Starting phenix.real_space_refine on Mon Mar 11 09:19:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lze_23605/03_2024/7lze_23605.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lze_23605/03_2024/7lze_23605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lze_23605/03_2024/7lze_23605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lze_23605/03_2024/7lze_23605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lze_23605/03_2024/7lze_23605.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lze_23605/03_2024/7lze_23605.pdb" } resolution = 3.23 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= 0.006 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 4899 2.51 5 N 1314 2.21 5 O 1560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C ASP 414": "OD1" <-> "OD2" Residue "C ASP 421": "OD1" <-> "OD2" Residue "C GLU 431": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2572 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2572 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain breaks: 1 Chain: "C" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2572 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.68, per 1000 atoms: 0.60 Number of scatterers: 7842 At special positions: 0 Unit cell: (88.7841, 86.5919, 107.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1560 8.00 N 1314 7.00 C 4899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 63 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS C 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.04 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 57 " " NAG B 601 " - " ASN B 57 " " NAG C 601 " - " ASN C 57 " " NAG D 1 " - " ASN A 353 " " NAG E 1 " - " ASN B 353 " " NAG F 1 " - " ASN C 353 " Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 16 sheets defined 25.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.716A pdb=" N GLU A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.545A pdb=" N MET A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.593A pdb=" N LEU A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.681A pdb=" N ARG A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 253' Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.166A pdb=" N ILE A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.990A pdb=" N THR B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.555A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.871A pdb=" N LEU B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.585A pdb=" N ARG B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.028A pdb=" N ILE B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 84 removed outlier: 3.649A pdb=" N GLU C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.639A pdb=" N SER C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.643A pdb=" N LEU C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.718A pdb=" N ARG C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 253' Processing helix chain 'C' and resid 348 through 353 removed outlier: 4.118A pdb=" N ILE C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 4.231A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A 36 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N THR A 281 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 38 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 279 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ARG A 40 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLY A 277 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY A 42 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 275 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 312 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 263 removed outlier: 7.080A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 47 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE C 437 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR A 49 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.514A pdb=" N SER A 291 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 303 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 376 removed outlier: 3.928A pdb=" N CYS A 384 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 406 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 393 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 438 removed outlier: 6.911A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 21 through 24 removed outlier: 4.007A pdb=" N GLY B 34 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS B 283 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU B 36 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR B 281 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 38 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 279 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG B 40 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY B 277 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY B 42 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 275 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 312 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 21 through 24 removed outlier: 8.181A pdb=" N VAL B 333 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 36 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 327 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 291 through 294 removed outlier: 3.702A pdb=" N ALA B 300 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 303 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 376 removed outlier: 3.798A pdb=" N CYS B 384 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B 406 " --> pdb=" O CYS B 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 401 through 402 removed outlier: 3.912A pdb=" N LYS B 401 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 391 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 434 through 438 removed outlier: 6.959A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 257 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 24 removed outlier: 4.236A pdb=" N GLY C 34 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N CYS C 283 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU C 36 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR C 281 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 38 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 279 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG C 40 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY C 277 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY C 42 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 275 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS C 312 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 291 through 295 removed outlier: 3.506A pdb=" N SER C 291 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 303 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 372 through 376 removed outlier: 3.952A pdb=" N CYS C 384 " --> pdb=" O GLY C 406 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 406 " --> pdb=" O CYS C 384 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 390 through 393 293 hydrogen bonds defined for protein. 807 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: 2.25 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2565 1.35 - 1.47: 1823 1.47 - 1.59: 3487 1.59 - 1.72: 0 1.72 - 1.84: 90 Bond restraints: 7965 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 7960 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 203 107.11 - 113.83: 4652 113.83 - 120.55: 2956 120.55 - 127.27: 2929 127.27 - 133.99: 60 Bond angle restraints: 10800 Sorted by residual: angle pdb=" CA CYS C 283 " pdb=" CB CYS C 283 " pdb=" SG CYS C 283 " ideal model delta sigma weight residual 114.40 119.61 -5.21 2.30e+00 1.89e-01 5.13e+00 angle pdb=" CA CYS A 283 " pdb=" CB CYS A 283 " pdb=" SG CYS A 283 " ideal model delta sigma weight residual 114.40 119.55 -5.15 2.30e+00 1.89e-01 5.00e+00 angle pdb=" C SER A 355 " pdb=" N THR A 356 " pdb=" CA THR A 356 " ideal model delta sigma weight residual 121.54 125.17 -3.63 1.91e+00 2.74e-01 3.61e+00 angle pdb=" C SER C 355 " pdb=" N THR C 356 " pdb=" CA THR C 356 " ideal model delta sigma weight residual 121.54 125.12 -3.58 1.91e+00 2.74e-01 3.52e+00 angle pdb=" C SER B 355 " pdb=" N THR B 356 " pdb=" CA THR B 356 " ideal model delta sigma weight residual 121.54 125.06 -3.52 1.91e+00 2.74e-01 3.40e+00 ... (remaining 10795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4494 17.13 - 34.27: 369 34.27 - 51.40: 127 51.40 - 68.53: 21 68.53 - 85.67: 11 Dihedral angle restraints: 5022 sinusoidal: 2091 harmonic: 2931 Sorted by residual: dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 63 " pdb=" CB CYS B 63 " ideal model delta sinusoidal sigma weight residual -86.00 -171.67 85.67 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS C 60 " pdb=" SG CYS C 60 " pdb=" SG CYS C 63 " pdb=" CB CYS C 63 " ideal model delta sinusoidal sigma weight residual 93.00 172.91 -79.91 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 63 " pdb=" CB CYS A 63 " ideal model delta sinusoidal sigma weight residual 93.00 172.51 -79.51 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 5019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 848 0.032 - 0.063: 279 0.063 - 0.095: 66 0.095 - 0.127: 94 0.127 - 0.158: 6 Chirality restraints: 1293 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA VAL C 38 " pdb=" N VAL C 38 " pdb=" C VAL C 38 " pdb=" CB VAL C 38 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 285 " pdb=" N ILE A 285 " pdb=" C ILE A 285 " pdb=" CB ILE A 285 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1290 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 355 " 0.004 2.00e-02 2.50e+03 8.38e-03 7.02e-01 pdb=" C SER B 355 " -0.014 2.00e-02 2.50e+03 pdb=" O SER B 355 " 0.005 2.00e-02 2.50e+03 pdb=" N THR B 356 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 355 " 0.004 2.00e-02 2.50e+03 8.30e-03 6.89e-01 pdb=" C SER C 355 " -0.014 2.00e-02 2.50e+03 pdb=" O SER C 355 " 0.005 2.00e-02 2.50e+03 pdb=" N THR C 356 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 355 " 0.004 2.00e-02 2.50e+03 8.20e-03 6.73e-01 pdb=" C SER A 355 " -0.014 2.00e-02 2.50e+03 pdb=" O SER A 355 " 0.005 2.00e-02 2.50e+03 pdb=" N THR A 356 " 0.005 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1072 2.76 - 3.29: 7484 3.29 - 3.83: 11854 3.83 - 4.36: 14177 4.36 - 4.90: 26051 Nonbonded interactions: 60638 Sorted by model distance: nonbonded pdb=" OE1 GLN A 206 " pdb=" OG SER A 218 " model vdw 2.222 2.440 nonbonded pdb=" OE1 GLN C 206 " pdb=" OG SER C 218 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU B 305 " pdb=" OG SER B 364 " model vdw 2.272 2.440 nonbonded pdb=" OE2 GLU C 305 " pdb=" OG SER C 364 " model vdw 2.286 2.440 nonbonded pdb=" OE1 GLN B 206 " pdb=" OG SER B 218 " model vdw 2.302 2.440 ... (remaining 60633 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.100 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: 4.320 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.480 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.003 0.029 7965 Z= 0.182 Angle : 0.453 5.208 10800 Z= 0.241 Chirality : 0.043 0.158 1293 Planarity : 0.002 0.020 1368 Dihedral : 13.958 82.348 3066 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % 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: -0.70 (0.28), residues: 999 helix: 2.96 (0.38), residues: 225 sheet: -1.15 (0.32), residues: 285 loop : -1.74 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 43 HIS 0.001 0.000 HIS B 435 PHE 0.003 0.000 PHE A 334 TYR 0.008 0.001 TYR A 310 ARG 0.002 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: C 189 MET cc_start: 0.7566 (mtt) cc_final: 0.6877 (mtt) REVERT: C 270 MET cc_start: 0.7362 (ttm) cc_final: 0.7162 (ttm) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1478 time to fit residues: 12.1359 Evaluate side-chains 39 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.0040 chunk 89 optimal weight: 4.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7965 Z= 0.223 Angle : 0.550 9.600 10800 Z= 0.287 Chirality : 0.046 0.254 1293 Planarity : 0.003 0.021 1368 Dihedral : 6.680 55.870 1281 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.46 % Allowed : 5.15 % Favored : 94.39 % 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: -0.76 (0.27), residues: 999 helix: 2.40 (0.35), residues: 231 sheet: -0.92 (0.32), residues: 294 loop : -1.74 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.002 0.001 HIS C 435 PHE 0.005 0.001 PHE B 200 TYR 0.018 0.001 TYR B 319 ARG 0.002 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: B 57 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6874 (m-40) REVERT: C 270 MET cc_start: 0.7669 (ttm) cc_final: 0.7465 (ttm) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.1334 time to fit residues: 10.9749 Evaluate side-chains 39 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7965 Z= 0.173 Angle : 0.507 9.650 10800 Z= 0.265 Chirality : 0.044 0.232 1293 Planarity : 0.002 0.020 1368 Dihedral : 6.305 54.417 1281 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.03 % Allowed : 8.82 % Favored : 90.15 % 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: -0.71 (0.27), residues: 999 helix: 2.37 (0.35), residues: 231 sheet: -0.84 (0.32), residues: 294 loop : -1.72 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 309 HIS 0.002 0.000 HIS B 435 PHE 0.005 0.001 PHE B 200 TYR 0.018 0.001 TYR B 319 ARG 0.001 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8896 (mtm) cc_final: 0.8595 (mtm) REVERT: B 57 ASN cc_start: 0.7177 (OUTLIER) cc_final: 0.6836 (m-40) outliers start: 9 outliers final: 3 residues processed: 49 average time/residue: 0.1429 time to fit residues: 11.4852 Evaluate side-chains 42 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7965 Z= 0.252 Angle : 0.551 9.808 10800 Z= 0.286 Chirality : 0.045 0.241 1293 Planarity : 0.003 0.024 1368 Dihedral : 6.257 54.989 1281 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.72 % Allowed : 9.16 % Favored : 89.12 % 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: -0.82 (0.27), residues: 999 helix: 2.32 (0.35), residues: 231 sheet: -1.11 (0.32), residues: 309 loop : -1.65 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 284 HIS 0.002 0.001 HIS B 435 PHE 0.005 0.001 PHE B 256 TYR 0.025 0.001 TYR B 319 ARG 0.002 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: C 319 TYR cc_start: 0.8364 (t80) cc_final: 0.8035 (t80) outliers start: 15 outliers final: 12 residues processed: 50 average time/residue: 0.1526 time to fit residues: 12.7657 Evaluate side-chains 50 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7965 Z= 0.202 Angle : 0.521 9.703 10800 Z= 0.270 Chirality : 0.044 0.236 1293 Planarity : 0.003 0.025 1368 Dihedral : 6.164 54.827 1281 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.83 % Allowed : 11.00 % Favored : 87.17 % 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: -0.79 (0.27), residues: 999 helix: 2.33 (0.35), residues: 231 sheet: -0.85 (0.32), residues: 300 loop : -1.80 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 284 HIS 0.002 0.000 HIS B 435 PHE 0.004 0.001 PHE B 256 TYR 0.015 0.001 TYR B 319 ARG 0.001 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8934 (mtm) cc_final: 0.8620 (mtm) REVERT: B 57 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6826 (m-40) REVERT: B 197 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7891 (m-40) outliers start: 16 outliers final: 13 residues processed: 50 average time/residue: 0.1402 time to fit residues: 11.7554 Evaluate side-chains 53 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.0070 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 0.0670 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7965 Z= 0.152 Angle : 0.492 9.650 10800 Z= 0.256 Chirality : 0.044 0.236 1293 Planarity : 0.002 0.024 1368 Dihedral : 6.012 54.995 1281 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.83 % Allowed : 11.57 % Favored : 86.60 % 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: -0.71 (0.27), residues: 999 helix: 2.41 (0.35), residues: 231 sheet: -0.65 (0.33), residues: 285 loop : -1.86 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 43 HIS 0.001 0.000 HIS B 435 PHE 0.004 0.001 PHE B 256 TYR 0.021 0.001 TYR B 319 ARG 0.001 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.946 Fit side-chains REVERT: A 244 MET cc_start: 0.8874 (mtm) cc_final: 0.8567 (mtm) REVERT: B 57 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6813 (m-40) REVERT: B 197 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7841 (m-40) outliers start: 16 outliers final: 13 residues processed: 58 average time/residue: 0.1354 time to fit residues: 12.9180 Evaluate side-chains 55 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7965 Z= 0.261 Angle : 0.541 9.735 10800 Z= 0.280 Chirality : 0.045 0.239 1293 Planarity : 0.003 0.025 1368 Dihedral : 6.104 54.926 1281 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.83 % Allowed : 12.83 % Favored : 85.34 % 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: -0.80 (0.27), residues: 999 helix: 2.35 (0.35), residues: 231 sheet: -0.64 (0.33), residues: 279 loop : -1.97 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 284 HIS 0.002 0.001 HIS B 435 PHE 0.005 0.001 PHE B 256 TYR 0.021 0.001 TYR B 319 ARG 0.002 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8954 (mtm) cc_final: 0.8635 (mtm) REVERT: B 197 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (m-40) REVERT: C 319 TYR cc_start: 0.8249 (t80) cc_final: 0.8041 (t80) REVERT: C 440 ARG cc_start: 0.7504 (mtm180) cc_final: 0.7148 (mtt180) outliers start: 16 outliers final: 13 residues processed: 53 average time/residue: 0.1567 time to fit residues: 13.0234 Evaluate side-chains 54 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.0060 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7965 Z= 0.176 Angle : 0.504 9.675 10800 Z= 0.262 Chirality : 0.044 0.235 1293 Planarity : 0.003 0.024 1368 Dihedral : 6.094 56.292 1281 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.83 % Allowed : 12.83 % Favored : 85.34 % 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: -0.72 (0.27), residues: 999 helix: 2.41 (0.35), residues: 231 sheet: -0.70 (0.33), residues: 294 loop : -1.86 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 284 HIS 0.001 0.000 HIS B 435 PHE 0.004 0.001 PHE B 256 TYR 0.020 0.001 TYR B 319 ARG 0.001 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.927 Fit side-chains REVERT: A 244 MET cc_start: 0.8909 (mtm) cc_final: 0.8609 (mtm) REVERT: B 197 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7871 (m-40) outliers start: 16 outliers final: 14 residues processed: 53 average time/residue: 0.1402 time to fit residues: 12.2079 Evaluate side-chains 53 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0980 chunk 91 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7965 Z= 0.143 Angle : 0.483 9.650 10800 Z= 0.252 Chirality : 0.043 0.236 1293 Planarity : 0.003 0.023 1368 Dihedral : 5.952 55.185 1281 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.95 % Allowed : 12.83 % Favored : 85.22 % 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: -0.65 (0.27), residues: 999 helix: 2.48 (0.35), residues: 231 sheet: -0.52 (0.33), residues: 279 loop : -1.90 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 43 HIS 0.001 0.000 HIS B 435 PHE 0.004 0.001 PHE B 256 TYR 0.025 0.001 TYR A 319 ARG 0.001 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.914 Fit side-chains REVERT: A 244 MET cc_start: 0.8870 (mtm) cc_final: 0.8574 (mtm) REVERT: B 197 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7794 (m-40) outliers start: 17 outliers final: 15 residues processed: 57 average time/residue: 0.1328 time to fit residues: 12.6748 Evaluate side-chains 55 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 39 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7965 Z= 0.324 Angle : 0.569 9.823 10800 Z= 0.296 Chirality : 0.046 0.240 1293 Planarity : 0.003 0.026 1368 Dihedral : 6.158 55.059 1281 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.95 % Allowed : 12.94 % Favored : 85.11 % 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: -0.92 (0.27), residues: 999 helix: 2.32 (0.35), residues: 231 sheet: -0.98 (0.32), residues: 294 loop : -1.91 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 284 HIS 0.002 0.001 HIS B 435 PHE 0.006 0.001 PHE C 207 TYR 0.021 0.001 TYR B 319 ARG 0.002 0.000 ARG C 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7903 (m-40) REVERT: C 440 ARG cc_start: 0.7504 (mtm180) cc_final: 0.7150 (mtt180) outliers start: 17 outliers final: 14 residues processed: 56 average time/residue: 0.1536 time to fit residues: 13.4999 Evaluate side-chains 56 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097480 restraints weight = 11753.034| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.69 r_work: 0.3146 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7965 Z= 0.256 Angle : 0.538 9.751 10800 Z= 0.280 Chirality : 0.045 0.236 1293 Planarity : 0.003 0.027 1368 Dihedral : 6.136 54.952 1281 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.95 % Allowed : 13.17 % Favored : 84.88 % 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: -0.92 (0.27), residues: 999 helix: 2.31 (0.35), residues: 231 sheet: -0.86 (0.32), residues: 294 loop : -1.99 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 284 HIS 0.002 0.000 HIS B 435 PHE 0.005 0.001 PHE A 256 TYR 0.017 0.001 TYR B 319 ARG 0.002 0.000 ARG C 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1612.15 seconds wall clock time: 30 minutes 19.27 seconds (1819.27 seconds total)