Starting phenix.real_space_refine on Sun Mar 17 06:15:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/03_2024/6xt9_10617.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/03_2024/6xt9_10617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/03_2024/6xt9_10617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/03_2024/6xt9_10617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/03_2024/6xt9_10617.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xt9_10617/03_2024/6xt9_10617.pdb" } resolution = 3.8 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= 0.002 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10811 2.51 5 N 2888 2.21 5 O 3127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 17": "NH1" <-> "NH2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "H ARG 227": "NH1" <-> "NH2" Residue "H PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H GLU 303": "OE1" <-> "OE2" Residue "H ARG 340": "NH1" <-> "NH2" Residue "H GLU 381": "OE1" <-> "OE2" Residue "H GLU 384": "OE1" <-> "OE2" Residue "H GLU 422": "OE1" <-> "OE2" Residue "H ARG 433": "NH1" <-> "NH2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 487": "OD1" <-> "OD2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 265": "OE1" <-> "OE2" Residue "I ASP 317": "OD1" <-> "OD2" Residue "I ASP 429": "OD1" <-> "OD2" Residue "I ARG 449": "NH1" <-> "NH2" Residue "I GLU 466": "OE1" <-> "OE2" Residue "I PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 587": "NH1" <-> "NH2" Residue "I TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 600": "NH1" <-> "NH2" Residue "I GLU 607": "OE1" <-> "OE2" Residue "I ARG 619": "NH1" <-> "NH2" Residue "I PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 668": "OE1" <-> "OE2" Residue "I ARG 674": "NH1" <-> "NH2" Residue "I ARG 678": "NH1" <-> "NH2" Residue "I ARG 679": "NH1" <-> "NH2" Residue "I ARG 683": "NH1" <-> "NH2" Residue "I ASP 686": "OD1" <-> "OD2" Residue "I ASP 696": "OD1" <-> "OD2" Residue "I ASP 700": "OD1" <-> "OD2" Residue "I GLU 715": "OE1" <-> "OE2" Residue "I GLU 761": "OE1" <-> "OE2" Residue "I GLU 769": "OE1" <-> "OE2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 67": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16916 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4378 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 38, 'TRANS': 528} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3069 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 10, 'TRANS': 385} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 61 Chain: "H" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3192 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5834 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 31, 'TRANS': 735} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "J" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 443 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Time building chain proxies: 9.09, per 1000 atoms: 0.54 Number of scatterers: 16916 At special positions: 0 Unit cell: (141.24, 160.5, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3127 8.00 N 2888 7.00 C 10811 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: 6.49 Conformation dependent library (CDL) restraints added in 3.1 seconds 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4144 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 25 sheets defined 40.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 132 through 140 removed outlier: 3.938A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.509A pdb=" N LEU A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.675A pdb=" N VAL A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 removed outlier: 3.587A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 472 removed outlier: 3.891A pdb=" N MET A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.944A pdb=" N ILE D 39 " --> pdb=" O GLN D 35 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 41 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.565A pdb=" N LYS D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.658A pdb=" N GLN D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 4.004A pdb=" N GLU D 88 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 removed outlier: 4.215A pdb=" N ALA D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 131 removed outlier: 3.541A pdb=" N ALA D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 147 removed outlier: 3.617A pdb=" N LEU D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 3.963A pdb=" N ASP D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 164 " --> pdb=" O ASN D 160 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.762A pdb=" N ILE D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 198 removed outlier: 4.162A pdb=" N GLU D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.598A pdb=" N LEU D 205 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 232 removed outlier: 3.790A pdb=" N GLU D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 248 removed outlier: 3.669A pdb=" N LEU D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 247 " --> pdb=" O GLY D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 263 removed outlier: 3.686A pdb=" N THR D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.533A pdb=" N ASN D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 282 " --> pdb=" O MET D 278 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS D 283 " --> pdb=" O CYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 300 removed outlier: 3.786A pdb=" N ILE D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D 296 " --> pdb=" O CYS D 292 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.857A pdb=" N TYR D 308 " --> pdb=" O TRP D 304 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 315 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 332 removed outlier: 3.532A pdb=" N PHE D 324 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN D 332 " --> pdb=" O SER D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 350 removed outlier: 3.564A pdb=" N ALA D 345 " --> pdb=" O TYR D 341 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 346 " --> pdb=" O MET D 342 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 367 removed outlier: 3.507A pdb=" N ARG D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 removed outlier: 3.835A pdb=" N ASN D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 381 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 407 through 422 removed outlier: 4.165A pdb=" N LEU D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP D 414 " --> pdb=" O SER D 410 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN D 422 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 removed outlier: 3.545A pdb=" N ARG H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 30 removed outlier: 4.165A pdb=" N ASP H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 50 removed outlier: 3.540A pdb=" N LEU H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.510A pdb=" N TYR H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 194 removed outlier: 3.807A pdb=" N GLU H 193 " --> pdb=" O ILE H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 210 removed outlier: 3.540A pdb=" N ALA H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP H 201 " --> pdb=" O LYS H 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU H 202 " --> pdb=" O THR H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 229 removed outlier: 3.521A pdb=" N GLY H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 243 removed outlier: 4.277A pdb=" N LYS H 239 " --> pdb=" O GLU H 235 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA H 241 " --> pdb=" O GLN H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.605A pdb=" N PHE H 251 " --> pdb=" O MET H 247 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS H 256 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL H 259 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.866A pdb=" N ASN H 269 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU H 270 " --> pdb=" O THR H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 277 No H-bonds generated for 'chain 'H' and resid 275 through 277' Processing helix chain 'H' and resid 281 through 292 removed outlier: 3.671A pdb=" N LEU H 285 " --> pdb=" O GLU H 281 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 289 " --> pdb=" O LEU H 285 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR H 292 " --> pdb=" O ILE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 302 removed outlier: 3.675A pdb=" N ALA H 302 " --> pdb=" O MET H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'H' and resid 315 through 318 removed outlier: 3.548A pdb=" N ALA H 318 " --> pdb=" O HIS H 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 315 through 318' Processing helix chain 'H' and resid 319 through 324 Processing helix chain 'H' and resid 333 through 345 removed outlier: 3.602A pdb=" N TYR H 339 " --> pdb=" O ALA H 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG H 341 " --> pdb=" O ARG H 337 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 342 " --> pdb=" O PHE H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 363 removed outlier: 3.522A pdb=" N ASN H 354 " --> pdb=" O GLY H 350 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS H 360 " --> pdb=" O LEU H 356 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 361 " --> pdb=" O GLY H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 378 removed outlier: 4.545A pdb=" N THR H 371 " --> pdb=" O ASP H 367 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER H 372 " --> pdb=" O MET H 368 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 401 removed outlier: 4.280A pdb=" N ASP H 388 " --> pdb=" O GLU H 384 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL H 389 " --> pdb=" O GLU H 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS H 395 " --> pdb=" O TYR H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 417 removed outlier: 3.719A pdb=" N GLN H 408 " --> pdb=" O ASN H 404 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE H 410 " --> pdb=" O ALA H 406 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG H 411 " --> pdb=" O HIS H 407 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 435 removed outlier: 3.790A pdb=" N ASN H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN H 426 " --> pdb=" O GLU H 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL H 429 " --> pdb=" O ASN H 425 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU H 430 " --> pdb=" O ASN H 426 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET H 432 " --> pdb=" O ALA H 428 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS H 434 " --> pdb=" O LEU H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 449 removed outlier: 3.653A pdb=" N ALA H 442 " --> pdb=" O GLU H 438 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 443 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN H 445 " --> pdb=" O ARG H 441 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 449 " --> pdb=" O GLN H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 462 removed outlier: 3.549A pdb=" N ALA H 462 " --> pdb=" O HIS H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 3.630A pdb=" N VAL H 476 " --> pdb=" O GLN H 472 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA H 478 " --> pdb=" O SER H 474 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU H 482 " --> pdb=" O ALA H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 493 removed outlier: 3.911A pdb=" N GLN H 492 " --> pdb=" O HIS H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 504 removed outlier: 3.690A pdb=" N GLN H 500 " --> pdb=" O LYS H 496 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS H 501 " --> pdb=" O GLN H 497 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA H 503 " --> pdb=" O ARG H 499 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET H 504 " --> pdb=" O GLN H 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.663A pdb=" N GLY I 145 " --> pdb=" O SER I 142 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL I 146 " --> pdb=" O PHE I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 146' Processing helix chain 'I' and resid 401 through 414 removed outlier: 3.605A pdb=" N THR I 405 " --> pdb=" O VAL I 401 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP I 410 " --> pdb=" O GLU I 406 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU I 411 " --> pdb=" O ARG I 407 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN I 412 " --> pdb=" O GLU I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 562 Processing helix chain 'I' and resid 609 through 625 removed outlier: 4.187A pdb=" N ASN I 614 " --> pdb=" O TRP I 610 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU I 615 " --> pdb=" O LEU I 611 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU I 625 " --> pdb=" O GLN I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 660 removed outlier: 3.987A pdb=" N GLU I 644 " --> pdb=" O ILE I 640 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU I 647 " --> pdb=" O GLN I 643 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU I 648 " --> pdb=" O GLU I 644 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 650 " --> pdb=" O PHE I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 684 removed outlier: 3.553A pdb=" N GLU I 668 " --> pdb=" O GLU I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 696 through 709 removed outlier: 3.590A pdb=" N ASP I 700 " --> pdb=" O ASP I 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY I 701 " --> pdb=" O THR I 697 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR I 702 " --> pdb=" O LEU I 698 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL I 706 " --> pdb=" O THR I 702 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE I 707 " --> pdb=" O TYR I 703 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU I 709 " --> pdb=" O GLN I 705 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 742 removed outlier: 3.899A pdb=" N ASN I 716 " --> pdb=" O ALA I 712 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN I 717 " --> pdb=" O VAL I 713 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG I 726 " --> pdb=" O GLN I 722 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU I 737 " --> pdb=" O LEU I 733 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA I 739 " --> pdb=" O ILE I 735 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU I 740 " --> pdb=" O LEU I 736 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN I 742 " --> pdb=" O ILE I 738 " (cutoff:3.500A) Processing helix chain 'I' and resid 747 through 756 removed outlier: 3.605A pdb=" N ALA I 754 " --> pdb=" O ALA I 750 " (cutoff:3.500A) Processing helix chain 'I' and resid 767 through 780 removed outlier: 3.830A pdb=" N ASP I 773 " --> pdb=" O GLU I 769 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA I 774 " --> pdb=" O GLU I 770 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS I 778 " --> pdb=" O ALA I 774 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU I 780 " --> pdb=" O ILE I 776 " (cutoff:3.500A) Processing helix chain 'I' and resid 788 through 799 removed outlier: 3.733A pdb=" N LEU I 795 " --> pdb=" O GLN I 791 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN I 798 " --> pdb=" O ASN I 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 80 removed outlier: 3.952A pdb=" N ASN J 75 " --> pdb=" O GLN J 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN J 79 " --> pdb=" O ASN J 75 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN J 80 " --> pdb=" O THR J 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 29 removed outlier: 5.410A pdb=" N ASP A 25 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 401 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 27 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 398 " --> pdb=" O MET A 390 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 400 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 388 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASP A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TYR A 381 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 375 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.646A pdb=" N ALA A 44 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 78 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A 72 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 92 removed outlier: 3.664A pdb=" N ALA A 88 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 114 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR A 121 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 207 removed outlier: 3.689A pdb=" N THR A 202 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 222 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 230 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 240 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253 removed outlier: 3.500A pdb=" N CYS A 267 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 274 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR A 284 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 297 removed outlier: 6.305A pdb=" N GLY A 305 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 295 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 303 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA8, first strand: chain 'A' and resid 330 through 337 removed outlier: 3.654A pdb=" N ASN A 334 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.707A pdb=" N HIS A 489 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.707A pdb=" N HIS A 489 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 501 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.814A pdb=" N VAL A 519 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.561A pdb=" N ILE I 41 " --> pdb=" O CYS I 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 51 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU I 70 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 78 through 82 removed outlier: 4.150A pdb=" N GLN I 80 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 98 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 95 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS I 102 " --> pdb=" O HIS I 99 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS I 124 " --> pdb=" O SER I 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 78 through 82 removed outlier: 4.150A pdb=" N GLN I 80 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 98 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 95 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS I 102 " --> pdb=" O HIS I 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 135 through 137 removed outlier: 7.345A pdb=" N GLN I 155 " --> pdb=" O CYS I 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'I' and resid 160 through 164 removed outlier: 3.840A pdb=" N PHE I 171 " --> pdb=" O VAL I 163 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 184 through 186 Processing sheet with id=AC1, first strand: chain 'I' and resid 245 through 252 removed outlier: 4.013A pdb=" N ASP I 247 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 263 " --> pdb=" O ASP I 247 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I 251 " --> pdb=" O SER I 259 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL I 262 " --> pdb=" O PHE I 269 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS I 270 " --> pdb=" O ARG I 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 290 through 291 Processing sheet with id=AC3, first strand: chain 'I' and resid 332 through 336 removed outlier: 3.776A pdb=" N ARG I 334 " --> pdb=" O VAL I 346 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY I 336 " --> pdb=" O VAL I 344 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL I 344 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 430 through 432 removed outlier: 3.690A pdb=" N VAL I 440 " --> pdb=" O VAL I 489 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 472 through 473 removed outlier: 3.628A pdb=" N LEU I 457 " --> pdb=" O PHE I 472 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER I 509 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 472 through 473 removed outlier: 3.628A pdb=" N LEU I 457 " --> pdb=" O PHE I 472 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER I 509 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 546 through 550 removed outlier: 3.520A pdb=" N HIS I 546 " --> pdb=" O SER I 603 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1683 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: 4.92 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5372 1.34 - 1.46: 2812 1.46 - 1.57: 8938 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 17260 Sorted by residual: bond pdb=" C ASN D 371 " pdb=" N PRO D 372 " ideal model delta sigma weight residual 1.330 1.367 -0.036 1.23e-02 6.61e+03 8.76e+00 bond pdb=" N ASP I 317 " pdb=" CA ASP I 317 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.77e+00 bond pdb=" N PRO A 419 " pdb=" CA PRO A 419 " ideal model delta sigma weight residual 1.473 1.453 0.020 8.50e-03 1.38e+04 5.58e+00 bond pdb=" N GLU A 410 " pdb=" CA GLU A 410 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.30e+00 bond pdb=" C THR I 688 " pdb=" N PRO I 689 " ideal model delta sigma weight residual 1.335 1.357 -0.022 9.40e-03 1.13e+04 5.27e+00 ... (remaining 17255 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.63: 491 106.63 - 113.53: 9484 113.53 - 120.43: 6692 120.43 - 127.32: 6565 127.32 - 134.22: 191 Bond angle restraints: 23423 Sorted by residual: angle pdb=" N PRO A 419 " pdb=" CA PRO A 419 " pdb=" CB PRO A 419 " ideal model delta sigma weight residual 101.88 110.61 -8.73 1.01e+00 9.80e-01 7.48e+01 angle pdb=" N PRO A 418 " pdb=" CA PRO A 418 " pdb=" CB PRO A 418 " ideal model delta sigma weight residual 103.08 111.26 -8.18 9.70e-01 1.06e+00 7.11e+01 angle pdb=" N PRO I 369 " pdb=" CA PRO I 369 " pdb=" CB PRO I 369 " ideal model delta sigma weight residual 103.25 111.37 -8.12 1.05e+00 9.07e-01 5.98e+01 angle pdb=" N PRO A 417 " pdb=" CA PRO A 417 " pdb=" CB PRO A 417 " ideal model delta sigma weight residual 103.08 109.96 -6.88 9.70e-01 1.06e+00 5.02e+01 angle pdb=" N PRO I 403 " pdb=" CA PRO I 403 " pdb=" CB PRO I 403 " ideal model delta sigma weight residual 103.51 110.19 -6.68 9.60e-01 1.09e+00 4.84e+01 ... (remaining 23418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9081 17.85 - 35.70: 1065 35.70 - 53.56: 188 53.56 - 71.41: 45 71.41 - 89.26: 23 Dihedral angle restraints: 10402 sinusoidal: 4005 harmonic: 6397 Sorted by residual: dihedral pdb=" CA VAL I 437 " pdb=" C VAL I 437 " pdb=" N PRO I 438 " pdb=" CA PRO I 438 " ideal model delta harmonic sigma weight residual -180.00 -111.84 -68.16 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA ALA I 633 " pdb=" C ALA I 633 " pdb=" N CYS I 634 " pdb=" CA CYS I 634 " ideal model delta harmonic sigma weight residual 180.00 127.53 52.47 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA GLN H 211 " pdb=" C GLN H 211 " pdb=" N TYR H 212 " pdb=" CA TYR H 212 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 10399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2421 0.089 - 0.178: 233 0.178 - 0.266: 30 0.266 - 0.355: 2 0.355 - 0.444: 2 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CB ILE I 534 " pdb=" CA ILE I 534 " pdb=" CG1 ILE I 534 " pdb=" CG2 ILE I 534 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CB VAL I 437 " pdb=" CA VAL I 437 " pdb=" CG1 VAL I 437 " pdb=" CG2 VAL I 437 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA PRO I 369 " pdb=" N PRO I 369 " pdb=" C PRO I 369 " pdb=" CB PRO I 369 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2685 not shown) Planarity restraints: 3011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 409 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL A 409 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL A 409 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 410 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 437 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO I 438 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO I 438 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO I 438 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 463 " -0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO I 464 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO I 464 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO I 464 " -0.049 5.00e-02 4.00e+02 ... (remaining 3008 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4811 2.81 - 3.33: 15432 3.33 - 3.85: 27153 3.85 - 4.38: 30345 4.38 - 4.90: 51167 Nonbonded interactions: 128908 Sorted by model distance: nonbonded pdb=" O SER D 86 " pdb=" OG SER D 86 " model vdw 2.285 2.440 nonbonded pdb=" O VAL I 444 " pdb=" OG1 THR I 484 " model vdw 2.294 2.440 nonbonded pdb=" OG SER I 156 " pdb=" OD1 ASP I 158 " model vdw 2.298 2.440 nonbonded pdb=" O PHE I 86 " pdb=" OH TYR I 127 " model vdw 2.299 2.440 nonbonded pdb=" O GLY I 767 " pdb=" OG1 THR I 771 " model vdw 2.306 2.440 ... (remaining 128903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.430 Check model and map are aligned: 0.280 Set scattering table: 0.150 Process input model: 44.620 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17260 Z= 0.344 Angle : 1.005 15.672 23423 Z= 0.564 Chirality : 0.057 0.444 2688 Planarity : 0.007 0.106 3011 Dihedral : 16.304 89.260 6258 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.41 % Favored : 90.31 % Rotamer: Outliers : 0.34 % Allowed : 10.91 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.24 % 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: -5.57 (0.13), residues: 2167 helix: -4.21 (0.09), residues: 813 sheet: -2.87 (0.22), residues: 416 loop : -3.45 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 139 HIS 0.008 0.001 HIS H 192 PHE 0.032 0.002 PHE I 632 TYR 0.025 0.002 TYR D 361 ARG 0.005 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 2.008 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 160 ARG cc_start: 0.8805 (ttp-170) cc_final: 0.8188 (mmt180) REVERT: A 347 MET cc_start: 0.8346 (mpp) cc_final: 0.8139 (mpp) REVERT: A 578 LEU cc_start: 0.8785 (pp) cc_final: 0.8360 (pp) REVERT: D 246 MET cc_start: 0.8110 (mmt) cc_final: 0.7568 (mmm) REVERT: D 251 ASP cc_start: 0.7759 (m-30) cc_final: 0.7406 (m-30) REVERT: D 260 ARG cc_start: 0.8655 (mtt180) cc_final: 0.8412 (mtt-85) REVERT: D 295 ARG cc_start: 0.8515 (ttt180) cc_final: 0.8304 (ttt90) REVERT: D 343 LEU cc_start: 0.9462 (mm) cc_final: 0.9177 (mm) REVERT: D 361 TYR cc_start: 0.6912 (t80) cc_final: 0.6679 (t80) REVERT: H 53 TYR cc_start: 0.8538 (t80) cc_final: 0.8137 (t80) REVERT: H 186 PHE cc_start: 0.8562 (t80) cc_final: 0.8183 (t80) REVERT: H 190 PHE cc_start: 0.8989 (m-80) cc_final: 0.8654 (m-80) REVERT: H 225 TYR cc_start: 0.8806 (m-10) cc_final: 0.8377 (m-10) REVERT: H 286 CYS cc_start: 0.8593 (t) cc_final: 0.8255 (t) REVERT: H 334 ILE cc_start: 0.9118 (mt) cc_final: 0.8910 (tt) REVERT: H 480 LYS cc_start: 0.9197 (mttt) cc_final: 0.8601 (mmmm) REVERT: I 98 LEU cc_start: 0.8625 (tp) cc_final: 0.8364 (tt) REVERT: I 123 MET cc_start: 0.7284 (mmp) cc_final: 0.7035 (mmp) REVERT: I 138 MET cc_start: 0.7847 (ptm) cc_final: 0.7587 (ptp) REVERT: I 284 ASP cc_start: 0.8432 (p0) cc_final: 0.8188 (p0) REVERT: I 477 MET cc_start: 0.3765 (mmt) cc_final: 0.1972 (mmt) REVERT: I 501 GLU cc_start: 0.8739 (pp20) cc_final: 0.8177 (pp20) REVERT: I 535 CYS cc_start: 0.7271 (t) cc_final: 0.6541 (p) REVERT: I 711 ASP cc_start: 0.9109 (m-30) cc_final: 0.8668 (p0) REVERT: J 69 MET cc_start: 0.8594 (tmm) cc_final: 0.7976 (tmm) REVERT: J 70 HIS cc_start: 0.8170 (t-90) cc_final: 0.7900 (t70) outliers start: 6 outliers final: 3 residues processed: 285 average time/residue: 0.2880 time to fit residues: 122.5769 Evaluate side-chains 204 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 230 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 308 GLN A 504 HIS A 581 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 103 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS D 366 HIS D 371 ASN D 377 ASN D 384 ASN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 ASN ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN ** H 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 500 GLN I 55 HIS I 166 GLN I 200 GLN I 307 ASN I 515 ASN I 553 ASN ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 GLN I 719 ASN I 748 GLN I 760 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17260 Z= 0.276 Angle : 0.695 14.086 23423 Z= 0.363 Chirality : 0.043 0.240 2688 Planarity : 0.006 0.101 3011 Dihedral : 6.327 57.702 2338 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.86 % Favored : 91.00 % Rotamer: Outliers : 2.75 % Allowed : 17.14 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % 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: -4.07 (0.15), residues: 2167 helix: -2.24 (0.15), residues: 864 sheet: -2.19 (0.24), residues: 375 loop : -3.30 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 610 HIS 0.011 0.001 HIS D 366 PHE 0.018 0.002 PHE A 521 TYR 0.029 0.002 TYR H 304 ARG 0.005 0.000 ARG I 669 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 222 time to evaluate : 2.174 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 137 ASP cc_start: 0.9527 (m-30) cc_final: 0.9321 (t70) REVERT: A 146 ARG cc_start: 0.8924 (tpt90) cc_final: 0.8686 (tpt90) REVERT: A 570 ARG cc_start: 0.7481 (mmm-85) cc_final: 0.7252 (mmm-85) REVERT: D 246 MET cc_start: 0.8300 (mmt) cc_final: 0.7833 (mmm) REVERT: D 251 ASP cc_start: 0.7652 (m-30) cc_final: 0.7342 (m-30) REVERT: D 260 ARG cc_start: 0.8765 (mtt180) cc_final: 0.8483 (mtt-85) REVERT: D 337 MET cc_start: 0.8973 (tpp) cc_final: 0.8136 (tpp) REVERT: D 339 GLU cc_start: 0.8673 (mp0) cc_final: 0.8133 (mp0) REVERT: D 373 LEU cc_start: 0.7523 (mt) cc_final: 0.7312 (pp) REVERT: H 61 GLN cc_start: 0.6373 (mm-40) cc_final: 0.5163 (mm-40) REVERT: H 186 PHE cc_start: 0.8599 (t80) cc_final: 0.8095 (t80) REVERT: H 190 PHE cc_start: 0.9090 (m-80) cc_final: 0.8504 (m-80) REVERT: H 230 MET cc_start: 0.7495 (mtp) cc_final: 0.6716 (mpp) REVERT: H 295 MET cc_start: 0.9318 (mmt) cc_final: 0.9034 (mpp) REVERT: H 479 GLN cc_start: 0.8888 (tp40) cc_final: 0.8647 (tp40) REVERT: H 480 LYS cc_start: 0.9197 (mttt) cc_final: 0.8685 (mmmm) REVERT: H 487 ASP cc_start: 0.8234 (t0) cc_final: 0.8031 (t0) REVERT: I 157 MET cc_start: 0.8712 (mmm) cc_final: 0.8495 (mmm) REVERT: I 239 LEU cc_start: 0.8649 (tp) cc_final: 0.8221 (mt) REVERT: I 284 ASP cc_start: 0.8443 (p0) cc_final: 0.8180 (p0) REVERT: I 477 MET cc_start: 0.4095 (mmt) cc_final: 0.2431 (mmt) REVERT: I 481 LEU cc_start: 0.5601 (OUTLIER) cc_final: 0.5084 (pt) REVERT: I 535 CYS cc_start: 0.6831 (t) cc_final: 0.5995 (p) REVERT: I 711 ASP cc_start: 0.9159 (m-30) cc_final: 0.8678 (p0) REVERT: I 770 GLU cc_start: 0.6444 (mt-10) cc_final: 0.6214 (tt0) REVERT: J 69 MET cc_start: 0.8272 (tmm) cc_final: 0.7657 (tmm) REVERT: J 70 HIS cc_start: 0.7895 (t-90) cc_final: 0.7609 (t70) REVERT: J 71 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8067 (tm-30) outliers start: 49 outliers final: 24 residues processed: 258 average time/residue: 0.2787 time to fit residues: 111.4182 Evaluate side-chains 218 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 590 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 211 optimal weight: 0.0000 chunk 174 optimal weight: 4.9990 chunk 193 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS A 581 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN I 339 HIS ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17260 Z= 0.181 Angle : 0.636 11.408 23423 Z= 0.322 Chirality : 0.042 0.227 2688 Planarity : 0.005 0.094 3011 Dihedral : 5.735 56.252 2338 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.21 % Favored : 91.69 % Rotamer: Outliers : 2.98 % Allowed : 19.73 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % 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: -3.25 (0.17), residues: 2167 helix: -1.28 (0.17), residues: 867 sheet: -1.92 (0.25), residues: 367 loop : -3.10 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 610 HIS 0.015 0.001 HIS A 581 PHE 0.019 0.001 PHE H 238 TYR 0.019 0.001 TYR H 304 ARG 0.003 0.000 ARG D 295 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 224 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.6819 (p-80) REVERT: A 584 MET cc_start: 0.8230 (ppp) cc_final: 0.7243 (ppp) REVERT: D 260 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8464 (mtt-85) REVERT: D 337 MET cc_start: 0.8841 (tpp) cc_final: 0.7883 (tpp) REVERT: D 339 GLU cc_start: 0.8678 (mp0) cc_final: 0.8233 (mp0) REVERT: D 361 TYR cc_start: 0.7941 (t80) cc_final: 0.7671 (t80) REVERT: H 43 LEU cc_start: 0.9594 (tp) cc_final: 0.9330 (tt) REVERT: H 186 PHE cc_start: 0.8611 (t80) cc_final: 0.8074 (t80) REVERT: H 190 PHE cc_start: 0.9090 (m-80) cc_final: 0.8498 (m-80) REVERT: H 230 MET cc_start: 0.7052 (mtp) cc_final: 0.6640 (mpp) REVERT: H 377 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8467 (mm) REVERT: H 391 TYR cc_start: 0.9330 (t80) cc_final: 0.8795 (t80) REVERT: H 480 LYS cc_start: 0.9174 (mttt) cc_final: 0.8678 (mmmm) REVERT: I 138 MET cc_start: 0.7586 (ptp) cc_final: 0.7340 (ppp) REVERT: I 157 MET cc_start: 0.8710 (mmm) cc_final: 0.8475 (mmm) REVERT: I 200 GLN cc_start: 0.8611 (mt0) cc_final: 0.8378 (mp10) REVERT: I 239 LEU cc_start: 0.8648 (tp) cc_final: 0.8332 (mt) REVERT: I 284 ASP cc_start: 0.8392 (p0) cc_final: 0.8142 (p0) REVERT: I 477 MET cc_start: 0.4129 (mmt) cc_final: 0.2550 (mmt) REVERT: I 481 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.4904 (pt) REVERT: I 535 CYS cc_start: 0.6923 (t) cc_final: 0.6526 (t) REVERT: I 580 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7698 (t80) REVERT: I 582 PHE cc_start: 0.5146 (m-80) cc_final: 0.4731 (m-80) REVERT: I 673 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: I 711 ASP cc_start: 0.9120 (m-30) cc_final: 0.8623 (p0) REVERT: I 770 GLU cc_start: 0.6391 (mt-10) cc_final: 0.6149 (tt0) REVERT: J 71 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8024 (tm-30) outliers start: 53 outliers final: 26 residues processed: 259 average time/residue: 0.2561 time to fit residues: 103.9107 Evaluate side-chains 228 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 673 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 101 optimal weight: 0.0050 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 50.0000 chunk 131 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 581 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN ** I 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 448 ASN ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17260 Z= 0.346 Angle : 0.711 10.835 23423 Z= 0.362 Chirality : 0.045 0.510 2688 Planarity : 0.005 0.092 3011 Dihedral : 5.804 55.539 2338 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.06 % Favored : 89.80 % Rotamer: Outliers : 3.88 % Allowed : 21.14 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % 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: -2.96 (0.17), residues: 2167 helix: -0.88 (0.17), residues: 870 sheet: -1.82 (0.26), residues: 352 loop : -3.08 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 610 HIS 0.016 0.001 HIS A 581 PHE 0.018 0.002 PHE H 238 TYR 0.022 0.002 TYR H 304 ARG 0.004 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 197 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.7107 (mmm-85) REVERT: A 581 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.6865 (p-80) REVERT: A 584 MET cc_start: 0.8274 (ppp) cc_final: 0.7411 (ppp) REVERT: D 173 MET cc_start: 0.8945 (mmm) cc_final: 0.8608 (mmm) REVERT: D 260 ARG cc_start: 0.8800 (mtt180) cc_final: 0.8545 (mtt-85) REVERT: D 337 MET cc_start: 0.8940 (tpp) cc_final: 0.8062 (tpp) REVERT: D 339 GLU cc_start: 0.8658 (mp0) cc_final: 0.8171 (mp0) REVERT: D 361 TYR cc_start: 0.8276 (t80) cc_final: 0.8076 (t80) REVERT: H 43 LEU cc_start: 0.9640 (tp) cc_final: 0.9406 (tt) REVERT: H 186 PHE cc_start: 0.8680 (t80) cc_final: 0.8125 (t80) REVERT: H 190 PHE cc_start: 0.9227 (m-80) cc_final: 0.8666 (m-80) REVERT: H 225 TYR cc_start: 0.8668 (m-10) cc_final: 0.8356 (m-10) REVERT: H 230 MET cc_start: 0.7066 (mtp) cc_final: 0.6834 (ttm) REVERT: H 295 MET cc_start: 0.8773 (mpp) cc_final: 0.8095 (mpp) REVERT: H 298 MET cc_start: 0.8587 (tmm) cc_final: 0.8247 (tmm) REVERT: H 377 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8513 (mm) REVERT: H 412 LEU cc_start: 0.9337 (mm) cc_final: 0.8832 (mm) REVERT: H 480 LYS cc_start: 0.9227 (mttt) cc_final: 0.8793 (mmmm) REVERT: H 482 GLU cc_start: 0.8408 (tt0) cc_final: 0.8097 (tt0) REVERT: I 239 LEU cc_start: 0.8692 (tp) cc_final: 0.8385 (mt) REVERT: I 284 ASP cc_start: 0.8467 (p0) cc_final: 0.8219 (p0) REVERT: I 311 MET cc_start: 0.8638 (mmm) cc_final: 0.8423 (mmt) REVERT: I 477 MET cc_start: 0.4160 (mmt) cc_final: 0.2590 (mmt) REVERT: I 535 CYS cc_start: 0.6892 (t) cc_final: 0.6462 (t) REVERT: I 580 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7864 (t80) REVERT: I 582 PHE cc_start: 0.4790 (m-80) cc_final: 0.4510 (m-80) REVERT: I 651 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6523 (p-80) REVERT: I 673 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: I 711 ASP cc_start: 0.9102 (m-30) cc_final: 0.8578 (p0) REVERT: I 770 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6119 (tt0) outliers start: 69 outliers final: 45 residues processed: 246 average time/residue: 0.2595 time to fit residues: 100.3365 Evaluate side-chains 237 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 187 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 651 HIS Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 154 optimal weight: 0.0040 chunk 85 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 ASN ** I 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 524 GLN I 569 GLN ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17260 Z= 0.232 Angle : 0.655 11.529 23423 Z= 0.329 Chirality : 0.043 0.267 2688 Planarity : 0.005 0.088 3011 Dihedral : 5.558 54.734 2338 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.68 % Favored : 91.23 % Rotamer: Outliers : 3.65 % Allowed : 22.93 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % 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: -2.63 (0.17), residues: 2167 helix: -0.54 (0.17), residues: 872 sheet: -1.64 (0.26), residues: 347 loop : -2.97 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 768 HIS 0.009 0.001 HIS A 581 PHE 0.018 0.001 PHE H 238 TYR 0.018 0.001 TYR H 304 ARG 0.003 0.000 ARG I 669 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 201 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TRP cc_start: 0.7471 (t-100) cc_final: 0.7220 (t-100) REVERT: A 581 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7166 (p90) REVERT: A 584 MET cc_start: 0.8259 (ppp) cc_final: 0.7374 (ppp) REVERT: D 173 MET cc_start: 0.8969 (mmm) cc_final: 0.8638 (mmm) REVERT: D 203 GLU cc_start: 0.8255 (mp0) cc_final: 0.7956 (mp0) REVERT: D 260 ARG cc_start: 0.8790 (mtt180) cc_final: 0.8544 (mtt-85) REVERT: D 337 MET cc_start: 0.8884 (tpp) cc_final: 0.7970 (tpp) REVERT: D 339 GLU cc_start: 0.8659 (mp0) cc_final: 0.8220 (mp0) REVERT: D 361 TYR cc_start: 0.8379 (t80) cc_final: 0.8173 (t80) REVERT: H 43 LEU cc_start: 0.9637 (tp) cc_final: 0.9397 (tt) REVERT: H 186 PHE cc_start: 0.8617 (t80) cc_final: 0.8023 (t80) REVERT: H 190 PHE cc_start: 0.9158 (m-80) cc_final: 0.8554 (m-80) REVERT: H 295 MET cc_start: 0.8758 (mpp) cc_final: 0.8118 (mpp) REVERT: H 377 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8497 (mm) REVERT: H 412 LEU cc_start: 0.9311 (mm) cc_final: 0.9036 (mm) REVERT: H 480 LYS cc_start: 0.9193 (mttt) cc_final: 0.8717 (mmmm) REVERT: I 239 LEU cc_start: 0.8682 (tp) cc_final: 0.8399 (mt) REVERT: I 284 ASP cc_start: 0.8433 (p0) cc_final: 0.8219 (p0) REVERT: I 477 MET cc_start: 0.4227 (mmt) cc_final: 0.2649 (mmt) REVERT: I 481 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.4962 (pt) REVERT: I 501 GLU cc_start: 0.8602 (pp20) cc_final: 0.8036 (pp20) REVERT: I 535 CYS cc_start: 0.6837 (t) cc_final: 0.6442 (t) REVERT: I 580 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7795 (t80) REVERT: I 582 PHE cc_start: 0.5128 (m-80) cc_final: 0.4840 (m-80) REVERT: I 622 GLU cc_start: 0.8574 (pt0) cc_final: 0.8041 (tp30) REVERT: I 673 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: I 711 ASP cc_start: 0.9091 (m-30) cc_final: 0.8564 (p0) REVERT: I 770 GLU cc_start: 0.6324 (mt-10) cc_final: 0.6084 (tt0) outliers start: 65 outliers final: 44 residues processed: 248 average time/residue: 0.2541 time to fit residues: 99.7603 Evaluate side-chains 244 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 195 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 640 ILE Chi-restraints excluded: chain I residue 673 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 0.0170 chunk 68 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17260 Z= 0.293 Angle : 0.682 10.904 23423 Z= 0.344 Chirality : 0.044 0.292 2688 Planarity : 0.005 0.086 3011 Dihedral : 5.574 53.539 2338 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.92 % Favored : 89.94 % Rotamer: Outliers : 4.22 % Allowed : 23.22 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % 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: -2.55 (0.18), residues: 2167 helix: -0.36 (0.18), residues: 870 sheet: -1.73 (0.26), residues: 366 loop : -3.01 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 322 HIS 0.005 0.001 HIS H 192 PHE 0.025 0.002 PHE H 238 TYR 0.024 0.002 TYR H 304 ARG 0.004 0.000 ARG I 669 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 198 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6241 (mmm) cc_final: 0.5857 (mmm) REVERT: A 570 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.7124 (mmm-85) REVERT: A 584 MET cc_start: 0.8269 (ppp) cc_final: 0.7436 (ppp) REVERT: D 173 MET cc_start: 0.9120 (mmm) cc_final: 0.8730 (mmm) REVERT: D 203 GLU cc_start: 0.8306 (mp0) cc_final: 0.7916 (mp0) REVERT: D 260 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8592 (mtt-85) REVERT: D 337 MET cc_start: 0.8918 (tpp) cc_final: 0.8094 (tpp) REVERT: D 339 GLU cc_start: 0.8657 (mp0) cc_final: 0.8223 (mp0) REVERT: D 361 TYR cc_start: 0.8469 (t80) cc_final: 0.8171 (t80) REVERT: H 43 LEU cc_start: 0.9649 (tp) cc_final: 0.9417 (tt) REVERT: H 190 PHE cc_start: 0.9225 (m-80) cc_final: 0.8900 (m-80) REVERT: H 230 MET cc_start: 0.7584 (ttm) cc_final: 0.7350 (ttm) REVERT: H 295 MET cc_start: 0.8775 (mpp) cc_final: 0.8138 (mpp) REVERT: H 377 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8495 (mm) REVERT: H 412 LEU cc_start: 0.9389 (mm) cc_final: 0.8769 (mm) REVERT: H 480 LYS cc_start: 0.9194 (mttt) cc_final: 0.8718 (mmmm) REVERT: I 157 MET cc_start: 0.8589 (mmm) cc_final: 0.8270 (mmm) REVERT: I 239 LEU cc_start: 0.8706 (tp) cc_final: 0.8428 (mt) REVERT: I 284 ASP cc_start: 0.8491 (p0) cc_final: 0.8261 (p0) REVERT: I 460 TYR cc_start: 0.8767 (m-80) cc_final: 0.8542 (m-80) REVERT: I 477 MET cc_start: 0.3957 (mmt) cc_final: 0.2375 (mmt) REVERT: I 481 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.4911 (pt) REVERT: I 535 CYS cc_start: 0.6955 (t) cc_final: 0.6505 (t) REVERT: I 580 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7761 (t80) REVERT: I 582 PHE cc_start: 0.5169 (m-80) cc_final: 0.4928 (m-80) REVERT: I 622 GLU cc_start: 0.8596 (pt0) cc_final: 0.8122 (tp30) REVERT: I 673 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8449 (m-80) REVERT: I 770 GLU cc_start: 0.6332 (mt-10) cc_final: 0.6094 (tt0) outliers start: 75 outliers final: 59 residues processed: 252 average time/residue: 0.2644 time to fit residues: 104.8308 Evaluate side-chains 250 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 187 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 640 ILE Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN H 61 GLN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 ASN I 22 GLN ** I 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17260 Z= 0.183 Angle : 0.636 11.598 23423 Z= 0.315 Chirality : 0.043 0.269 2688 Planarity : 0.004 0.081 3011 Dihedral : 5.289 52.473 2338 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.21 % Favored : 91.69 % Rotamer: Outliers : 3.99 % Allowed : 24.51 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % 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: -2.20 (0.18), residues: 2167 helix: -0.04 (0.18), residues: 876 sheet: -1.55 (0.27), residues: 362 loop : -2.87 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 768 HIS 0.005 0.001 HIS D 178 PHE 0.020 0.001 PHE H 238 TYR 0.015 0.001 TYR H 304 ARG 0.003 0.000 ARG I 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 213 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6055 (mmm) cc_final: 0.5726 (mmm) REVERT: A 584 MET cc_start: 0.8277 (ppp) cc_final: 0.7496 (ppp) REVERT: D 173 MET cc_start: 0.9104 (mmm) cc_final: 0.8673 (mmm) REVERT: D 203 GLU cc_start: 0.8364 (mp0) cc_final: 0.7987 (mp0) REVERT: D 260 ARG cc_start: 0.8823 (mtt180) cc_final: 0.8578 (mtt-85) REVERT: D 339 GLU cc_start: 0.8639 (mp0) cc_final: 0.8203 (mp0) REVERT: H 5 MET cc_start: 0.8088 (pmm) cc_final: 0.7768 (ppp) REVERT: H 43 LEU cc_start: 0.9626 (tp) cc_final: 0.9375 (tt) REVERT: H 190 PHE cc_start: 0.9075 (m-80) cc_final: 0.8812 (m-80) REVERT: H 295 MET cc_start: 0.8745 (mpp) cc_final: 0.8121 (mpp) REVERT: H 377 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8427 (mm) REVERT: H 388 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: H 412 LEU cc_start: 0.9319 (mm) cc_final: 0.8688 (mm) REVERT: H 479 GLN cc_start: 0.8726 (tp40) cc_final: 0.8267 (tt0) REVERT: H 480 LYS cc_start: 0.9196 (mttt) cc_final: 0.8708 (mmmm) REVERT: I 239 LEU cc_start: 0.8718 (tp) cc_final: 0.8469 (mt) REVERT: I 477 MET cc_start: 0.3962 (mmt) cc_final: 0.2339 (mmt) REVERT: I 481 LEU cc_start: 0.5582 (OUTLIER) cc_final: 0.4862 (pt) REVERT: I 501 GLU cc_start: 0.8695 (pp20) cc_final: 0.8020 (pp20) REVERT: I 580 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7638 (t80) REVERT: I 622 GLU cc_start: 0.8517 (pt0) cc_final: 0.8140 (tp30) REVERT: I 673 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: I 770 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5737 (tt0) outliers start: 71 outliers final: 51 residues processed: 266 average time/residue: 0.2522 time to fit residues: 105.1472 Evaluate side-chains 250 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 194 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 388 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 673 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 19 optimal weight: 0.2980 chunk 162 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 ASN I 22 GLN ** I 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17260 Z= 0.169 Angle : 0.658 11.823 23423 Z= 0.321 Chirality : 0.043 0.260 2688 Planarity : 0.004 0.080 3011 Dihedral : 5.147 51.164 2338 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.32 % Rotamer: Outliers : 3.65 % Allowed : 25.80 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % 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: -2.03 (0.18), residues: 2167 helix: 0.10 (0.18), residues: 876 sheet: -1.40 (0.28), residues: 346 loop : -2.78 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 768 HIS 0.008 0.001 HIS H 209 PHE 0.026 0.001 PHE H 271 TYR 0.026 0.001 TYR D 361 ARG 0.004 0.000 ARG I 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 208 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6076 (mmm) cc_final: 0.5803 (mmm) REVERT: A 584 MET cc_start: 0.8242 (ppp) cc_final: 0.7092 (ppp) REVERT: D 173 MET cc_start: 0.9179 (mmm) cc_final: 0.8749 (mmm) REVERT: D 203 GLU cc_start: 0.8350 (mp0) cc_final: 0.7986 (mp0) REVERT: D 260 ARG cc_start: 0.8819 (mtt180) cc_final: 0.8568 (mtt-85) REVERT: D 339 GLU cc_start: 0.8631 (mp0) cc_final: 0.8267 (mp0) REVERT: D 361 TYR cc_start: 0.6442 (t80) cc_final: 0.6190 (t80) REVERT: H 43 LEU cc_start: 0.9587 (tp) cc_final: 0.9320 (tt) REVERT: H 190 PHE cc_start: 0.9066 (m-80) cc_final: 0.8805 (m-80) REVERT: H 295 MET cc_start: 0.8715 (mpp) cc_final: 0.8086 (mpp) REVERT: H 377 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8437 (mm) REVERT: H 383 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7357 (tp30) REVERT: H 388 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8520 (m-30) REVERT: H 412 LEU cc_start: 0.9319 (mm) cc_final: 0.8762 (mm) REVERT: H 416 ASN cc_start: 0.9047 (t0) cc_final: 0.8349 (t0) REVERT: H 479 GLN cc_start: 0.8669 (tp40) cc_final: 0.8218 (tt0) REVERT: H 480 LYS cc_start: 0.9176 (mttt) cc_final: 0.8721 (mmmm) REVERT: H 482 GLU cc_start: 0.8335 (tt0) cc_final: 0.8108 (tt0) REVERT: I 239 LEU cc_start: 0.8730 (tp) cc_final: 0.8512 (mt) REVERT: I 477 MET cc_start: 0.4058 (mmt) cc_final: 0.2474 (mmt) REVERT: I 481 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.4883 (pt) REVERT: I 501 GLU cc_start: 0.8614 (pp20) cc_final: 0.7999 (pp20) REVERT: I 535 CYS cc_start: 0.6895 (t) cc_final: 0.6620 (t) REVERT: I 580 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7643 (t80) REVERT: I 622 GLU cc_start: 0.8505 (pt0) cc_final: 0.8138 (tp30) REVERT: I 635 SER cc_start: 0.7433 (OUTLIER) cc_final: 0.7046 (p) REVERT: I 673 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8405 (m-80) REVERT: I 770 GLU cc_start: 0.6118 (mt-10) cc_final: 0.5674 (tt0) outliers start: 65 outliers final: 48 residues processed: 257 average time/residue: 0.2519 time to fit residues: 102.9909 Evaluate side-chains 250 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 388 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 20.0000 chunk 181 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17260 Z= 0.172 Angle : 0.664 11.556 23423 Z= 0.324 Chirality : 0.043 0.240 2688 Planarity : 0.004 0.078 3011 Dihedral : 5.108 50.555 2338 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.08 % Favored : 91.83 % Rotamer: Outliers : 3.09 % Allowed : 26.03 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % 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: -1.84 (0.18), residues: 2167 helix: 0.24 (0.18), residues: 871 sheet: -1.20 (0.28), residues: 351 loop : -2.70 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 139 HIS 0.006 0.001 HIS H 209 PHE 0.019 0.001 PHE H 271 TYR 0.031 0.001 TYR I 703 ARG 0.004 0.000 ARG I 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 208 time to evaluate : 2.156 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 94 MET cc_start: 0.6111 (mmm) cc_final: 0.5845 (mmm) REVERT: A 584 MET cc_start: 0.8223 (ppp) cc_final: 0.7033 (ppp) REVERT: D 173 MET cc_start: 0.9141 (mmm) cc_final: 0.8676 (mmm) REVERT: D 203 GLU cc_start: 0.8330 (mp0) cc_final: 0.7977 (mp0) REVERT: D 246 MET cc_start: 0.8193 (mmt) cc_final: 0.7839 (mmm) REVERT: D 260 ARG cc_start: 0.8799 (mtt180) cc_final: 0.8556 (mtt-85) REVERT: D 339 GLU cc_start: 0.8641 (mp0) cc_final: 0.8251 (mp0) REVERT: H 43 LEU cc_start: 0.9575 (tp) cc_final: 0.9307 (tt) REVERT: H 190 PHE cc_start: 0.9037 (m-80) cc_final: 0.8786 (m-80) REVERT: H 295 MET cc_start: 0.8737 (mpp) cc_final: 0.8065 (mpp) REVERT: H 377 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8447 (mm) REVERT: H 388 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8536 (m-30) REVERT: H 412 LEU cc_start: 0.9282 (mm) cc_final: 0.8852 (mm) REVERT: H 479 GLN cc_start: 0.8688 (tp40) cc_final: 0.8236 (tt0) REVERT: H 480 LYS cc_start: 0.9186 (mttt) cc_final: 0.8767 (mmmm) REVERT: H 482 GLU cc_start: 0.8333 (tt0) cc_final: 0.8095 (tt0) REVERT: I 477 MET cc_start: 0.4064 (mmt) cc_final: 0.2517 (mmt) REVERT: I 481 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.4843 (pt) REVERT: I 501 GLU cc_start: 0.8597 (pp20) cc_final: 0.7979 (pp20) REVERT: I 535 CYS cc_start: 0.6938 (t) cc_final: 0.6706 (t) REVERT: I 635 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.7024 (p) REVERT: I 673 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: I 770 GLU cc_start: 0.6095 (mt-10) cc_final: 0.5648 (tt0) outliers start: 55 outliers final: 45 residues processed: 251 average time/residue: 0.2501 time to fit residues: 99.6655 Evaluate side-chains 250 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 200 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 388 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 640 ILE Chi-restraints excluded: chain I residue 673 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 HIS ** H 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17260 Z= 0.208 Angle : 0.681 11.251 23423 Z= 0.332 Chirality : 0.045 0.594 2688 Planarity : 0.004 0.085 3011 Dihedral : 5.173 56.499 2338 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.72 % Favored : 91.23 % Rotamer: Outliers : 3.20 % Allowed : 26.31 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % 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: -1.78 (0.18), residues: 2167 helix: 0.34 (0.18), residues: 868 sheet: -1.25 (0.27), residues: 354 loop : -2.67 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 139 HIS 0.005 0.001 HIS H 209 PHE 0.025 0.001 PHE H 271 TYR 0.019 0.001 TYR D 361 ARG 0.003 0.000 ARG I 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 199 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6080 (mmm) cc_final: 0.5823 (mmm) REVERT: A 584 MET cc_start: 0.8238 (ppp) cc_final: 0.7025 (ppp) REVERT: D 173 MET cc_start: 0.9182 (mmm) cc_final: 0.8677 (mmm) REVERT: D 203 GLU cc_start: 0.8350 (mp0) cc_final: 0.7980 (mp0) REVERT: D 246 MET cc_start: 0.8179 (mmt) cc_final: 0.7853 (mmm) REVERT: D 260 ARG cc_start: 0.8807 (mtt180) cc_final: 0.8558 (mtt-85) REVERT: D 339 GLU cc_start: 0.8619 (mp0) cc_final: 0.8291 (mp0) REVERT: H 43 LEU cc_start: 0.9580 (tp) cc_final: 0.9318 (tt) REVERT: H 190 PHE cc_start: 0.9069 (m-80) cc_final: 0.8782 (m-80) REVERT: H 295 MET cc_start: 0.8768 (mpp) cc_final: 0.8074 (mpp) REVERT: H 377 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8434 (mm) REVERT: H 383 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7506 (tp30) REVERT: H 388 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8553 (m-30) REVERT: H 412 LEU cc_start: 0.9334 (mm) cc_final: 0.8774 (mm) REVERT: H 432 MET cc_start: 0.7971 (tpt) cc_final: 0.7718 (tpp) REVERT: H 479 GLN cc_start: 0.8720 (tp40) cc_final: 0.8254 (tt0) REVERT: H 480 LYS cc_start: 0.9191 (mttt) cc_final: 0.8774 (mmmm) REVERT: I 477 MET cc_start: 0.4146 (mmt) cc_final: 0.2592 (mmt) REVERT: I 481 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5014 (pt) REVERT: I 535 CYS cc_start: 0.7025 (t) cc_final: 0.6723 (t) REVERT: I 622 GLU cc_start: 0.8502 (pt0) cc_final: 0.8184 (tp30) REVERT: I 635 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.6999 (p) REVERT: I 673 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: I 770 GLU cc_start: 0.6161 (mt-10) cc_final: 0.5698 (tt0) outliers start: 57 outliers final: 48 residues processed: 242 average time/residue: 0.2456 time to fit residues: 93.9844 Evaluate side-chains 246 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 193 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 388 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 640 ILE Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 0.0270 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.103071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073056 restraints weight = 56313.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075408 restraints weight = 31058.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.076855 restraints weight = 21829.755| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 17260 Z= 0.389 Angle : 0.784 10.799 23423 Z= 0.392 Chirality : 0.048 0.612 2688 Planarity : 0.005 0.093 3011 Dihedral : 5.720 56.896 2338 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.57 % Favored : 89.34 % Rotamer: Outliers : 3.20 % Allowed : 26.48 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % 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: -2.18 (0.18), residues: 2167 helix: -0.06 (0.18), residues: 876 sheet: -1.58 (0.26), residues: 368 loop : -2.78 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 139 HIS 0.007 0.001 HIS H 192 PHE 0.019 0.002 PHE H 238 TYR 0.020 0.002 TYR I 703 ARG 0.005 0.000 ARG I 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.24 seconds wall clock time: 60 minutes 19.50 seconds (3619.50 seconds total)