Starting phenix.real_space_refine on Sat Mar 16 13:21:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yup_10933/03_2024/6yup_10933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yup_10933/03_2024/6yup_10933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yup_10933/03_2024/6yup_10933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yup_10933/03_2024/6yup_10933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yup_10933/03_2024/6yup_10933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yup_10933/03_2024/6yup_10933.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 76 5.16 5 C 9620 2.51 5 N 2366 2.21 5 O 2710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ASP 391": "OD1" <-> "OD2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 532": "OD1" <-> "OD2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 641": "OD1" <-> "OD2" Residue "A ARG 665": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C ASP 338": "OD1" <-> "OD2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C ASP 391": "OD1" <-> "OD2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 437": "OE1" <-> "OE2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C ASP 499": "OD1" <-> "OD2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 532": "OD1" <-> "OD2" Residue "C TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 539": "OD1" <-> "OD2" Residue "C ARG 546": "NH1" <-> "NH2" Residue "C TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C GLU 585": "OE1" <-> "OE2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 641": "OD1" <-> "OD2" Residue "C ARG 665": "NH1" <-> "NH2" Residue "C ARG 671": "NH1" <-> "NH2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E GLU 282": "OE1" <-> "OE2" Residue "E ASP 295": "OD1" <-> "OD2" Residue "E TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14774 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4834 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain: "C" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4834 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain: "D" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2496 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 7 Chain: "E" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2496 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 7 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.99, per 1000 atoms: 0.54 Number of scatterers: 14774 At special positions: 0 Unit cell: (133.92, 92.907, 127.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 76 16.00 O 2710 8.00 N 2366 7.00 C 9620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.16 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.04 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " distance=2.10 Simple disulfide: pdb=" SG CYS C 673 " - pdb=" SG CYS C 685 " distance=2.04 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 Atom "HETATM14700 O5 NAG A 703 .*. O " rejected from bonding due to valence issues. Atom "HETATM14771 O5 NAG C 704 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 332 " " NAG A 702 " - " ASN A 513 " " NAG A 703 " - " ASN A 575 " " NAG A 704 " - " ASN A 261 " " NAG C 701 " - " ASN C 332 " " NAG C 702 " - " ASN C 513 " " NAG C 703 " - " ASN C 575 " " NAG C 704 " - " ASN C 261 " Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 2.2 seconds 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 18 sheets defined 47.2% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 92 through 111 removed outlier: 4.259A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.649A pdb=" N ILE A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.578A pdb=" N ILE A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.567A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.597A pdb=" N TYR A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.762A pdb=" N LYS A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.672A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.982A pdb=" N SER A 507 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.775A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'C' and resid 93 through 111 removed outlier: 4.258A pdb=" N LEU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.648A pdb=" N ILE C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.578A pdb=" N ILE C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.566A pdb=" N LYS C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.596A pdb=" N TYR C 233 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 307 removed outlier: 3.759A pdb=" N LYS C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 420 through 435 removed outlier: 3.671A pdb=" N ASN C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 503 through 507 removed outlier: 3.980A pdb=" N SER C 507 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.774A pdb=" N ASN C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 659 Processing helix chain 'D' and resid 32 through 42 Processing helix chain 'D' and resid 50 through 60 removed outlier: 4.267A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 87 removed outlier: 3.567A pdb=" N GLU D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 116 Processing helix chain 'D' and resid 120 through 137 removed outlier: 3.564A pdb=" N CYS D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 167 Processing helix chain 'D' and resid 179 through 197 removed outlier: 3.716A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.916A pdb=" N ALA D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 242 removed outlier: 3.804A pdb=" N THR D 242 " --> pdb=" O ASN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.637A pdb=" N ILE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 276 removed outlier: 3.727A pdb=" N SER D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR D 274 " --> pdb=" O MET D 270 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 285 removed outlier: 3.711A pdb=" N LEU D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 279 through 285' Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.735A pdb=" N THR D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 297 " --> pdb=" O PHE D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 removed outlier: 3.694A pdb=" N ALA D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY D 315 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 361 removed outlier: 3.645A pdb=" N ILE D 361 " --> pdb=" O PHE D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.518A pdb=" N ILE D 366 " --> pdb=" O THR D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 395 removed outlier: 3.962A pdb=" N VAL D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN D 376 " --> pdb=" O ASN D 372 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 380 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 427 removed outlier: 3.678A pdb=" N LEU D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 50 through 60 removed outlier: 4.265A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 87 removed outlier: 3.566A pdb=" N GLU E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 116 Processing helix chain 'E' and resid 120 through 137 removed outlier: 3.563A pdb=" N CYS E 129 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 167 Processing helix chain 'E' and resid 179 through 197 removed outlier: 3.716A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 230 removed outlier: 3.917A pdb=" N ALA E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.806A pdb=" N THR E 242 " --> pdb=" O ASN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.637A pdb=" N ILE E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 276 removed outlier: 3.725A pdb=" N SER E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR E 274 " --> pdb=" O MET E 270 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE E 275 " --> pdb=" O ASN E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 285 removed outlier: 3.711A pdb=" N LEU E 283 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 279 through 285' Processing helix chain 'E' and resid 288 through 297 removed outlier: 3.735A pdb=" N THR E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 297 " --> pdb=" O PHE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.694A pdb=" N ALA E 310 " --> pdb=" O PRO E 306 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY E 315 " --> pdb=" O PHE E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 361 removed outlier: 3.645A pdb=" N ILE E 361 " --> pdb=" O PHE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 removed outlier: 3.520A pdb=" N ILE E 366 " --> pdb=" O THR E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 395 removed outlier: 3.962A pdb=" N VAL E 375 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN E 376 " --> pdb=" O ASN E 372 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE E 380 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 427 removed outlier: 3.678A pdb=" N LEU E 419 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 423 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 445 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.295A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 removed outlier: 7.285A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 169 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLY A 176 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.588A pdb=" N GLY A 382 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 645 through 650 Processing sheet with id=AA7, first strand: chain 'A' and resid 604 through 606 removed outlier: 3.564A pdb=" N LEU A 605 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 619 Processing sheet with id=AA9, first strand: chain 'A' and resid 673 through 674 Processing sheet with id=AB1, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.296A pdb=" N MET C 123 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP C 443 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR C 479 " --> pdb=" O TRP C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 167 through 170 removed outlier: 7.284A pdb=" N LYS C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 169 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLY C 176 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 211 removed outlier: 3.588A pdb=" N GLY C 382 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB6, first strand: chain 'C' and resid 645 through 650 Processing sheet with id=AB7, first strand: chain 'C' and resid 604 through 606 Processing sheet with id=AB8, first strand: chain 'C' and resid 617 through 618 Processing sheet with id=AB9, first strand: chain 'C' and resid 673 through 674 549 hydrogen bonds defined for protein. 1554 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: 4.44 Time building geometry restraints manager: 6.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2330 1.31 - 1.44: 4277 1.44 - 1.56: 8413 1.56 - 1.69: 4 1.69 - 1.82: 120 Bond restraints: 15144 Sorted by residual: bond pdb=" C THR C 624 " pdb=" N ASN C 625 " ideal model delta sigma weight residual 1.333 1.507 -0.174 1.41e-02 5.03e+03 1.52e+02 bond pdb=" C THR A 624 " pdb=" N ASN A 625 " ideal model delta sigma weight residual 1.332 1.417 -0.084 1.40e-02 5.10e+03 3.62e+01 bond pdb=" C7 NAG A 702 " pdb=" N2 NAG A 702 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C7 NAG C 702 " pdb=" N2 NAG C 702 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C7 NAG A 701 " pdb=" N2 NAG A 701 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 15139 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.27: 497 107.27 - 113.99: 8656 113.99 - 120.71: 6288 120.71 - 127.43: 5003 127.43 - 134.15: 176 Bond angle restraints: 20620 Sorted by residual: angle pdb=" O THR A 624 " pdb=" C THR A 624 " pdb=" N ASN A 625 " ideal model delta sigma weight residual 122.59 132.25 -9.66 1.33e+00 5.65e-01 5.27e+01 angle pdb=" CA THR A 624 " pdb=" C THR A 624 " pdb=" N ASN A 625 " ideal model delta sigma weight residual 116.84 104.64 12.20 1.71e+00 3.42e-01 5.09e+01 angle pdb=" C ILE E 107 " pdb=" CA ILE E 107 " pdb=" CB ILE E 107 " ideal model delta sigma weight residual 114.35 108.30 6.05 1.06e+00 8.90e-01 3.26e+01 angle pdb=" C ILE D 107 " pdb=" CA ILE D 107 " pdb=" CB ILE D 107 " ideal model delta sigma weight residual 114.35 108.37 5.98 1.06e+00 8.90e-01 3.18e+01 angle pdb=" N VAL E 50 " pdb=" CA VAL E 50 " pdb=" C VAL E 50 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 ... (remaining 20615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 8418 22.41 - 44.83: 443 44.83 - 67.24: 59 67.24 - 89.65: 20 89.65 - 112.06: 16 Dihedral angle restraints: 8956 sinusoidal: 3572 harmonic: 5384 Sorted by residual: dihedral pdb=" CB CYS C 673 " pdb=" SG CYS C 673 " pdb=" SG CYS C 685 " pdb=" CB CYS C 685 " ideal model delta sinusoidal sigma weight residual -86.00 -26.44 -59.56 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS A 673 " pdb=" SG CYS A 673 " pdb=" SG CYS A 685 " pdb=" CB CYS A 685 " ideal model delta sinusoidal sigma weight residual -86.00 -26.57 -59.43 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CA ASN C 261 " pdb=" C ASN C 261 " pdb=" N SER C 262 " pdb=" CA SER C 262 " ideal model delta harmonic sigma weight residual 180.00 152.14 27.86 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 8953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 2371 0.270 - 0.540: 6 0.540 - 0.809: 1 0.809 - 1.079: 0 1.079 - 1.349: 2 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 575 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" C1 NAG C 704 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG C 704 " pdb=" O5 NAG C 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.41e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -3.05 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2377 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 513 " 0.247 2.00e-02 2.50e+03 2.21e-01 6.12e+02 pdb=" CG ASN C 513 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C 513 " -0.112 2.00e-02 2.50e+03 pdb=" ND2 ASN C 513 " -0.314 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 261 " 0.091 2.00e-02 2.50e+03 1.09e-01 1.48e+02 pdb=" CG ASN C 261 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 261 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN C 261 " -0.165 2.00e-02 2.50e+03 pdb=" C1 NAG C 704 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 332 " 0.088 2.00e-02 2.50e+03 1.05e-01 1.39e+02 pdb=" CG ASN C 332 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 332 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 332 " -0.166 2.00e-02 2.50e+03 pdb=" C1 NAG C 701 " 0.135 2.00e-02 2.50e+03 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 32 2.39 - 3.01: 7786 3.01 - 3.64: 22088 3.64 - 4.27: 34152 4.27 - 4.90: 56143 Nonbonded interactions: 120201 Sorted by model distance: nonbonded pdb=" NZ LYS D 152 " pdb=" O ILE D 366 " model vdw 1.758 2.520 nonbonded pdb=" OD1 ASP A 150 " pdb=" NZ LYS A 203 " model vdw 1.762 2.520 nonbonded pdb=" CB PRO C 375 " pdb=" CG2 VAL D 142 " model vdw 1.790 3.860 nonbonded pdb=" NH2 ARG C 574 " pdb=" OH TYR C 579 " model vdw 1.869 2.520 nonbonded pdb=" NH2 ARG A 574 " pdb=" OH TYR A 579 " model vdw 1.957 2.520 ... (remaining 120196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.550 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 39.460 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 0.174 15144 Z= 0.342 Angle : 0.597 12.197 20620 Z= 0.351 Chirality : 0.060 1.349 2380 Planarity : 0.004 0.058 2558 Dihedral : 14.627 112.063 5474 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.04 % Favored : 96.57 % Rotamer: Outliers : 1.98 % Allowed : 12.52 % Favored : 85.50 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.16), residues: 1808 helix: -3.06 (0.12), residues: 748 sheet: -1.94 (0.40), residues: 152 loop : -2.27 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 383 HIS 0.002 0.001 HIS A 215 PHE 0.009 0.001 PHE A 407 TYR 0.006 0.001 TYR D 110 ARG 0.002 0.000 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 221 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 ASP cc_start: 0.6991 (p0) cc_final: 0.6779 (p0) REVERT: C 368 MET cc_start: 0.8770 (mtp) cc_final: 0.8502 (mtp) REVERT: C 664 ASP cc_start: 0.7287 (p0) cc_final: 0.6980 (p0) REVERT: C 680 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7207 (pp) REVERT: E 303 TRP cc_start: 0.7254 (p-90) cc_final: 0.7019 (p-90) outliers start: 32 outliers final: 15 residues processed: 249 average time/residue: 1.1553 time to fit residues: 318.0857 Evaluate side-chains 146 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 244 HIS A 272 GLN A 366 GLN A 488 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN A 544 GLN A 572 HIS A 659 GLN C 220 HIS C 244 HIS C 272 GLN C 366 GLN C 488 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN C 530 ASN C 544 GLN ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN C 659 GLN E 148 GLN E 227 ASN E 237 GLN E 287 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15144 Z= 0.181 Angle : 0.563 9.766 20620 Z= 0.281 Chirality : 0.043 0.454 2380 Planarity : 0.004 0.049 2558 Dihedral : 8.165 87.455 2174 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.82 % Favored : 95.96 % Rotamer: Outliers : 4.09 % Allowed : 15.92 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.34 (0.18), residues: 1808 helix: -1.00 (0.17), residues: 780 sheet: -1.35 (0.43), residues: 134 loop : -2.08 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 230 HIS 0.005 0.001 HIS A 276 PHE 0.018 0.001 PHE A 407 TYR 0.013 0.001 TYR D 451 ARG 0.007 0.001 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 147 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 610 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7458 (mtm) REVERT: A 664 ASP cc_start: 0.7231 (p0) cc_final: 0.6937 (p0) REVERT: C 664 ASP cc_start: 0.7354 (p0) cc_final: 0.7006 (p0) REVERT: D 49 PHE cc_start: 0.5879 (OUTLIER) cc_final: 0.5477 (p90) REVERT: E 303 TRP cc_start: 0.7506 (p-90) cc_final: 0.6913 (p-90) outliers start: 66 outliers final: 24 residues processed: 191 average time/residue: 1.0072 time to fit residues: 217.8890 Evaluate side-chains 147 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 0.0570 chunk 178 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 277 GLN A 358 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN C 358 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN E 227 ASN E 236 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15144 Z= 0.278 Angle : 0.599 11.164 20620 Z= 0.304 Chirality : 0.045 0.395 2380 Planarity : 0.004 0.048 2558 Dihedral : 6.307 57.891 2160 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Rotamer: Outliers : 3.66 % Allowed : 17.72 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1808 helix: -0.05 (0.19), residues: 794 sheet: -1.40 (0.45), residues: 126 loop : -1.74 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 69 HIS 0.007 0.001 HIS A 276 PHE 0.028 0.002 PHE E 161 TYR 0.016 0.001 TYR C 166 ARG 0.010 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 131 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: A 610 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7585 (mtm) REVERT: A 664 ASP cc_start: 0.7421 (p0) cc_final: 0.7128 (p0) REVERT: A 684 SER cc_start: 0.7924 (m) cc_final: 0.7716 (m) REVERT: C 658 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7686 (mtt-85) REVERT: C 664 ASP cc_start: 0.7428 (p0) cc_final: 0.7123 (p0) REVERT: C 684 SER cc_start: 0.7846 (m) cc_final: 0.7537 (m) REVERT: D 49 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6275 (p90) REVERT: E 303 TRP cc_start: 0.7752 (p-90) cc_final: 0.7131 (p-90) outliers start: 59 outliers final: 27 residues processed: 169 average time/residue: 1.1453 time to fit residues: 215.6049 Evaluate side-chains 148 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15144 Z= 0.152 Angle : 0.507 9.555 20620 Z= 0.254 Chirality : 0.042 0.558 2380 Planarity : 0.004 0.048 2558 Dihedral : 5.917 59.787 2155 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 2.85 % Allowed : 19.27 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1808 helix: 0.38 (0.19), residues: 794 sheet: -1.44 (0.42), residues: 152 loop : -1.69 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.003 0.001 HIS A 265 PHE 0.016 0.001 PHE E 161 TYR 0.009 0.001 TYR C 582 ARG 0.009 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 time to evaluate : 1.719 Fit side-chains REVERT: A 265 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6931 (m90) REVERT: A 610 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7556 (mtm) REVERT: A 664 ASP cc_start: 0.7363 (p0) cc_final: 0.7072 (p0) REVERT: C 184 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6998 (p0) REVERT: C 664 ASP cc_start: 0.7420 (p0) cc_final: 0.7116 (p0) REVERT: E 303 TRP cc_start: 0.7706 (p-90) cc_final: 0.7063 (p-90) outliers start: 46 outliers final: 14 residues processed: 152 average time/residue: 1.1954 time to fit residues: 201.6140 Evaluate side-chains 132 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 370 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 0.0170 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 157 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN C 215 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15144 Z= 0.162 Angle : 0.514 9.759 20620 Z= 0.255 Chirality : 0.043 0.591 2380 Planarity : 0.004 0.049 2558 Dihedral : 5.586 55.258 2152 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 2.73 % Allowed : 19.95 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1808 helix: 0.69 (0.19), residues: 794 sheet: -1.32 (0.44), residues: 142 loop : -1.55 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 383 HIS 0.003 0.001 HIS A 276 PHE 0.014 0.001 PHE C 407 TYR 0.010 0.001 TYR A 582 ARG 0.009 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 1.722 Fit side-chains REVERT: A 610 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7577 (mtm) REVERT: A 664 ASP cc_start: 0.7417 (p0) cc_final: 0.7113 (p0) REVERT: C 184 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6971 (p0) REVERT: C 664 ASP cc_start: 0.7422 (p0) cc_final: 0.7121 (p0) REVERT: E 303 TRP cc_start: 0.7711 (p-90) cc_final: 0.7037 (p-90) outliers start: 44 outliers final: 19 residues processed: 149 average time/residue: 1.2197 time to fit residues: 201.6645 Evaluate side-chains 137 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 370 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 0.0370 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 287 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15144 Z= 0.185 Angle : 0.524 9.597 20620 Z= 0.261 Chirality : 0.043 0.499 2380 Planarity : 0.004 0.050 2558 Dihedral : 5.279 53.844 2150 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 2.85 % Allowed : 20.14 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1808 helix: 0.88 (0.19), residues: 800 sheet: -1.33 (0.44), residues: 142 loop : -1.49 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 383 HIS 0.004 0.001 HIS A 276 PHE 0.016 0.001 PHE C 407 TYR 0.009 0.001 TYR C 582 ARG 0.010 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 126 time to evaluate : 1.790 Fit side-chains REVERT: A 265 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6924 (m90) REVERT: A 610 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7635 (mtm) REVERT: A 664 ASP cc_start: 0.7403 (p0) cc_final: 0.7124 (p0) REVERT: C 184 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7053 (p0) REVERT: C 664 ASP cc_start: 0.7437 (p0) cc_final: 0.7124 (p0) REVERT: E 303 TRP cc_start: 0.7709 (p-90) cc_final: 0.7065 (p-90) outliers start: 46 outliers final: 21 residues processed: 158 average time/residue: 1.1634 time to fit residues: 204.4586 Evaluate side-chains 142 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 370 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 422 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 287 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15144 Z= 0.305 Angle : 0.577 10.365 20620 Z= 0.289 Chirality : 0.045 0.501 2380 Planarity : 0.004 0.050 2558 Dihedral : 5.385 57.196 2150 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.73 % Allowed : 20.88 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1808 helix: 0.90 (0.19), residues: 794 sheet: -1.35 (0.42), residues: 152 loop : -1.49 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 383 HIS 0.007 0.001 HIS A 276 PHE 0.017 0.002 PHE C 407 TYR 0.011 0.001 TYR C 582 ARG 0.010 0.001 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 124 time to evaluate : 1.656 Fit side-chains REVERT: A 265 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6927 (m90) REVERT: A 334 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8639 (m) REVERT: A 610 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: A 664 ASP cc_start: 0.7462 (p0) cc_final: 0.7158 (p0) REVERT: C 184 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7154 (p0) REVERT: C 664 ASP cc_start: 0.7447 (p0) cc_final: 0.7127 (p0) REVERT: E 303 TRP cc_start: 0.7781 (p-90) cc_final: 0.7024 (p-90) outliers start: 44 outliers final: 27 residues processed: 154 average time/residue: 1.2343 time to fit residues: 210.3033 Evaluate side-chains 150 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 445 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 287 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15144 Z= 0.157 Angle : 0.521 11.134 20620 Z= 0.257 Chirality : 0.042 0.441 2380 Planarity : 0.004 0.050 2558 Dihedral : 4.885 53.827 2150 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.92 % Allowed : 22.00 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1808 helix: 1.11 (0.19), residues: 798 sheet: -1.22 (0.44), residues: 142 loop : -1.47 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 114 HIS 0.004 0.001 HIS A 265 PHE 0.014 0.001 PHE C 662 TYR 0.009 0.001 TYR A 274 ARG 0.013 0.001 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.742 Fit side-chains REVERT: A 265 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.6905 (m90) REVERT: A 610 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: A 664 ASP cc_start: 0.7463 (p0) cc_final: 0.7172 (p0) REVERT: C 184 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7096 (p0) REVERT: C 664 ASP cc_start: 0.7464 (p0) cc_final: 0.7171 (p0) REVERT: E 303 TRP cc_start: 0.7742 (p-90) cc_final: 0.6989 (p-90) outliers start: 31 outliers final: 18 residues processed: 147 average time/residue: 1.2920 time to fit residues: 210.1905 Evaluate side-chains 137 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 370 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.0670 chunk 168 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 287 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15144 Z= 0.144 Angle : 0.512 11.713 20620 Z= 0.253 Chirality : 0.041 0.386 2380 Planarity : 0.004 0.058 2558 Dihedral : 4.508 48.851 2150 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.43 % Allowed : 22.68 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1808 helix: 1.25 (0.19), residues: 802 sheet: -1.33 (0.48), residues: 122 loop : -1.40 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 383 HIS 0.003 0.001 HIS A 265 PHE 0.031 0.001 PHE C 165 TYR 0.008 0.001 TYR A 582 ARG 0.014 0.001 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.697 Fit side-chains REVERT: A 265 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6907 (m90) REVERT: A 610 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7651 (mtm) REVERT: A 664 ASP cc_start: 0.7445 (p0) cc_final: 0.7149 (p0) REVERT: C 184 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7010 (p0) REVERT: C 633 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8455 (p) REVERT: E 303 TRP cc_start: 0.7656 (p-90) cc_final: 0.6984 (p-90) outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 1.3038 time to fit residues: 201.4400 Evaluate side-chains 131 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 370 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 287 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15144 Z= 0.253 Angle : 0.563 13.224 20620 Z= 0.281 Chirality : 0.044 0.423 2380 Planarity : 0.004 0.060 2558 Dihedral : 4.803 52.476 2150 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.80 % Allowed : 22.24 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1808 helix: 1.19 (0.19), residues: 798 sheet: -1.18 (0.43), residues: 152 loop : -1.39 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 383 HIS 0.008 0.001 HIS C 276 PHE 0.018 0.001 PHE A 165 TYR 0.011 0.001 TYR A 582 ARG 0.014 0.001 ARG A 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6920 (m90) REVERT: A 610 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7722 (mtm) REVERT: A 664 ASP cc_start: 0.7485 (p0) cc_final: 0.7182 (p0) REVERT: C 184 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7094 (p0) REVERT: C 664 ASP cc_start: 0.7473 (p0) cc_final: 0.7169 (p0) REVERT: E 303 TRP cc_start: 0.7724 (p-90) cc_final: 0.7007 (p-90) outliers start: 29 outliers final: 20 residues processed: 141 average time/residue: 1.3199 time to fit residues: 205.0140 Evaluate side-chains 138 residues out of total 1614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 370 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 44 optimal weight: 0.0980 chunk 133 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 144 optimal weight: 0.0070 chunk 60 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 18 optimal weight: 0.0030 chunk 26 optimal weight: 5.9990 overall best weight: 1.6212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 287 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.119294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076888 restraints weight = 25570.135| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.38 r_work: 0.2909 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15144 Z= 0.225 Angle : 0.549 13.253 20620 Z= 0.274 Chirality : 0.043 0.416 2380 Planarity : 0.004 0.058 2558 Dihedral : 4.803 53.009 2150 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.55 % Allowed : 22.55 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1808 helix: 1.21 (0.19), residues: 796 sheet: -1.19 (0.43), residues: 152 loop : -1.37 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 383 HIS 0.005 0.001 HIS A 276 PHE 0.017 0.001 PHE A 407 TYR 0.009 0.001 TYR A 582 ARG 0.014 0.001 ARG A 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4605.42 seconds wall clock time: 82 minutes 34.17 seconds (4954.17 seconds total)