Starting phenix.real_space_refine on Wed Feb 14 14:31:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x14_21988/02_2024/6x14_21988_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x14_21988/02_2024/6x14_21988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x14_21988/02_2024/6x14_21988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x14_21988/02_2024/6x14_21988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x14_21988/02_2024/6x14_21988_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x14_21988/02_2024/6x14_21988_updated.pdb" } resolution = 3.71 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 54 5.16 5 C 6243 2.51 5 N 1500 2.21 5 O 1674 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 312": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9486 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3071 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 18, 'TRANS': 394} Chain: "B" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3071 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 18, 'TRANS': 394} Chain: "C" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3071 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 18, 'TRANS': 394} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'6OU': 2, '7O9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'6OU': 2, '7O9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'6OU': 2, '7O9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.71, per 1000 atoms: 0.60 Number of scatterers: 9486 At special positions: 0 Unit cell: (114.838, 115.911, 70.8345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 F 9 9.00 O 1674 8.00 N 1500 7.00 C 6243 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: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 0 sheets defined 75.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 No H-bonds generated for 'chain 'A' and resid 5 through 8' Processing helix chain 'A' and resid 12 through 33 removed outlier: 3.746A pdb=" N ILE A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 44 through 72 removed outlier: 3.718A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET A 59 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.562A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 105 Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.829A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 134' Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.821A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 removed outlier: 3.640A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 219 removed outlier: 3.591A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 4.527A pdb=" N PHE A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 252 removed outlier: 3.798A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 removed outlier: 3.671A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 273 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 291 removed outlier: 3.649A pdb=" N ARG A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 313 through 328 removed outlier: 3.605A pdb=" N GLY A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.613A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.300A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 415 removed outlier: 3.882A pdb=" N ALA A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 8 No H-bonds generated for 'chain 'B' and resid 5 through 8' Processing helix chain 'B' and resid 12 through 33 removed outlier: 3.745A pdb=" N ILE B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 44 through 72 removed outlier: 3.717A pdb=" N PHE B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET B 59 " --> pdb=" O CYS B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 3.563A pdb=" N PHE B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 105 Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.829A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 130 through 134' Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.821A pdb=" N LEU B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 169 removed outlier: 3.640A pdb=" N PHE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 219 removed outlier: 3.592A pdb=" N ASN B 199 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Proline residue: B 206 - end of helix removed outlier: 4.528A pdb=" N PHE B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 252 removed outlier: 3.797A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.671A pdb=" N HIS B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 273 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.649A pdb=" N ARG B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 313 through 328 removed outlier: 3.605A pdb=" N GLY B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 322 " --> pdb=" O GLN B 318 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 351 removed outlier: 3.612A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 4.299A pdb=" N LEU B 363 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 415 removed outlier: 3.882A pdb=" N ALA B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 12 through 33 removed outlier: 3.746A pdb=" N ILE C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 44 through 72 removed outlier: 3.718A pdb=" N PHE C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET C 59 " --> pdb=" O CYS C 55 " (cutoff:3.500A) Proline residue: C 60 - end of helix removed outlier: 3.562A pdb=" N PHE C 63 " --> pdb=" O MET C 59 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 105 Processing helix chain 'C' and resid 130 through 134 removed outlier: 3.830A pdb=" N LEU C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 130 through 134' Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.822A pdb=" N LEU C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 169 removed outlier: 3.640A pdb=" N PHE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C 157 " --> pdb=" O PRO C 153 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 219 removed outlier: 3.591A pdb=" N ASN C 199 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Proline residue: C 206 - end of helix removed outlier: 4.528A pdb=" N PHE C 210 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 252 removed outlier: 3.797A pdb=" N GLY C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.671A pdb=" N HIS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE C 273 " --> pdb=" O MET C 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.649A pdb=" N ARG C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 299 No H-bonds generated for 'chain 'C' and resid 296 through 299' Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 313 through 328 removed outlier: 3.604A pdb=" N GLY C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 326 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.612A pdb=" N LEU C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.300A pdb=" N LEU C 363 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL C 366 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 369 " --> pdb=" O MET C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 415 removed outlier: 3.882A pdb=" N ALA C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1656 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: 3.86 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1455 1.31 - 1.43: 2360 1.43 - 1.55: 5686 1.55 - 1.68: 63 1.68 - 1.80: 102 Bond restraints: 9666 Sorted by residual: bond pdb=" N 7O9 A 501 " pdb=" C8 7O9 A 501 " ideal model delta sigma weight residual 1.354 1.450 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N 7O9 B 501 " pdb=" C8 7O9 B 501 " ideal model delta sigma weight residual 1.354 1.450 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N 7O9 C 501 " pdb=" C8 7O9 C 501 " ideal model delta sigma weight residual 1.354 1.449 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C16 6OU B 502 " pdb=" O18 6OU B 502 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C16 6OU C 502 " pdb=" O18 6OU C 502 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 9661 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.47: 222 105.47 - 112.12: 4842 112.12 - 118.78: 2895 118.78 - 125.43: 5103 125.43 - 132.09: 93 Bond angle restraints: 13155 Sorted by residual: angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 109.57 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU C 503 " pdb=" P23 6OU C 503 " pdb=" O26 6OU C 503 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU B 503 " pdb=" P23 6OU B 503 " pdb=" O26 6OU B 503 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU C 502 " pdb=" P23 6OU C 502 " pdb=" O26 6OU C 502 " ideal model delta sigma weight residual 93.95 109.41 -15.46 3.00e+00 1.11e-01 2.66e+01 angle pdb=" O22 6OU B 502 " pdb=" P23 6OU B 502 " pdb=" O26 6OU B 502 " ideal model delta sigma weight residual 93.95 109.36 -15.41 3.00e+00 1.11e-01 2.64e+01 ... (remaining 13150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.79: 5323 25.79 - 51.59: 326 51.59 - 77.38: 51 77.38 - 103.17: 30 103.17 - 128.97: 6 Dihedral angle restraints: 5736 sinusoidal: 2214 harmonic: 3522 Sorted by residual: dihedral pdb=" C11 6OU C 502 " pdb=" C12 6OU C 502 " pdb=" C13 6OU C 502 " pdb=" C14 6OU C 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.68 128.97 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 6OU A 502 " pdb=" C12 6OU A 502 " pdb=" C13 6OU A 502 " pdb=" C14 6OU A 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.71 128.94 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 6OU B 502 " pdb=" C12 6OU B 502 " pdb=" C13 6OU B 502 " pdb=" C14 6OU B 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.75 128.90 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 5733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1144 0.050 - 0.101: 379 0.101 - 0.151: 81 0.151 - 0.201: 4 0.201 - 0.252: 9 Chirality restraints: 1617 Sorted by residual: chirality pdb=" C1 7O9 A 501 " pdb=" C 7O9 A 501 " pdb=" C2 7O9 A 501 " pdb=" N1 7O9 A 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 7O9 C 501 " pdb=" C 7O9 C 501 " pdb=" C2 7O9 C 501 " pdb=" N1 7O9 C 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1 7O9 B 501 " pdb=" C 7O9 B 501 " pdb=" C2 7O9 B 501 " pdb=" N1 7O9 B 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1614 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 7O9 C 501 " -0.071 2.00e-02 2.50e+03 4.56e-02 2.60e+01 pdb=" C7 7O9 C 501 " 0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 C 501 " -0.013 2.00e-02 2.50e+03 pdb=" C9 7O9 C 501 " 0.042 2.00e-02 2.50e+03 pdb=" O5 7O9 C 501 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 7O9 A 501 " 0.071 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" C7 7O9 A 501 " -0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 A 501 " 0.013 2.00e-02 2.50e+03 pdb=" C9 7O9 A 501 " -0.042 2.00e-02 2.50e+03 pdb=" O5 7O9 A 501 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 7O9 B 501 " 0.071 2.00e-02 2.50e+03 4.54e-02 2.57e+01 pdb=" C7 7O9 B 501 " -0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 B 501 " 0.012 2.00e-02 2.50e+03 pdb=" C9 7O9 B 501 " -0.041 2.00e-02 2.50e+03 pdb=" O5 7O9 B 501 " 0.015 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2604 2.81 - 3.33: 8869 3.33 - 3.85: 15558 3.85 - 4.38: 17781 4.38 - 4.90: 30187 Nonbonded interactions: 74999 Sorted by model distance: nonbonded pdb=" OH TYR B 247 " pdb=" OD2 ASP B 312 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR C 247 " pdb=" OD2 ASP C 312 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.282 2.440 nonbonded pdb=" O THR C 271 " pdb=" OG1 THR C 275 " model vdw 2.348 2.440 nonbonded pdb=" O THR A 271 " pdb=" OG1 THR A 275 " model vdw 2.348 2.440 ... (remaining 74994 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 'B' selection = chain 'C' } 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: 0.850 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: 4.120 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.060 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.008 0.096 9666 Z= 0.503 Angle : 1.105 15.622 13155 Z= 0.516 Chirality : 0.052 0.252 1617 Planarity : 0.008 0.068 1608 Dihedral : 18.679 128.965 3504 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % 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: -4.81 (0.16), residues: 1233 helix: -3.09 (0.11), residues: 993 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 132 PHE 0.018 0.002 PHE C 323 TYR 0.018 0.002 TYR B 299 ARG 0.003 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.967 Fit side-chains REVERT: A 42 TYR cc_start: 0.8027 (m-10) cc_final: 0.7798 (m-80) REVERT: A 195 TYR cc_start: 0.8904 (m-10) cc_final: 0.8568 (m-10) REVERT: A 241 LEU cc_start: 0.8820 (tt) cc_final: 0.8570 (tp) REVERT: A 263 LYS cc_start: 0.8936 (ptpp) cc_final: 0.8531 (ptpp) REVERT: A 318 GLN cc_start: 0.8659 (mt0) cc_final: 0.8451 (mt0) REVERT: B 17 LEU cc_start: 0.8554 (tp) cc_final: 0.8211 (tt) REVERT: B 269 MET cc_start: 0.7687 (ttp) cc_final: 0.7413 (ttm) REVERT: B 318 GLN cc_start: 0.8718 (mt0) cc_final: 0.8433 (mt0) REVERT: C 263 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8418 (ptpp) REVERT: C 269 MET cc_start: 0.7825 (ttp) cc_final: 0.7325 (ttp) REVERT: C 318 GLN cc_start: 0.8465 (mt0) cc_final: 0.8109 (mt0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1723 time to fit residues: 55.4026 Evaluate side-chains 178 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 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 318 GLN A 337 GLN A 338 GLN B 318 GLN B 337 GLN C 40 HIS C 318 GLN C 337 GLN C 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9666 Z= 0.197 Angle : 0.545 6.828 13155 Z= 0.280 Chirality : 0.039 0.194 1617 Planarity : 0.005 0.052 1608 Dihedral : 15.072 92.119 1533 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.14 % Allowed : 16.00 % Favored : 82.87 % 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: -2.36 (0.21), residues: 1233 helix: -1.35 (0.15), residues: 975 sheet: None (None), residues: 0 loop : -1.63 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 40 PHE 0.011 0.001 PHE C 323 TYR 0.022 0.001 TYR B 42 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 0.905 Fit side-chains REVERT: A 241 LEU cc_start: 0.8848 (tt) cc_final: 0.8449 (tp) REVERT: A 263 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8586 (ptpp) REVERT: A 362 MET cc_start: 0.8293 (ttp) cc_final: 0.8092 (ttp) REVERT: B 17 LEU cc_start: 0.8606 (tp) cc_final: 0.8241 (tt) REVERT: B 286 MET cc_start: 0.7523 (mmt) cc_final: 0.7297 (mmm) REVERT: B 298 ILE cc_start: 0.8480 (mp) cc_final: 0.8257 (mm) REVERT: B 395 MET cc_start: 0.7420 (mtt) cc_final: 0.7218 (mtp) REVERT: C 132 HIS cc_start: 0.8105 (t70) cc_final: 0.7888 (t70) REVERT: C 263 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8487 (ptpp) REVERT: C 318 GLN cc_start: 0.8451 (mt0) cc_final: 0.8028 (mt0) outliers start: 11 outliers final: 8 residues processed: 219 average time/residue: 0.1558 time to fit residues: 51.6597 Evaluate side-chains 202 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 308 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 110 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9666 Z= 0.156 Angle : 0.508 7.962 13155 Z= 0.259 Chirality : 0.038 0.181 1617 Planarity : 0.004 0.047 1608 Dihedral : 12.724 86.860 1533 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.65 % Allowed : 19.40 % Favored : 78.95 % 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: -1.34 (0.23), residues: 1233 helix: -0.62 (0.16), residues: 987 sheet: None (None), residues: 0 loop : -1.33 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 40 PHE 0.005 0.001 PHE C 323 TYR 0.027 0.001 TYR A 42 ARG 0.001 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 209 time to evaluate : 0.979 Fit side-chains REVERT: A 42 TYR cc_start: 0.7837 (m-80) cc_final: 0.7635 (m-10) REVERT: A 132 HIS cc_start: 0.7974 (t70) cc_final: 0.7619 (t70) REVERT: A 241 LEU cc_start: 0.8841 (tt) cc_final: 0.8432 (tp) REVERT: A 263 LYS cc_start: 0.8881 (ptpp) cc_final: 0.8550 (ptpp) REVERT: B 286 MET cc_start: 0.7575 (mmt) cc_final: 0.7230 (mmt) REVERT: B 340 THR cc_start: 0.7982 (m) cc_final: 0.7679 (m) REVERT: C 160 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8644 (tp) REVERT: C 263 LYS cc_start: 0.8791 (ptpp) cc_final: 0.8405 (ptpp) REVERT: C 269 MET cc_start: 0.7730 (ttp) cc_final: 0.7083 (ttp) REVERT: C 318 GLN cc_start: 0.8400 (mt0) cc_final: 0.7983 (mt0) REVERT: C 399 MET cc_start: 0.8861 (tpp) cc_final: 0.8354 (tpt) outliers start: 16 outliers final: 8 residues processed: 219 average time/residue: 0.1543 time to fit residues: 51.7528 Evaluate side-chains 208 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 308 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN B 203 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9666 Z= 0.187 Angle : 0.512 6.365 13155 Z= 0.261 Chirality : 0.038 0.170 1617 Planarity : 0.004 0.043 1608 Dihedral : 11.182 82.336 1533 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.68 % Allowed : 20.85 % Favored : 76.47 % 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: -0.69 (0.24), residues: 1233 helix: -0.15 (0.17), residues: 987 sheet: None (None), residues: 0 loop : -1.14 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS C 132 PHE 0.008 0.001 PHE A 323 TYR 0.023 0.001 TYR C 299 ARG 0.002 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 0.964 Fit side-chains REVERT: A 132 HIS cc_start: 0.8046 (t70) cc_final: 0.7677 (t70) REVERT: A 241 LEU cc_start: 0.8849 (tt) cc_final: 0.8449 (tp) REVERT: A 263 LYS cc_start: 0.8883 (ptpp) cc_final: 0.8573 (ptpp) REVERT: B 286 MET cc_start: 0.7563 (mmt) cc_final: 0.7283 (mmt) REVERT: C 263 LYS cc_start: 0.8812 (ptpp) cc_final: 0.8444 (ptpp) REVERT: C 318 GLN cc_start: 0.8253 (mt0) cc_final: 0.7841 (mt0) REVERT: C 399 MET cc_start: 0.8916 (tpp) cc_final: 0.8273 (tpt) outliers start: 26 outliers final: 17 residues processed: 216 average time/residue: 0.1558 time to fit residues: 51.5607 Evaluate side-chains 216 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 308 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.0570 chunk 30 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9666 Z= 0.151 Angle : 0.500 8.015 13155 Z= 0.253 Chirality : 0.038 0.119 1617 Planarity : 0.003 0.041 1608 Dihedral : 10.105 78.704 1533 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 21.57 % Favored : 75.85 % 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: -0.21 (0.24), residues: 1233 helix: 0.21 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -1.07 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS C 132 PHE 0.005 0.001 PHE A 323 TYR 0.022 0.001 TYR C 299 ARG 0.001 0.000 ARG B 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.033 Fit side-chains REVERT: A 42 TYR cc_start: 0.7569 (m-80) cc_final: 0.7180 (m-10) REVERT: A 132 HIS cc_start: 0.8010 (t70) cc_final: 0.7696 (t70) REVERT: A 160 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8639 (tp) REVERT: A 263 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8571 (ptpp) REVERT: B 170 ASN cc_start: 0.8064 (p0) cc_final: 0.7848 (m-40) REVERT: B 286 MET cc_start: 0.7552 (mmt) cc_final: 0.7269 (mmt) REVERT: C 4 TYR cc_start: 0.8042 (t80) cc_final: 0.7691 (t80) REVERT: C 160 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8650 (tp) REVERT: C 263 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8424 (ptpp) REVERT: C 269 MET cc_start: 0.7724 (ttp) cc_final: 0.7002 (ttp) REVERT: C 318 GLN cc_start: 0.8298 (mt0) cc_final: 0.7879 (mt0) REVERT: C 399 MET cc_start: 0.8887 (tpp) cc_final: 0.8235 (tpt) outliers start: 25 outliers final: 19 residues processed: 217 average time/residue: 0.1553 time to fit residues: 51.6780 Evaluate side-chains 216 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9666 Z= 0.236 Angle : 0.549 12.357 13155 Z= 0.276 Chirality : 0.039 0.109 1617 Planarity : 0.003 0.038 1608 Dihedral : 10.015 80.834 1533 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.30 % Allowed : 21.57 % Favored : 75.13 % 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: -0.17 (0.24), residues: 1233 helix: 0.22 (0.17), residues: 987 sheet: None (None), residues: 0 loop : -0.99 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 132 PHE 0.011 0.001 PHE A 323 TYR 0.022 0.001 TYR C 299 ARG 0.002 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 0.853 Fit side-chains REVERT: A 42 TYR cc_start: 0.7563 (m-80) cc_final: 0.7207 (m-10) REVERT: A 132 HIS cc_start: 0.8092 (t70) cc_final: 0.7809 (t70) REVERT: A 241 LEU cc_start: 0.8860 (tt) cc_final: 0.8453 (tp) REVERT: A 263 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8668 (ptpp) REVERT: A 387 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8341 (mp) REVERT: B 160 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8755 (tp) REVERT: B 174 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7774 (tp30) REVERT: B 286 MET cc_start: 0.7646 (mmt) cc_final: 0.7356 (mmt) REVERT: C 18 ILE cc_start: 0.8498 (tp) cc_final: 0.8265 (tp) REVERT: C 160 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8748 (tp) REVERT: C 174 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7954 (tm-30) REVERT: C 399 MET cc_start: 0.9019 (tpp) cc_final: 0.8163 (tpt) outliers start: 32 outliers final: 20 residues processed: 222 average time/residue: 0.1541 time to fit residues: 53.1709 Evaluate side-chains 218 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9666 Z= 0.193 Angle : 0.533 12.761 13155 Z= 0.268 Chirality : 0.038 0.129 1617 Planarity : 0.003 0.039 1608 Dihedral : 9.779 79.781 1533 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.99 % Allowed : 22.08 % Favored : 74.92 % 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: -0.01 (0.24), residues: 1233 helix: 0.33 (0.17), residues: 987 sheet: None (None), residues: 0 loop : -0.94 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 132 PHE 0.010 0.001 PHE A 323 TYR 0.022 0.001 TYR C 299 ARG 0.001 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 0.904 Fit side-chains REVERT: A 42 TYR cc_start: 0.7595 (m-80) cc_final: 0.7281 (m-10) REVERT: A 132 HIS cc_start: 0.8038 (t70) cc_final: 0.7741 (t70) REVERT: A 241 LEU cc_start: 0.8849 (tt) cc_final: 0.8463 (tp) REVERT: A 263 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8591 (ptpp) REVERT: A 387 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8309 (mp) REVERT: B 160 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8724 (tp) REVERT: B 174 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7730 (tp30) REVERT: B 286 MET cc_start: 0.7648 (mmt) cc_final: 0.7349 (mmt) REVERT: B 387 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8151 (mp) REVERT: C 18 ILE cc_start: 0.8516 (tp) cc_final: 0.8263 (tp) REVERT: C 160 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8715 (tp) REVERT: C 174 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7951 (tm-30) REVERT: C 389 ILE cc_start: 0.8274 (tp) cc_final: 0.8012 (tp) outliers start: 29 outliers final: 20 residues processed: 216 average time/residue: 0.1472 time to fit residues: 49.5869 Evaluate side-chains 220 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9666 Z= 0.240 Angle : 0.564 13.185 13155 Z= 0.282 Chirality : 0.040 0.132 1617 Planarity : 0.004 0.038 1608 Dihedral : 9.802 80.270 1533 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.41 % Allowed : 22.39 % Favored : 74.20 % 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: -0.13 (0.24), residues: 1233 helix: 0.25 (0.17), residues: 1005 sheet: None (None), residues: 0 loop : -1.10 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.013 0.001 PHE A 323 TYR 0.023 0.002 TYR A 88 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 0.905 Fit side-chains REVERT: A 42 TYR cc_start: 0.7776 (m-80) cc_final: 0.7464 (m-10) REVERT: A 132 HIS cc_start: 0.8052 (t70) cc_final: 0.7780 (t70) REVERT: A 174 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 241 LEU cc_start: 0.8864 (tt) cc_final: 0.8481 (tp) REVERT: A 387 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8353 (mp) REVERT: B 132 HIS cc_start: 0.8037 (t70) cc_final: 0.7658 (t70) REVERT: B 160 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8753 (tp) REVERT: B 174 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7803 (tp30) REVERT: B 286 MET cc_start: 0.7684 (mmt) cc_final: 0.7376 (mmt) REVERT: B 368 HIS cc_start: 0.8191 (m170) cc_final: 0.7945 (m-70) REVERT: B 387 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8225 (mp) REVERT: C 42 TYR cc_start: 0.7739 (m-80) cc_final: 0.6853 (m-10) REVERT: C 160 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8730 (tp) REVERT: C 174 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8052 (tm-30) REVERT: C 389 ILE cc_start: 0.8372 (tp) cc_final: 0.8122 (tp) REVERT: C 399 MET cc_start: 0.8984 (tpp) cc_final: 0.8217 (tpt) outliers start: 33 outliers final: 22 residues processed: 221 average time/residue: 0.1421 time to fit residues: 48.9869 Evaluate side-chains 226 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 0.0010 chunk 113 optimal weight: 0.7980 chunk 66 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9666 Z= 0.157 Angle : 0.522 12.260 13155 Z= 0.261 Chirality : 0.038 0.134 1617 Planarity : 0.003 0.037 1608 Dihedral : 9.304 76.389 1533 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 23.22 % Favored : 74.20 % 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: 0.18 (0.24), residues: 1233 helix: 0.48 (0.17), residues: 1005 sheet: None (None), residues: 0 loop : -1.06 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 132 PHE 0.006 0.001 PHE C 323 TYR 0.021 0.001 TYR A 88 ARG 0.001 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 0.953 Fit side-chains REVERT: A 42 TYR cc_start: 0.7531 (m-80) cc_final: 0.7259 (m-10) REVERT: A 132 HIS cc_start: 0.7945 (t70) cc_final: 0.7637 (t70) REVERT: A 241 LEU cc_start: 0.8840 (tt) cc_final: 0.8474 (tp) REVERT: A 263 LYS cc_start: 0.8847 (ptpp) cc_final: 0.8582 (ptpp) REVERT: A 387 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8150 (mp) REVERT: B 132 HIS cc_start: 0.7953 (t70) cc_final: 0.7562 (t70) REVERT: B 160 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8617 (tp) REVERT: B 387 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8064 (mp) REVERT: C 4 TYR cc_start: 0.8143 (t80) cc_final: 0.7861 (t80) REVERT: C 30 LEU cc_start: 0.8264 (mt) cc_final: 0.8037 (mt) REVERT: C 42 TYR cc_start: 0.7777 (m-80) cc_final: 0.6984 (m-10) REVERT: C 160 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8616 (tp) REVERT: C 263 LYS cc_start: 0.8812 (ptpp) cc_final: 0.8417 (ptpp) REVERT: C 312 ASP cc_start: 0.7860 (m-30) cc_final: 0.7534 (m-30) REVERT: C 389 ILE cc_start: 0.8101 (tp) cc_final: 0.7729 (tp) REVERT: C 399 MET cc_start: 0.8791 (tpp) cc_final: 0.8115 (tpt) outliers start: 25 outliers final: 19 residues processed: 222 average time/residue: 0.1550 time to fit residues: 53.1317 Evaluate side-chains 223 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9666 Z= 0.190 Angle : 0.552 12.685 13155 Z= 0.272 Chirality : 0.039 0.214 1617 Planarity : 0.003 0.035 1608 Dihedral : 9.232 74.184 1533 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.58 % Allowed : 23.53 % Favored : 73.89 % 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: 0.21 (0.24), residues: 1233 helix: 0.50 (0.17), residues: 1005 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.009 0.001 PHE A 323 TYR 0.022 0.001 TYR C 299 ARG 0.001 0.000 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.002 Fit side-chains REVERT: A 42 TYR cc_start: 0.7720 (m-80) cc_final: 0.7427 (m-10) REVERT: A 132 HIS cc_start: 0.7912 (t70) cc_final: 0.7641 (t70) REVERT: A 241 LEU cc_start: 0.8832 (tt) cc_final: 0.8454 (tp) REVERT: A 263 LYS cc_start: 0.8863 (ptpp) cc_final: 0.8602 (ptpp) REVERT: A 387 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 132 HIS cc_start: 0.8024 (t70) cc_final: 0.7646 (t70) REVERT: B 160 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8695 (tp) REVERT: B 174 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7732 (tp30) REVERT: B 269 MET cc_start: 0.7601 (ttt) cc_final: 0.7356 (ttp) REVERT: B 387 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 399 MET cc_start: 0.8931 (tpp) cc_final: 0.8588 (tpt) REVERT: C 30 LEU cc_start: 0.8295 (mt) cc_final: 0.8057 (mt) REVERT: C 42 TYR cc_start: 0.7788 (m-80) cc_final: 0.7028 (m-10) REVERT: C 160 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8682 (tp) REVERT: C 174 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8000 (tm-30) REVERT: C 399 MET cc_start: 0.8844 (tpp) cc_final: 0.8032 (tpt) outliers start: 25 outliers final: 19 residues processed: 214 average time/residue: 0.1512 time to fit residues: 50.0377 Evaluate side-chains 220 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.106240 restraints weight = 11726.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.109026 restraints weight = 7232.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.110996 restraints weight = 5140.683| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9666 Z= 0.201 Angle : 0.552 12.731 13155 Z= 0.273 Chirality : 0.039 0.171 1617 Planarity : 0.003 0.032 1608 Dihedral : 9.218 73.835 1533 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.48 % Allowed : 23.84 % Favored : 73.68 % 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: 0.21 (0.24), residues: 1233 helix: 0.50 (0.17), residues: 1005 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.010 0.001 PHE A 323 TYR 0.022 0.002 TYR C 299 ARG 0.001 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.48 seconds wall clock time: 35 minutes 7.61 seconds (2107.61 seconds total)