERT: A 118 VAL cc_start: 0.8072 (p) cc_final: 0.7860 (m) REVERT: A 120 ASP cc_start: 0.7180 (m-30) cc_final: 0.6732 (t0) REVERT: A 154 MET cc_start: 0.7895 (mmm) cc_final: 0.7161 (mmm) REVERT: A 187 SER cc_start: 0.8274 (m) cc_final: 0.7840 (p) REVERT: A 209 ILE cc_start: 0.8220 (mm) cc_final: 0.7841 (mt) REVERT: A 211 ASP cc_start: 0.7924 (m-30) cc_final: 0.7654 (m-30) REVERT: A 215 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7051 (mtt180) REVERT: A 226 ASN cc_start: 0.7468 (m110) cc_final: 0.7202 (m110) REVERT: A 254 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6797 (mt-10) REVERT: A 280 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8153 (mtmm) REVERT: A 284 GLU cc_start: 0.7894 (tt0) cc_final: 0.7296 (tt0) REVERT: A 297 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7226 (mm-30) REVERT: A 302 MET cc_start: 0.8006 (mmm) cc_final: 0.7659 (mmm) REVERT: A 304 LYS cc_start: 0.8159 (tppt) cc_final: 0.7874 (tppt) REVERT: A 309 HIS cc_start: 0.6790 (m-70) cc_final: 0.6352 (m-70) REVERT: A 356 ASN cc_start: 0.8041 (t0) cc_final: 0.7594 (t0) REVERT: A 376 CYS cc_start: 0.8363 (t) cc_final: 0.8028 (t) REVERT: A 402 ARG cc_start: 0.7391 (mpt180) cc_final: 0.7045 (mmt-90) REVERT: A 433 GLU cc_start: 0.7387 (tp30) cc_final: 0.6928 (pt0) REVERT: A 435 VAL cc_start: 0.8506 (p) cc_final: 0.8297 (m) REVERT: B 53 GLU cc_start: 0.6831 (tp30) cc_final: 0.6283 (tp30) REVERT: B 73 MET cc_start: 0.7547 (mmm) cc_final: 0.7181 (mmm) REVERT: B 86 ARG cc_start: 0.7745 (mtt180) cc_final: 0.6684 (tpm170) REVERT: B 99 ASN cc_start: 0.8180 (m-40) cc_final: 0.7906 (m-40) REVERT: B 197 ASP cc_start: 0.7596 (m-30) cc_final: 0.7062 (m-30) REVERT: B 209 ASP cc_start: 0.7703 (t70) cc_final: 0.7346 (t0) REVERT: B 213 ARG cc_start: 0.7424 (ptm160) cc_final: 0.7031 (ptm160) REVERT: B 237 THR cc_start: 0.8005 (p) cc_final: 0.7672 (t) REVERT: B 241 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8416 (mtp180) REVERT: B 247 ASN cc_start: 0.8023 (m110) cc_final: 0.7566 (m-40) REVERT: B 280 GLN cc_start: 0.7606 (mt0) cc_final: 0.7253 (mt0) REVERT: B 299 MET cc_start: 0.6374 (tpp) cc_final: 0.6090 (mmm) REVERT: B 318 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7495 (mtm-85) REVERT: B 380 ARG cc_start: 0.7248 (ptp-170) cc_final: 0.6989 (ptp-170) REVERT: B 412 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7696 (tm-30) REVERT: B 418 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7914 (tp) REVERT: E 53 GLU cc_start: 0.7151 (tp30) cc_final: 0.6549 (tp30) REVERT: E 86 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7646 (ttp-170) REVERT: E 108 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7001 (tm-30) REVERT: E 123 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7423 (mm-30) REVERT: E 131 GLN cc_start: 0.7594 (tm-30) cc_final: 0.6612 (tm-30) REVERT: E 135 LEU cc_start: 0.7188 (mp) cc_final: 0.6890 (mp) REVERT: E 154 LYS cc_start: 0.7612 (mmtp) cc_final: 0.7365 (mmtm) REVERT: E 167 PHE cc_start: 0.7853 (m-80) cc_final: 0.7532 (m-10) REVERT: E 174 LYS cc_start: 0.8211 (mptt) cc_final: 0.7905 (mptt) REVERT: E 175 VAL cc_start: 0.7771 (m) cc_final: 0.7492 (t) REVERT: E 197 ASP cc_start: 0.7696 (m-30) cc_final: 0.7011 (m-30) REVERT: E 199 THR cc_start: 0.7884 (m) cc_final: 0.7651 (p) REVERT: E 205 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6829 (tm-30) REVERT: E 225 LEU cc_start: 0.8235 (mp) cc_final: 0.7957 (mp) REVERT: E 257 MET cc_start: 0.6985 (mpp) cc_final: 0.6154 (mpp) REVERT: E 262 ARG cc_start: 0.7009 (mtp180) cc_final: 0.6782 (ttm-80) REVERT: E 279 GLN cc_start: 0.7821 (pt0) cc_final: 0.7398 (pt0) REVERT: E 280 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7519 (mm-40) REVERT: E 366 THR cc_start: 0.8328 (m) cc_final: 0.7912 (t) REVERT: E 391 ARG cc_start: 0.4795 (ptt180) cc_final: 0.2796 (mtm180) REVERT: E 399 THR cc_start: 0.7439 (m) cc_final: 0.6651 (t) REVERT: E 405 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6720 (mt-10) REVERT: E 421 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6769 (mt-10) REVERT: F 24 TYR cc_start: 0.7933 (m-10) cc_final: 0.7639 (m-10) REVERT: F 51 THR cc_start: 0.8438 (p) cc_final: 0.8218 (t) REVERT: F 69 ASP cc_start: 0.7858 (t0) cc_final: 0.7350 (t0) REVERT: F 70 LEU cc_start: 0.7659 (mm) cc_final: 0.7272 (mt) REVERT: F 77 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6888 (tm-30) REVERT: F 78 VAL cc_start: 0.7695 (t) cc_final: 0.7358 (t) REVERT: F 97 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6674 (tm-30) REVERT: F 123 ARG cc_start: 0.7024 (tpp-160) cc_final: 0.6501 (tpp-160) REVERT: F 154 MET cc_start: 0.7555 (mmm) cc_final: 0.7328 (mmm) REVERT: F 155 GLU cc_start: 0.6874 (tp30) cc_final: 0.6356 (tp30) REVERT: F 215 ARG cc_start: 0.6800 (mtm110) cc_final: 0.6386 (mtm110) REVERT: F 301 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6611 (mt0) REVERT: F 306 ASP cc_start: 0.7709 (t0) cc_final: 0.7091 (t0) REVERT: F 352 LYS cc_start: 0.7862 (tptt) cc_final: 0.5974 (mmtt) REVERT: F 367 ASP cc_start: 0.7524 (t0) cc_final: 0.6848 (t0) REVERT: F 413 MET cc_start: 0.7091 (mmm) cc_final: 0.6867 (tpp) REVERT: F 432 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.5590 (t80) outliers start: 69 outliers final: 46 residues processed: 546 average time/residue: 0.3285 time to fit residues: 244.8161 Evaluate side-chains 554 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 506 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 93 optimal weight: 0.0270 chunk 166 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 101 optimal weight: 0.3980 chunk 76 optimal weight: 0.1980 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 107 HIS B 8 GLN B 43 GLN B 137 HIS B 291 GLN B 298 ASN E 99 ASN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 298 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14163 Z= 0.171 Angle : 0.559 10.038 19237 Z= 0.283 Chirality : 0.043 0.174 2106 Planarity : 0.004 0.056 2502 Dihedral : 9.436 169.128 1994 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.90 % Allowed : 25.37 % Favored : 70.73 % 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: 0.14 (0.20), residues: 1738 helix: 1.32 (0.19), residues: 779 sheet: -0.91 (0.30), residues: 269 loop : -0.83 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 21 HIS 0.007 0.001 HIS F 88 PHE 0.024 0.001 PHE E 167 TYR 0.012 0.001 TYR F 432 ARG 0.006 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 530 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7064 (mp0) cc_final: 0.6446 (mp0) REVERT: A 24 TYR cc_start: 0.7700 (m-80) cc_final: 0.7295 (m-80) REVERT: A 67 PHE cc_start: 0.8158 (m-80) cc_final: 0.7702 (m-80) REVERT: A 118 VAL cc_start: 0.8072 (p) cc_final: 0.7853 (m) REVERT: A 120 ASP cc_start: 0.7179 (m-30) cc_final: 0.6737 (t0) REVERT: A 141 PHE cc_start: 0.7600 (m-10) cc_final: 0.7234 (m-10) REVERT: A 154 MET cc_start: 0.7864 (mmm) cc_final: 0.7124 (mmm) REVERT: A 168 GLU cc_start: 0.6745 (mp0) cc_final: 0.6192 (mp0) REVERT: A 187 SER cc_start: 0.8260 (m) cc_final: 0.7756 (p) REVERT: A 209 ILE cc_start: 0.8233 (mm) cc_final: 0.7971 (mt) REVERT: A 211 ASP cc_start: 0.7871 (m-30) cc_final: 0.7574 (m-30) REVERT: A 215 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7040 (mtt180) REVERT: A 217 LEU cc_start: 0.8196 (mp) cc_final: 0.7921 (mt) REVERT: A 226 ASN cc_start: 0.7455 (m110) cc_final: 0.7194 (m110) REVERT: A 254 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6847 (mt-10) REVERT: A 280 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8202 (mtmm) REVERT: A 284 GLU cc_start: 0.7856 (tt0) cc_final: 0.7185 (tt0) REVERT: A 297 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 302 MET cc_start: 0.8002 (mmm) cc_final: 0.7686 (mmm) REVERT: A 304 LYS cc_start: 0.8156 (tppt) cc_final: 0.7903 (tppt) REVERT: A 309 HIS cc_start: 0.6792 (m-70) cc_final: 0.6330 (m-70) REVERT: A 356 ASN cc_start: 0.8022 (t0) cc_final: 0.7528 (t0) REVERT: A 376 CYS cc_start: 0.8229 (t) cc_final: 0.8005 (t) REVERT: A 391 LEU cc_start: 0.8109 (mt) cc_final: 0.7672 (tt) REVERT: A 402 ARG cc_start: 0.7324 (mpt180) cc_final: 0.7056 (mmt-90) REVERT: A 414 GLU cc_start: 0.6060 (mp0) cc_final: 0.5575 (mp0) REVERT: A 424 ASP cc_start: 0.7729 (m-30) cc_final: 0.7358 (m-30) REVERT: A 433 GLU cc_start: 0.7325 (tp30) cc_final: 0.6877 (pt0) REVERT: A 435 VAL cc_start: 0.8556 (p) cc_final: 0.8326 (m) REVERT: B 53 GLU cc_start: 0.6849 (tp30) cc_final: 0.6291 (tp30) REVERT: B 86 ARG cc_start: 0.7754 (mtt180) cc_final: 0.6713 (tpm170) REVERT: B 99 ASN cc_start: 0.8076 (m-40) cc_final: 0.7741 (m-40) REVERT: B 197 ASP cc_start: 0.7541 (m-30) cc_final: 0.6787 (m-30) REVERT: B 209 ASP cc_start: 0.7753 (t70) cc_final: 0.7325 (t0) REVERT: B 213 ARG cc_start: 0.7447 (ptm160) cc_final: 0.7243 (ptm160) REVERT: B 216 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7996 (mmmm) REVERT: B 221 THR cc_start: 0.8158 (p) cc_final: 0.7951 (t) REVERT: B 237 THR cc_start: 0.8036 (p) cc_final: 0.7709 (t) REVERT: B 247 ASN cc_start: 0.8001 (m110) cc_final: 0.7511 (m-40) REVERT: B 280 GLN cc_start: 0.7609 (mt0) cc_final: 0.7280 (mt0) REVERT: B 299 MET cc_start: 0.6197 (tpp) cc_final: 0.5934 (mmm) REVERT: B 304 ASP cc_start: 0.7725 (t0) cc_final: 0.7449 (t70) REVERT: B 309 ARG cc_start: 0.7066 (mtt-85) cc_final: 0.6138 (mtt-85) REVERT: B 318 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: B 324 LYS cc_start: 0.7508 (tptp) cc_final: 0.7091 (tptp) REVERT: B 370 ASN cc_start: 0.7329 (t0) cc_final: 0.6946 (t0) REVERT: B 380 ARG cc_start: 0.7226 (ptp-170) cc_final: 0.6992 (ptp-170) REVERT: B 412 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 422 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.4921 (t80) REVERT: E 53 GLU cc_start: 0.7149 (tp30) cc_final: 0.6652 (tp30) REVERT: E 86 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7559 (ttp-170) REVERT: E 108 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6991 (tm-30) REVERT: E 123 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7503 (mm-30) REVERT: E 154 LYS cc_start: 0.7603 (mmtp) cc_final: 0.7339 (mmtm) REVERT: E 174 LYS cc_start: 0.8169 (mptt) cc_final: 0.7916 (mptt) REVERT: E 175 VAL cc_start: 0.7852 (m) cc_final: 0.7603 (t) REVERT: E 197 ASP cc_start: 0.7707 (m-30) cc_final: 0.7162 (m-30) REVERT: E 199 THR cc_start: 0.7884 (m) cc_final: 0.7628 (p) REVERT: E 205 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6756 (tm-30) REVERT: E 225 LEU cc_start: 0.8235 (mp) cc_final: 0.7991 (mp) REVERT: E 257 MET cc_start: 0.6958 (mpp) cc_final: 0.6166 (mpp) REVERT: E 262 ARG cc_start: 0.7047 (mtp180) cc_final: 0.6792 (mtp-110) REVERT: E 366 THR cc_start: 0.8298 (m) cc_final: 0.7907 (t) REVERT: E 391 ARG cc_start: 0.4858 (ptt180) cc_final: 0.3506 (ptt90) REVERT: E 399 THR cc_start: 0.7374 (m) cc_final: 0.6792 (t) REVERT: E 405 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6705 (mt-10) REVERT: F 3 GLU cc_start: 0.6334 (mp0) cc_final: 0.5861 (mp0) REVERT: F 24 TYR cc_start: 0.7889 (m-10) cc_final: 0.7596 (m-10) REVERT: F 50 ASN cc_start: 0.8050 (t0) cc_final: 0.7210 (t0) REVERT: F 51 THR cc_start: 0.8461 (p) cc_final: 0.8112 (t) REVERT: F 69 ASP cc_start: 0.7856 (t0) cc_final: 0.7351 (t0) REVERT: F 70 LEU cc_start: 0.7713 (mm) cc_final: 0.7296 (mt) REVERT: F 77 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6839 (tm-30) REVERT: F 78 VAL cc_start: 0.7653 (t) cc_final: 0.6905 (t) REVERT: F 102 ASN cc_start: 0.6723 (t0) cc_final: 0.6375 (t0) REVERT: F 123 ARG cc_start: 0.6911 (tpp-160) cc_final: 0.6344 (tpp-160) REVERT: F 154 MET cc_start: 0.7565 (mmm) cc_final: 0.7256 (mmm) REVERT: F 155 GLU cc_start: 0.6912 (tp30) cc_final: 0.6464 (tp30) REVERT: F 199 ASP cc_start: 0.7971 (t0) cc_final: 0.7393 (t0) REVERT: F 215 ARG cc_start: 0.6759 (mtm110) cc_final: 0.6328 (mtm110) REVERT: F 216 ASN cc_start: 0.8309 (m-40) cc_final: 0.8096 (m110) REVERT: F 239 THR cc_start: 0.7805 (m) cc_final: 0.7141 (t) REVERT: F 301 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6697 (mp10) REVERT: F 306 ASP cc_start: 0.7702 (t0) cc_final: 0.7063 (t0) REVERT: F 322 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6840 (p0) REVERT: F 352 LYS cc_start: 0.7871 (tptt) cc_final: 0.6023 (mmtt) REVERT: F 367 ASP cc_start: 0.7541 (t0) cc_final: 0.6878 (t0) REVERT: F 413 MET cc_start: 0.7078 (mmm) cc_final: 0.6852 (tpp) REVERT: F 432 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.5740 (t80) outliers start: 58 outliers final: 45 residues processed: 552 average time/residue: 0.3354 time to fit residues: 254.6824 Evaluate side-chains 559 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 511 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 131 optimal weight: 0.0870 chunk 151 optimal weight: 0.8980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 107 HIS ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 137 HIS B 424 GLN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14163 Z= 0.237 Angle : 0.588 9.875 19237 Z= 0.301 Chirality : 0.045 0.186 2106 Planarity : 0.004 0.055 2502 Dihedral : 9.537 168.366 1994 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.31 % Allowed : 25.77 % Favored : 69.92 % 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: 0.14 (0.20), residues: 1738 helix: 1.23 (0.19), residues: 786 sheet: -0.80 (0.30), residues: 266 loop : -0.79 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 101 HIS 0.005 0.001 HIS F 88 PHE 0.042 0.002 PHE E 167 TYR 0.014 0.001 TYR F 432 ARG 0.007 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 523 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7759 (m-80) cc_final: 0.7282 (m-80) REVERT: A 67 PHE cc_start: 0.8208 (m-80) cc_final: 0.7756 (m-80) REVERT: A 118 VAL cc_start: 0.8079 (p) cc_final: 0.7849 (m) REVERT: A 120 ASP cc_start: 0.7209 (m-30) cc_final: 0.6774 (t0) REVERT: A 154 MET cc_start: 0.7897 (mmm) cc_final: 0.7121 (mmm) REVERT: A 168 GLU cc_start: 0.6761 (mp0) cc_final: 0.6174 (mp0) REVERT: A 187 SER cc_start: 0.8310 (m) cc_final: 0.7836 (p) REVERT: A 199 ASP cc_start: 0.7549 (t0) cc_final: 0.7235 (t0) REVERT: A 209 ILE cc_start: 0.8246 (mm) cc_final: 0.7995 (mt) REVERT: A 211 ASP cc_start: 0.7895 (m-30) cc_final: 0.7625 (m-30) REVERT: A 215 ARG cc_start: 0.7521 (mtt180) cc_final: 0.7052 (mtt180) REVERT: A 217 LEU cc_start: 0.8235 (mp) cc_final: 0.7989 (mt) REVERT: A 226 ASN cc_start: 0.7508 (m110) cc_final: 0.7277 (m110) REVERT: A 254 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 280 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8147 (mtmm) REVERT: A 284 GLU cc_start: 0.7879 (tt0) cc_final: 0.7194 (tt0) REVERT: A 297 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 302 MET cc_start: 0.8003 (mmm) cc_final: 0.7695 (mmm) REVERT: A 304 LYS cc_start: 0.8165 (tppt) cc_final: 0.7946 (tppt) REVERT: A 309 HIS cc_start: 0.6823 (m-70) cc_final: 0.6368 (m-70) REVERT: A 349 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8229 (p) REVERT: A 356 ASN cc_start: 0.8064 (t0) cc_final: 0.7590 (t0) REVERT: A 376 CYS cc_start: 0.8409 (t) cc_final: 0.8075 (t) REVERT: A 414 GLU cc_start: 0.6116 (mp0) cc_final: 0.5638 (mp0) REVERT: A 424 ASP cc_start: 0.7745 (m-30) cc_final: 0.7375 (m-30) REVERT: A 433 GLU cc_start: 0.7351 (tp30) cc_final: 0.6964 (pt0) REVERT: A 435 VAL cc_start: 0.8553 (p) cc_final: 0.8310 (m) REVERT: B 53 GLU cc_start: 0.6896 (tp30) cc_final: 0.6321 (tp30) REVERT: B 86 ARG cc_start: 0.7792 (mtt180) cc_final: 0.6723 (tpm170) REVERT: B 99 ASN cc_start: 0.8194 (m-40) cc_final: 0.7895 (m-40) REVERT: B 197 ASP cc_start: 0.7561 (m-30) cc_final: 0.6838 (m-30) REVERT: B 209 ASP cc_start: 0.7777 (t70) cc_final: 0.7363 (t0) REVERT: B 221 THR cc_start: 0.8194 (p) cc_final: 0.7985 (t) REVERT: B 237 THR cc_start: 0.8068 (p) cc_final: 0.7706 (t) REVERT: B 247 ASN cc_start: 0.8035 (m110) cc_final: 0.7589 (m-40) REVERT: B 279 GLN cc_start: 0.7851 (pm20) cc_final: 0.7377 (pp30) REVERT: B 280 GLN cc_start: 0.7595 (mt0) cc_final: 0.7104 (mt0) REVERT: B 304 ASP cc_start: 0.7723 (t0) cc_final: 0.7358 (t70) REVERT: B 309 ARG cc_start: 0.7060 (mtt-85) cc_final: 0.6125 (mtt-85) REVERT: B 318 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7439 (mtm-85) REVERT: B 324 LYS cc_start: 0.7773 (tptp) cc_final: 0.7311 (tptp) REVERT: B 329 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: B 380 ARG cc_start: 0.7247 (ptp-170) cc_final: 0.7000 (ptp-170) REVERT: B 412 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7725 (tm-30) REVERT: E 53 GLU cc_start: 0.7185 (tp30) cc_final: 0.6753 (tp30) REVERT: E 86 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7619 (ttp-170) REVERT: E 108 GLU cc_start: 0.7839 (tm-30) cc_final: 0.6994 (tm-30) REVERT: E 123 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7516 (mm-30) REVERT: E 154 LYS cc_start: 0.7604 (mmtp) cc_final: 0.7326 (mmtm) REVERT: E 174 LYS cc_start: 0.8214 (mptt) cc_final: 0.7925 (mptt) REVERT: E 175 VAL cc_start: 0.7905 (m) cc_final: 0.7599 (t) REVERT: E 197 ASP cc_start: 0.7756 (m-30) cc_final: 0.7191 (m-30) REVERT: E 199 THR cc_start: 0.7831 (m) cc_final: 0.7607 (p) REVERT: E 225 LEU cc_start: 0.8253 (mp) cc_final: 0.8007 (mp) REVERT: E 257 MET cc_start: 0.6951 (mpp) cc_final: 0.5993 (mpp) REVERT: E 262 ARG cc_start: 0.7089 (mtp180) cc_final: 0.6824 (mtp-110) REVERT: E 267 MET cc_start: 0.7283 (ttm) cc_final: 0.6942 (ttp) REVERT: E 280 GLN cc_start: 0.7962 (mm110) cc_final: 0.7683 (mm-40) REVERT: E 299 MET cc_start: 0.6476 (mmm) cc_final: 0.6014 (mmm) REVERT: E 366 THR cc_start: 0.8303 (m) cc_final: 0.7951 (t) REVERT: E 391 ARG cc_start: 0.4693 (ptt180) cc_final: 0.3342 (ptt90) REVERT: E 399 THR cc_start: 0.7405 (m) cc_final: 0.6602 (t) REVERT: E 405 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6678 (mt-10) REVERT: F 3 GLU cc_start: 0.6420 (mp0) cc_final: 0.6026 (mp0) REVERT: F 24 TYR cc_start: 0.7937 (m-10) cc_final: 0.7617 (m-10) REVERT: F 51 THR cc_start: 0.8450 (p) cc_final: 0.8208 (t) REVERT: F 69 ASP cc_start: 0.7812 (t0) cc_final: 0.7350 (t0) REVERT: F 70 LEU cc_start: 0.7696 (mm) cc_final: 0.7325 (mt) REVERT: F 77 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6859 (tm-30) REVERT: F 78 VAL cc_start: 0.7640 (t) cc_final: 0.7202 (t) REVERT: F 102 ASN cc_start: 0.6864 (t0) cc_final: 0.6388 (t0) REVERT: F 123 ARG cc_start: 0.7088 (tpp-160) cc_final: 0.6712 (tpp-160) REVERT: F 154 MET cc_start: 0.7580 (mmm) cc_final: 0.7278 (mmm) REVERT: F 161 TYR cc_start: 0.7769 (m-80) cc_final: 0.7370 (m-10) REVERT: F 199 ASP cc_start: 0.8051 (t0) cc_final: 0.7450 (t0) REVERT: F 215 ARG cc_start: 0.6769 (mtm110) cc_final: 0.6323 (mtm110) REVERT: F 216 ASN cc_start: 0.8349 (m-40) cc_final: 0.8127 (m110) REVERT: F 239 THR cc_start: 0.7853 (m) cc_final: 0.7237 (t) REVERT: F 301 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6738 (mp10) REVERT: F 306 ASP cc_start: 0.7719 (t0) cc_final: 0.7079 (t0) REVERT: F 352 LYS cc_start: 0.7629 (tptt) cc_final: 0.6645 (tppt) REVERT: F 367 ASP cc_start: 0.7680 (t0) cc_final: 0.7003 (t0) REVERT: F 413 MET cc_start: 0.7128 (mmm) cc_final: 0.6897 (tpp) REVERT: F 432 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.5538 (t80) outliers start: 64 outliers final: 50 residues processed: 550 average time/residue: 0.3158 time to fit residues: 238.2169 Evaluate side-chains 571 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 518 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 376 CYS Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 155 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 0.0370 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 140 optimal weight: 0.8980 chunk 146 optimal weight: 0.0000 chunk 154 optimal weight: 0.4980 chunk 102 optimal weight: 0.2980 overall best weight: 0.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14163 Z= 0.180 Angle : 0.573 9.966 19237 Z= 0.290 Chirality : 0.044 0.177 2106 Planarity : 0.004 0.055 2502 Dihedral : 9.402 172.132 1994 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.10 % Allowed : 26.65 % Favored : 69.25 % 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: 0.25 (0.20), residues: 1738 helix: 1.34 (0.19), residues: 779 sheet: -0.73 (0.31), residues: 257 loop : -0.77 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 101 HIS 0.005 0.001 HIS F 88 PHE 0.017 0.001 PHE E 167 TYR 0.012 0.001 TYR F 432 ARG 0.006 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 506 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7717 (m-80) cc_final: 0.7241 (m-80) REVERT: A 67 PHE cc_start: 0.8193 (m-80) cc_final: 0.7687 (m-80) REVERT: A 71 GLU cc_start: 0.6527 (tt0) cc_final: 0.6138 (tt0) REVERT: A 118 VAL cc_start: 0.8050 (p) cc_final: 0.7843 (m) REVERT: A 120 ASP cc_start: 0.7187 (m-30) cc_final: 0.6732 (t0) REVERT: A 141 PHE cc_start: 0.7690 (m-10) cc_final: 0.7425 (m-10) REVERT: A 154 MET cc_start: 0.7859 (mmm) cc_final: 0.7148 (mmm) REVERT: A 187 SER cc_start: 0.8252 (m) cc_final: 0.7819 (p) REVERT: A 199 ASP cc_start: 0.7558 (t0) cc_final: 0.7225 (t0) REVERT: A 209 ILE cc_start: 0.8253 (mm) cc_final: 0.7993 (mt) REVERT: A 211 ASP cc_start: 0.7875 (m-30) cc_final: 0.7601 (m-30) REVERT: A 215 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7030 (mtt180) REVERT: A 217 LEU cc_start: 0.8242 (mp) cc_final: 0.8025 (mt) REVERT: A 254 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6825 (mt-10) REVERT: A 280 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8136 (mtmm) REVERT: A 284 GLU cc_start: 0.7859 (tt0) cc_final: 0.7173 (tt0) REVERT: A 297 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 302 MET cc_start: 0.7982 (mmm) cc_final: 0.7687 (mmm) REVERT: A 304 LYS cc_start: 0.8160 (tppt) cc_final: 0.7912 (tppt) REVERT: A 309 HIS cc_start: 0.6816 (m-70) cc_final: 0.6348 (m-70) REVERT: A 349 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8202 (p) REVERT: A 356 ASN cc_start: 0.8019 (t0) cc_final: 0.7568 (t0) REVERT: A 376 CYS cc_start: 0.8208 (t) cc_final: 0.7991 (t) REVERT: A 402 ARG cc_start: 0.7324 (mpt180) cc_final: 0.7072 (mmt-90) REVERT: A 414 GLU cc_start: 0.6070 (mp0) cc_final: 0.5579 (mp0) REVERT: A 424 ASP cc_start: 0.7614 (m-30) cc_final: 0.7238 (m-30) REVERT: A 433 GLU cc_start: 0.7277 (tp30) cc_final: 0.6899 (pt0) REVERT: A 434 GLU cc_start: 0.7939 (tt0) cc_final: 0.7490 (tm-30) REVERT: A 435 VAL cc_start: 0.8575 (p) cc_final: 0.8181 (m) REVERT: B 53 GLU cc_start: 0.6917 (tp30) cc_final: 0.6397 (tp30) REVERT: B 86 ARG cc_start: 0.7748 (mtt180) cc_final: 0.6723 (tpm170) REVERT: B 99 ASN cc_start: 0.8104 (m-40) cc_final: 0.7684 (m-40) REVERT: B 197 ASP cc_start: 0.7535 (m-30) cc_final: 0.6792 (m-30) REVERT: B 209 ASP cc_start: 0.7788 (t70) cc_final: 0.7440 (t0) REVERT: B 221 THR cc_start: 0.8192 (p) cc_final: 0.7983 (t) REVERT: B 237 THR cc_start: 0.8057 (p) cc_final: 0.7704 (t) REVERT: B 247 ASN cc_start: 0.7991 (m110) cc_final: 0.7506 (m-40) REVERT: B 299 MET cc_start: 0.6103 (tpp) cc_final: 0.5884 (mmm) REVERT: B 304 ASP cc_start: 0.7731 (t0) cc_final: 0.7418 (t70) REVERT: B 309 ARG cc_start: 0.7059 (mtt-85) cc_final: 0.6134 (mtt-85) REVERT: B 324 LYS cc_start: 0.7705 (tptp) cc_final: 0.7252 (tptp) REVERT: B 329 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: B 380 ARG cc_start: 0.7238 (ptp-170) cc_final: 0.6996 (ptp-170) REVERT: B 412 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 422 TYR cc_start: 0.5471 (OUTLIER) cc_final: 0.4496 (t80) REVERT: E 53 GLU cc_start: 0.7152 (tp30) cc_final: 0.6711 (tp30) REVERT: E 108 GLU cc_start: 0.7839 (tm-30) cc_final: 0.6987 (tm-30) REVERT: E 123 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7505 (mm-30) REVERT: E 174 LYS cc_start: 0.8217 (mptt) cc_final: 0.7938 (mptt) REVERT: E 175 VAL cc_start: 0.7754 (m) cc_final: 0.7507 (t) REVERT: E 199 THR cc_start: 0.7909 (m) cc_final: 0.7664 (p) REVERT: E 225 LEU cc_start: 0.8240 (mp) cc_final: 0.7857 (tt) REVERT: E 257 MET cc_start: 0.6913 (mpp) cc_final: 0.6105 (mpp) REVERT: E 262 ARG cc_start: 0.7050 (mtp180) cc_final: 0.6830 (mtp-110) REVERT: E 267 MET cc_start: 0.7297 (ttm) cc_final: 0.6892 (ttp) REVERT: E 279 GLN cc_start: 0.7740 (pt0) cc_final: 0.7281 (pt0) REVERT: E 280 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7562 (mm-40) REVERT: E 299 MET cc_start: 0.6551 (mmm) cc_final: 0.6122 (mmm) REVERT: E 300 MET cc_start: 0.8444 (mtp) cc_final: 0.8240 (mtm) REVERT: E 327 ASP cc_start: 0.7091 (m-30) cc_final: 0.6889 (m-30) REVERT: E 366 THR cc_start: 0.8255 (m) cc_final: 0.7899 (t) REVERT: E 391 ARG cc_start: 0.4836 (ptt180) cc_final: 0.3560 (ptt90) REVERT: E 399 THR cc_start: 0.7347 (m) cc_final: 0.6760 (t) REVERT: E 405 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6727 (mt-10) REVERT: F 3 GLU cc_start: 0.6403 (mp0) cc_final: 0.5967 (mp0) REVERT: F 24 TYR cc_start: 0.7901 (m-10) cc_final: 0.7597 (m-10) REVERT: F 51 THR cc_start: 0.8483 (p) cc_final: 0.8242 (t) REVERT: F 69 ASP cc_start: 0.7781 (t0) cc_final: 0.7308 (t0) REVERT: F 70 LEU cc_start: 0.7771 (mm) cc_final: 0.7384 (mt) REVERT: F 77 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6823 (tm-30) REVERT: F 78 VAL cc_start: 0.7545 (t) cc_final: 0.6757 (t) REVERT: F 123 ARG cc_start: 0.6962 (tpp-160) cc_final: 0.6356 (tpp-160) REVERT: F 154 MET cc_start: 0.7572 (mmm) cc_final: 0.7262 (mmm) REVERT: F 155 GLU cc_start: 0.6906 (tp30) cc_final: 0.6476 (tp30) REVERT: F 199 ASP cc_start: 0.8000 (t0) cc_final: 0.7454 (t0) REVERT: F 215 ARG cc_start: 0.6751 (mtm110) cc_final: 0.6272 (mtm110) REVERT: F 216 ASN cc_start: 0.8353 (m-40) cc_final: 0.8127 (m110) REVERT: F 217 LEU cc_start: 0.8060 (mp) cc_final: 0.7706 (mm) REVERT: F 239 THR cc_start: 0.7738 (m) cc_final: 0.7155 (t) REVERT: F 301 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6691 (mp10) REVERT: F 306 ASP cc_start: 0.7689 (t0) cc_final: 0.7064 (t0) REVERT: F 352 LYS cc_start: 0.7632 (tptt) cc_final: 0.6518 (tppt) REVERT: F 367 ASP cc_start: 0.7678 (t0) cc_final: 0.6612 (t0) REVERT: F 413 MET cc_start: 0.7110 (mmm) cc_final: 0.6890 (tpp) REVERT: F 432 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.5618 (t80) outliers start: 61 outliers final: 51 residues processed: 530 average time/residue: 0.3182 time to fit residues: 230.6210 Evaluate side-chains 556 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 501 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 376 CYS Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 43 GLN B 137 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 197 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14163 Z= 0.327 Angle : 0.648 9.603 19237 Z= 0.334 Chirality : 0.047 0.195 2106 Planarity : 0.004 0.066 2502 Dihedral : 9.710 168.611 1994 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.90 % Allowed : 26.78 % Favored : 69.31 % 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: 0.02 (0.20), residues: 1738 helix: 1.10 (0.19), residues: 782 sheet: -0.83 (0.30), residues: 269 loop : -0.80 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 101 HIS 0.005 0.001 HIS E 105 PHE 0.016 0.002 PHE B 133 TYR 0.018 0.002 TYR F 312 ARG 0.015 0.001 ARG B 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 533 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7802 (m-80) cc_final: 0.7273 (m-80) REVERT: A 118 VAL cc_start: 0.8046 (p) cc_final: 0.7816 (m) REVERT: A 120 ASP cc_start: 0.7224 (m-30) cc_final: 0.6775 (t0) REVERT: A 154 MET cc_start: 0.7927 (mmm) cc_final: 0.7068 (mmm) REVERT: A 168 GLU cc_start: 0.6633 (mp0) cc_final: 0.6025 (mp0) REVERT: A 187 SER cc_start: 0.8338 (m) cc_final: 0.7861 (p) REVERT: A 209 ILE cc_start: 0.8270 (mm) cc_final: 0.7896 (mt) REVERT: A 211 ASP cc_start: 0.7959 (m-30) cc_final: 0.7660 (m-30) REVERT: A 215 ARG cc_start: 0.7499 (mtt180) cc_final: 0.7042 (mtt180) REVERT: A 217 LEU cc_start: 0.8336 (mp) cc_final: 0.8116 (mt) REVERT: A 254 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6759 (mt-10) REVERT: A 280 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8239 (mtmm) REVERT: A 284 GLU cc_start: 0.7906 (tt0) cc_final: 0.7312 (tt0) REVERT: A 290 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6854 (mt-10) REVERT: A 297 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 302 MET cc_start: 0.8029 (mmm) cc_final: 0.7667 (mmm) REVERT: A 309 HIS cc_start: 0.6851 (m-70) cc_final: 0.6391 (m-70) REVERT: A 349 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 356 ASN cc_start: 0.8113 (t0) cc_final: 0.7667 (t0) REVERT: A 376 CYS cc_start: 0.8435 (t) cc_final: 0.8104 (t) REVERT: A 402 ARG cc_start: 0.7375 (mpt180) cc_final: 0.7099 (ptm160) REVERT: A 414 GLU cc_start: 0.6152 (mp0) cc_final: 0.5674 (mp0) REVERT: A 433 GLU cc_start: 0.7387 (tp30) cc_final: 0.7061 (pt0) REVERT: A 435 VAL cc_start: 0.8537 (p) cc_final: 0.8280 (m) REVERT: B 53 GLU cc_start: 0.6924 (tp30) cc_final: 0.6339 (tp30) REVERT: B 73 MET cc_start: 0.7735 (mmm) cc_final: 0.7434 (mmm) REVERT: B 86 ARG cc_start: 0.7821 (mtt180) cc_final: 0.6714 (tpm170) REVERT: B 164 MET cc_start: 0.6789 (tpp) cc_final: 0.5949 (tpp) REVERT: B 197 ASP cc_start: 0.7652 (m-30) cc_final: 0.7063 (m-30) REVERT: B 209 ASP cc_start: 0.7777 (t70) cc_final: 0.7461 (t0) REVERT: B 216 LYS cc_start: 0.8270 (mmmm) cc_final: 0.8051 (mmmm) REVERT: B 237 THR cc_start: 0.8105 (p) cc_final: 0.7665 (t) REVERT: B 241 ARG cc_start: 0.8624 (mtp180) cc_final: 0.8369 (mtp-110) REVERT: B 247 ASN cc_start: 0.8062 (m110) cc_final: 0.7644 (m-40) REVERT: B 251 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7469 (ttm110) REVERT: B 263 LEU cc_start: 0.7747 (tp) cc_final: 0.7509 (tp) REVERT: B 299 MET cc_start: 0.6455 (tpp) cc_final: 0.6158 (mmm) REVERT: B 318 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: B 324 LYS cc_start: 0.7865 (tptp) cc_final: 0.7664 (tptp) REVERT: B 376 GLU cc_start: 0.7251 (mp0) cc_final: 0.6790 (mp0) REVERT: B 380 ARG cc_start: 0.7296 (ptp-170) cc_final: 0.7030 (ptp-170) REVERT: B 381 ILE cc_start: 0.8270 (mm) cc_final: 0.7924 (tt) REVERT: B 391 ARG cc_start: 0.7048 (tpp80) cc_final: 0.6787 (mpt180) REVERT: B 412 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 422 TYR cc_start: 0.5817 (OUTLIER) cc_final: 0.4790 (t80) REVERT: E 53 GLU cc_start: 0.7222 (tp30) cc_final: 0.6773 (tp30) REVERT: E 86 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7740 (ttp-170) REVERT: E 108 GLU cc_start: 0.7873 (tm-30) cc_final: 0.6964 (tm-30) REVERT: E 123 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7500 (mm-30) REVERT: E 154 LYS cc_start: 0.7587 (mmtp) cc_final: 0.7341 (mmtm) REVERT: E 174 LYS cc_start: 0.8260 (mptt) cc_final: 0.7946 (mptt) REVERT: E 175 VAL cc_start: 0.7937 (m) cc_final: 0.7556 (t) REVERT: E 197 ASP cc_start: 0.7582 (m-30) cc_final: 0.7323 (m-30) REVERT: E 216 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8005 (mmtt) REVERT: E 225 LEU cc_start: 0.8241 (mp) cc_final: 0.7870 (tt) REVERT: E 257 MET cc_start: 0.6960 (mpp) cc_final: 0.6003 (mpp) REVERT: E 262 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6903 (mtp-110) REVERT: E 267 MET cc_start: 0.7356 (ttm) cc_final: 0.6968 (ttp) REVERT: E 279 GLN cc_start: 0.7774 (pt0) cc_final: 0.7335 (pt0) REVERT: E 280 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7584 (mm-40) REVERT: E 299 MET cc_start: 0.6653 (mmm) cc_final: 0.6297 (mmm) REVERT: E 366 THR cc_start: 0.8292 (m) cc_final: 0.7973 (t) REVERT: E 391 ARG cc_start: 0.4632 (ptt180) cc_final: 0.3147 (ptt-90) REVERT: E 405 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6640 (mt-10) REVERT: F 3 GLU cc_start: 0.6565 (mp0) cc_final: 0.6092 (mp0) REVERT: F 24 TYR cc_start: 0.7960 (m-10) cc_final: 0.7663 (m-10) REVERT: F 51 THR cc_start: 0.8523 (p) cc_final: 0.8278 (t) REVERT: F 69 ASP cc_start: 0.7823 (t0) cc_final: 0.7389 (t0) REVERT: F 70 LEU cc_start: 0.7764 (mm) cc_final: 0.7379 (mt) REVERT: F 77 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6965 (tm-30) REVERT: F 78 VAL cc_start: 0.7561 (t) cc_final: 0.7155 (t) REVERT: F 102 ASN cc_start: 0.7018 (t0) cc_final: 0.6421 (t0) REVERT: F 123 ARG cc_start: 0.7083 (tpp-160) cc_final: 0.6693 (tpp-160) REVERT: F 154 MET cc_start: 0.7577 (mmm) cc_final: 0.7331 (mmm) REVERT: F 155 GLU cc_start: 0.6944 (tp30) cc_final: 0.6532 (tp30) REVERT: F 161 TYR cc_start: 0.7750 (m-80) cc_final: 0.7203 (m-10) REVERT: F 199 ASP cc_start: 0.7997 (t0) cc_final: 0.7405 (t0) REVERT: F 215 ARG cc_start: 0.6769 (mtm110) cc_final: 0.6159 (mtm110) REVERT: F 216 ASN cc_start: 0.8381 (m-40) cc_final: 0.8060 (m110) REVERT: F 229 ARG cc_start: 0.7068 (mmt90) cc_final: 0.6642 (mpt-90) REVERT: F 239 THR cc_start: 0.7876 (m) cc_final: 0.7320 (t) REVERT: F 272 TYR cc_start: 0.8545 (t80) cc_final: 0.8097 (t80) REVERT: F 301 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6802 (mt0) REVERT: F 306 ASP cc_start: 0.7699 (t0) cc_final: 0.7057 (t0) REVERT: F 352 LYS cc_start: 0.7616 (tptt) cc_final: 0.6598 (tppt) REVERT: F 367 ASP cc_start: 0.7679 (t0) cc_final: 0.6986 (t0) REVERT: F 380 ASN cc_start: 0.8108 (t0) cc_final: 0.7730 (t0) REVERT: F 413 MET cc_start: 0.7224 (mmm) cc_final: 0.7019 (tpp) REVERT: F 432 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.5403 (t80) outliers start: 58 outliers final: 46 residues processed: 558 average time/residue: 0.3292 time to fit residues: 253.5621 Evaluate side-chains 582 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 533 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 376 CYS Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 120 optimal weight: 0.2980 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 102 ASN A 226 ASN B 137 HIS E 99 ASN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 285 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.126977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113672 restraints weight = 19803.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117552 restraints weight = 8899.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.120085 restraints weight = 4762.782| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14163 Z= 0.275 Angle : 0.624 9.591 19237 Z= 0.320 Chirality : 0.046 0.188 2106 Planarity : 0.004 0.061 2502 Dihedral : 9.619 168.416 1994 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.84 % Allowed : 27.19 % Favored : 68.98 % 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: 0.03 (0.20), residues: 1738 helix: 1.07 (0.19), residues: 782 sheet: -0.67 (0.31), residues: 255 loop : -0.84 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 101 HIS 0.004 0.001 HIS F 88 PHE 0.019 0.002 PHE E 167 TYR 0.016 0.001 TYR F 432 ARG 0.014 0.001 ARG B 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4736.31 seconds wall clock time: 85 minutes 11.36 seconds (5111.36 seconds total)