Starting phenix.real_space_refine on Mon Mar 18 14:04:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1d_7329/03_2024/6c1d_7329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1d_7329/03_2024/6c1d_7329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1d_7329/03_2024/6c1d_7329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1d_7329/03_2024/6c1d_7329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1d_7329/03_2024/6c1d_7329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1d_7329/03_2024/6c1d_7329_updated.pdb" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 127 5.16 5 C 13150 2.51 5 N 3638 2.21 5 O 4116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 498": "NH1" <-> "NH2" Residue "P ARG 536": "NH1" <-> "NH2" Residue "P ARG 566": "NH1" <-> "NH2" Residue "P ARG 635": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21049 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "P" Number of atoms: 5570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5570 Classifications: {'peptide': 729} Incomplete info: {'backbone_only': 71, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 4, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 701} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 185 Chain: "R" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 591 Classifications: {'peptide': 148} Incomplete info: {'backbone_only': 136, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 143} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 842 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 17, 'PHE:plan': 8, 'GLU:plan': 21, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 308 Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1, '2TL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.28, per 1000 atoms: 0.54 Number of scatterers: 21049 At special positions: 0 Unit cell: (202.8, 104, 193.7, 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 127 16.00 P 12 15.00 Mg 6 11.99 O 4116 8.00 N 3638 7.00 C 13150 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.76 Conformation dependent library (CDL) restraints added in 3.7 seconds 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DCY F 3 " Input volumes are d-peptide like pdb=" CB 2TL F 2 " Number of C-beta restraints generated: 4724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 26 sheets defined 43.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.702A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.784A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.820A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 351 through 354 removed outlier: 4.031A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 362 through 373 Proline residue: A 367 - end of helix removed outlier: 5.716A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.703A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.784A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.819A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 351 through 354 removed outlier: 4.031A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 362 through 373 Proline residue: B 367 - end of helix removed outlier: 5.717A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 143 Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.702A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.785A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.819A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 351 through 354 removed outlier: 4.031A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 362 through 373 Proline residue: C 367 - end of helix removed outlier: 5.715A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 143 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 203 through 215 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.702A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.784A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.820A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 351 through 354 removed outlier: 4.031A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 362 through 373 Proline residue: D 367 - end of helix removed outlier: 5.716A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 143 Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.702A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.784A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 320 removed outlier: 3.820A pdb=" N ALA E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 351 through 354 removed outlier: 4.031A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 362 through 373 Proline residue: E 367 - end of helix removed outlier: 5.716A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 40 removed outlier: 3.709A pdb=" N ASN P 34 " --> pdb=" O THR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 71 Processing helix chain 'P' and resid 84 through 96 Processing helix chain 'P' and resid 114 through 128 Processing helix chain 'P' and resid 135 through 153 Proline residue: P 147 - end of helix Processing helix chain 'P' and resid 207 through 213 Processing helix chain 'P' and resid 217 through 222 Processing helix chain 'P' and resid 229 through 231 No H-bonds generated for 'chain 'P' and resid 229 through 231' Processing helix chain 'P' and resid 250 through 261 Processing helix chain 'P' and resid 265 through 283 removed outlier: 4.078A pdb=" N GLY P 282 " --> pdb=" O VAL P 278 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN P 283 " --> pdb=" O LEU P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 313 Processing helix chain 'P' and resid 317 through 325 removed outlier: 3.821A pdb=" N SER P 325 " --> pdb=" O GLU P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 342 through 369 Processing helix chain 'P' and resid 399 through 416 Processing helix chain 'P' and resid 418 through 429 Processing helix chain 'P' and resid 443 through 449 Processing helix chain 'P' and resid 456 through 465 Processing helix chain 'P' and resid 472 through 481 Processing helix chain 'P' and resid 526 through 529 No H-bonds generated for 'chain 'P' and resid 526 through 529' Processing helix chain 'P' and resid 536 through 544 removed outlier: 4.204A pdb=" N LYS P 544 " --> pdb=" O GLN P 540 " (cutoff:3.500A) Processing helix chain 'P' and resid 550 through 553 No H-bonds generated for 'chain 'P' and resid 550 through 553' Processing helix chain 'P' and resid 555 through 557 No H-bonds generated for 'chain 'P' and resid 555 through 557' Processing helix chain 'P' and resid 571 through 583 Processing helix chain 'P' and resid 609 through 619 Processing helix chain 'P' and resid 621 through 628 Processing helix chain 'P' and resid 638 through 648 removed outlier: 5.753A pdb=" N MET P 647 " --> pdb=" O GLU P 643 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU P 648 " --> pdb=" O ARG P 644 " (cutoff:3.500A) Processing helix chain 'P' and resid 660 through 670 Processing helix chain 'P' and resid 690 through 731 removed outlier: 3.548A pdb=" N ASP P 706 " --> pdb=" O GLN P 702 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN P 731 " --> pdb=" O MET P 727 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 19 Processing helix chain 'R' and resid 32 through 39 Processing helix chain 'R' and resid 45 through 55 Processing helix chain 'R' and resid 65 through 76 Processing helix chain 'R' and resid 82 through 92 Processing helix chain 'R' and resid 102 through 111 Processing helix chain 'R' and resid 118 through 129 Processing helix chain 'R' and resid 138 through 145 removed outlier: 3.732A pdb=" N GLN R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 163 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= F, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= G, first strand: chain 'B' and resid 163 through 165 Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= K, first strand: chain 'C' and resid 163 through 165 Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 8 through 12 Processing sheet with id= N, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= O, first strand: chain 'D' and resid 163 through 165 Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 8 through 12 Processing sheet with id= R, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= S, first strand: chain 'E' and resid 163 through 165 Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'P' and resid 45 through 47 removed outlier: 9.662A pdb=" N VAL P 52 " --> pdb=" O PRO P 590 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR P 592 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER P 54 " --> pdb=" O TYR P 592 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG P 594 " --> pdb=" O SER P 54 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 286 through 289 Processing sheet with id= W, first strand: chain 'P' and resid 326 through 329 Processing sheet with id= X, first strand: chain 'P' and resid 509 through 513 Processing sheet with id= Y, first strand: chain 'P' and resid 634 through 637 removed outlier: 3.541A pdb=" N PHE P 686 " --> pdb=" O SER P 679 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'R' and resid 99 through 101 809 hydrogen bonds defined for protein. 2202 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: 6.77 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3628 1.28 - 1.42: 5366 1.42 - 1.56: 12233 1.56 - 1.69: 24 1.69 - 1.83: 217 Bond restraints: 21468 Sorted by residual: bond pdb=" CA ALA F 1 " pdb=" C ALA F 1 " ideal model delta sigma weight residual 1.525 1.318 0.207 2.10e-02 2.27e+03 9.67e+01 bond pdb=" NE1 TRP F 6 " pdb=" CE2 TRP F 6 " ideal model delta sigma weight residual 1.370 1.294 0.076 1.10e-02 8.26e+03 4.82e+01 bond pdb=" CA TRP F 6 " pdb=" C TRP F 6 " ideal model delta sigma weight residual 1.525 1.384 0.141 2.10e-02 2.27e+03 4.53e+01 bond pdb=" CA ALA F 5 " pdb=" C ALA F 5 " ideal model delta sigma weight residual 1.525 1.386 0.139 2.10e-02 2.27e+03 4.38e+01 bond pdb=" CD1 TRP F 6 " pdb=" NE1 TRP F 6 " ideal model delta sigma weight residual 1.374 1.236 0.138 2.10e-02 2.27e+03 4.35e+01 ... (remaining 21463 not shown) Histogram of bond angle deviations from ideal: 95.16 - 104.43: 404 104.43 - 113.71: 11727 113.71 - 122.98: 15234 122.98 - 132.25: 1585 132.25 - 141.52: 50 Bond angle restraints: 29000 Sorted by residual: angle pdb=" CA DCY F 3 " pdb=" C DCY F 3 " pdb=" N HYP F 4 " ideal model delta sigma weight residual 116.20 141.52 -25.32 2.00e+00 2.50e-01 1.60e+02 angle pdb=" CA DCY F 3 " pdb=" C DCY F 3 " pdb=" O DCY F 3 " ideal model delta sigma weight residual 120.80 104.70 16.10 1.70e+00 3.46e-01 8.97e+01 angle pdb=" O 2TL F 2 " pdb=" C 2TL F 2 " pdb=" N DCY F 3 " ideal model delta sigma weight residual 123.00 109.40 13.60 1.60e+00 3.91e-01 7.23e+01 angle pdb=" N TRP F 6 " pdb=" CA TRP F 6 " pdb=" CB TRP F 6 " ideal model delta sigma weight residual 110.50 98.65 11.85 1.70e+00 3.46e-01 4.86e+01 angle pdb=" CA DCY F 3 " pdb=" CB DCY F 3 " pdb=" SG DCY F 3 " ideal model delta sigma weight residual 114.40 130.36 -15.96 2.30e+00 1.89e-01 4.82e+01 ... (remaining 28995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.93: 12360 26.93 - 53.86: 261 53.86 - 80.78: 27 80.78 - 107.71: 1 107.71 - 134.64: 5 Dihedral angle restraints: 12654 sinusoidal: 5073 harmonic: 7581 Sorted by residual: dihedral pdb=" CA DCY F 3 " pdb=" C DCY F 3 " pdb=" N HYP F 4 " pdb=" CA HYP F 4 " ideal model delta harmonic sigma weight residual -180.00 -112.33 -67.67 0 5.00e+00 4.00e-02 1.83e+02 dihedral pdb=" CA 2TL F 2 " pdb=" C 2TL F 2 " pdb=" N DCY F 3 " pdb=" CA DCY F 3 " ideal model delta harmonic sigma weight residual 180.00 115.30 64.70 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CA HIS P 436 " pdb=" C HIS P 436 " pdb=" N ILE P 437 " pdb=" CA ILE P 437 " ideal model delta harmonic sigma weight residual -180.00 -145.76 -34.24 0 5.00e+00 4.00e-02 4.69e+01 ... (remaining 12651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.324: 3076 0.324 - 0.648: 10 0.648 - 0.972: 0 0.972 - 1.295: 0 1.295 - 1.619: 1 Chirality restraints: 3087 Sorted by residual: chirality pdb=" CA DCY F 3 " pdb=" N DCY F 3 " pdb=" C DCY F 3 " pdb=" CB DCY F 3 " both_signs ideal model delta sigma weight residual False -2.51 -0.89 -1.62 2.00e-01 2.50e+01 6.56e+01 chirality pdb=" CA 2TL F 2 " pdb=" N 2TL F 2 " pdb=" C 2TL F 2 " pdb=" CB 2TL F 2 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" CA ALA F 5 " pdb=" N ALA F 5 " pdb=" C ALA F 5 " pdb=" CB ALA F 5 " both_signs ideal model delta sigma weight residual False 2.48 1.98 0.50 2.00e-01 2.50e+01 6.26e+00 ... (remaining 3084 not shown) Planarity restraints: 3810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 6 " -0.148 2.00e-02 2.50e+03 1.26e-01 3.96e+02 pdb=" CG TRP F 6 " 0.166 2.00e-02 2.50e+03 pdb=" CD1 TRP F 6 " -0.193 2.00e-02 2.50e+03 pdb=" CD2 TRP F 6 " 0.071 2.00e-02 2.50e+03 pdb=" NE1 TRP F 6 " 0.097 2.00e-02 2.50e+03 pdb=" CE2 TRP F 6 " 0.137 2.00e-02 2.50e+03 pdb=" CE3 TRP F 6 " 0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 6 " -0.045 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 6 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 6 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 332 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C PRO E 332 " -0.047 2.00e-02 2.50e+03 pdb=" O PRO E 332 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO E 333 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 332 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C PRO B 332 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO B 332 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO B 333 " -0.016 2.00e-02 2.50e+03 ... (remaining 3807 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 7 2.26 - 2.92: 8595 2.92 - 3.58: 30297 3.58 - 4.24: 52748 4.24 - 4.90: 86122 Nonbonded interactions: 177769 Sorted by model distance: nonbonded pdb=" SG DCY F 3 " pdb=" CD1 TRP F 6 " model vdw 1.605 3.620 nonbonded pdb=" CD LYS A 238 " pdb=" NH1 ARG A 254 " model vdw 1.823 3.520 nonbonded pdb=" CD LYS B 238 " pdb=" NH1 ARG B 254 " model vdw 1.824 3.520 nonbonded pdb=" SG DCY F 3 " pdb=" NE1 TRP F 6 " model vdw 2.078 2.880 nonbonded pdb=" NH2 ARG P 231 " pdb=" OE2 GLU P 305 " model vdw 2.093 2.520 ... (remaining 177764 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' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.280 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 55.090 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.010 0.207 21468 Z= 0.680 Angle : 1.217 25.321 29000 Z= 0.670 Chirality : 0.077 1.619 3087 Planarity : 0.008 0.126 3810 Dihedral : 11.595 134.637 7930 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.06 % Allowed : 4.24 % Favored : 94.71 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.37 (0.12), residues: 2738 helix: -2.91 (0.10), residues: 1215 sheet: -2.84 (0.21), residues: 400 loop : -2.67 (0.15), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.193 0.010 TRP F 6 HIS 0.029 0.004 HIS A 161 PHE 0.041 0.004 PHE P 415 TYR 0.026 0.003 TYR P 389 ARG 0.009 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 351 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.7555 (tpt) cc_final: 0.7215 (tpt) REVERT: D 263 GLN cc_start: 0.7984 (tt0) cc_final: 0.7723 (tt0) REVERT: D 325 MET cc_start: 0.7639 (mmp) cc_final: 0.7281 (mmt) outliers start: 23 outliers final: 4 residues processed: 373 average time/residue: 0.3897 time to fit residues: 210.4101 Evaluate side-chains 165 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 246 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 40 HIS A 73 HIS A 115 ASN A 121 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 40 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN C 12 ASN C 59 GLN C 73 HIS C 115 ASN C 128 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 40 HIS D 73 HIS D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN E 12 ASN E 40 HIS E 73 HIS E 115 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 ASN P 42 ASN P 83 HIS P 137 GLN P 293 ASN P 375 GLN ** P 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 442 ASN P 454 ASN ** P 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 584 ASN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 614 HIS P 624 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21468 Z= 0.199 Angle : 0.662 17.522 29000 Z= 0.337 Chirality : 0.045 0.592 3087 Planarity : 0.005 0.042 3810 Dihedral : 8.958 127.623 3079 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.39 % Allowed : 8.15 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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: -2.32 (0.15), residues: 2738 helix: -0.84 (0.14), residues: 1228 sheet: -2.25 (0.23), residues: 381 loop : -1.93 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 434 HIS 0.009 0.001 HIS C 161 PHE 0.012 0.001 PHE E 90 TYR 0.012 0.001 TYR P 389 ARG 0.007 0.001 ARG P 688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.7433 (tmm) cc_final: 0.6788 (tmm) REVERT: C 325 MET cc_start: 0.6953 (mmm) cc_final: 0.6740 (mmt) REVERT: E 40 HIS cc_start: 0.6901 (OUTLIER) cc_final: 0.6620 (p-80) outliers start: 52 outliers final: 29 residues processed: 233 average time/residue: 0.3156 time to fit residues: 115.0596 Evaluate side-chains 174 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 266 optimal weight: 40.0000 chunk 219 optimal weight: 6.9990 chunk 244 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 197 optimal weight: 0.4980 overall best weight: 2.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN B 128 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 ASN P 408 ASN ** P 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 454 ASN ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21468 Z= 0.343 Angle : 0.678 14.300 29000 Z= 0.344 Chirality : 0.046 0.506 3087 Planarity : 0.004 0.039 3810 Dihedral : 8.630 118.946 3079 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.95 % Allowed : 9.53 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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 (0.16), residues: 2738 helix: 0.26 (0.15), residues: 1201 sheet: -2.26 (0.23), residues: 416 loop : -1.52 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 434 HIS 0.017 0.002 HIS E 40 PHE 0.013 0.002 PHE P 176 TYR 0.013 0.001 TYR P 58 ARG 0.009 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 143 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6497 (p90) REVERT: A 47 MET cc_start: 0.7021 (tpp) cc_final: 0.6616 (tpp) REVERT: B 40 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7309 (p90) outliers start: 64 outliers final: 33 residues processed: 199 average time/residue: 0.2747 time to fit residues: 91.3787 Evaluate side-chains 165 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 243 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 247 optimal weight: 9.9990 chunk 261 optimal weight: 50.0000 chunk 129 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 12 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 413 GLN ** P 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21468 Z= 0.360 Angle : 0.680 10.921 29000 Z= 0.346 Chirality : 0.046 0.331 3087 Planarity : 0.004 0.039 3810 Dihedral : 8.153 113.500 3079 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.76 % Allowed : 9.67 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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: -0.84 (0.16), residues: 2738 helix: 0.59 (0.15), residues: 1239 sheet: -2.09 (0.24), residues: 409 loop : -1.17 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P 434 HIS 0.007 0.001 HIS P 221 PHE 0.015 0.002 PHE P 176 TYR 0.013 0.001 TYR A 188 ARG 0.006 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 130 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6741 (p90) REVERT: C 40 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7295 (p90) outliers start: 60 outliers final: 37 residues processed: 178 average time/residue: 0.2629 time to fit residues: 80.2644 Evaluate side-chains 164 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 218 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 424 GLN P 488 HIS ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21468 Z= 0.175 Angle : 0.588 8.734 29000 Z= 0.293 Chirality : 0.043 0.267 3087 Planarity : 0.003 0.034 3810 Dihedral : 7.573 108.374 3079 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.16 % Allowed : 10.59 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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: -0.32 (0.16), residues: 2738 helix: 0.96 (0.15), residues: 1233 sheet: -1.70 (0.24), residues: 391 loop : -0.88 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P 434 HIS 0.004 0.001 HIS P 221 PHE 0.010 0.001 PHE P 176 TYR 0.008 0.001 TYR B 143 ARG 0.004 0.000 ARG P 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 141 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 29 residues processed: 182 average time/residue: 0.2870 time to fit residues: 87.6128 Evaluate side-chains 163 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 88 optimal weight: 0.0970 chunk 235 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 262 optimal weight: 0.3980 chunk 217 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21468 Z= 0.163 Angle : 0.579 8.386 29000 Z= 0.287 Chirality : 0.043 0.262 3087 Planarity : 0.003 0.035 3810 Dihedral : 7.337 104.476 3078 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.80 % Allowed : 10.82 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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: -0.10 (0.17), residues: 2738 helix: 1.14 (0.15), residues: 1229 sheet: -1.48 (0.25), residues: 386 loop : -0.82 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP P 434 HIS 0.008 0.001 HIS C 40 PHE 0.009 0.001 PHE P 176 TYR 0.012 0.001 TYR C 143 ARG 0.009 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6312 (pp30) outliers start: 39 outliers final: 26 residues processed: 172 average time/residue: 0.2977 time to fit residues: 86.7457 Evaluate side-chains 158 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 252 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 261 optimal weight: 30.0000 chunk 163 optimal weight: 10.0000 chunk 159 optimal weight: 0.0980 chunk 120 optimal weight: 0.4980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 250 ASN ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 21468 Z= 0.470 Angle : 0.730 12.211 29000 Z= 0.369 Chirality : 0.048 0.307 3087 Planarity : 0.004 0.034 3810 Dihedral : 7.857 111.677 3078 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.35 % Allowed : 10.77 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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: -0.30 (0.16), residues: 2738 helix: 0.89 (0.15), residues: 1244 sheet: -1.56 (0.25), residues: 381 loop : -0.83 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 434 HIS 0.016 0.001 HIS B 40 PHE 0.017 0.002 PHE P 176 TYR 0.014 0.002 TYR C 143 ARG 0.015 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 127 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.6916 (p90) REVERT: B 40 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7517 (p90) REVERT: E 299 MET cc_start: 0.6767 (ppp) cc_final: 0.6367 (ppp) outliers start: 51 outliers final: 32 residues processed: 173 average time/residue: 0.2811 time to fit residues: 82.2817 Evaluate side-chains 155 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 526 PHE Chi-restraints excluded: chain P residue 613 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 161 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 78 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 115 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21468 Z= 0.161 Angle : 0.595 12.319 29000 Z= 0.292 Chirality : 0.043 0.252 3087 Planarity : 0.003 0.034 3810 Dihedral : 7.331 108.390 3078 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.80 % Allowed : 11.92 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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: 0.12 (0.17), residues: 2738 helix: 1.43 (0.16), residues: 1191 sheet: -1.33 (0.25), residues: 391 loop : -0.78 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 434 HIS 0.006 0.001 HIS B 40 PHE 0.014 0.001 PHE P 263 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: E 299 MET cc_start: 0.6652 (ppp) cc_final: 0.6238 (ppp) outliers start: 39 outliers final: 30 residues processed: 162 average time/residue: 0.2661 time to fit residues: 73.4453 Evaluate side-chains 152 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 237 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 chunk 228 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21468 Z= 0.274 Angle : 0.627 13.142 29000 Z= 0.309 Chirality : 0.044 0.261 3087 Planarity : 0.003 0.034 3810 Dihedral : 7.291 107.793 3078 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.80 % Allowed : 11.83 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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: 0.11 (0.17), residues: 2738 helix: 1.33 (0.15), residues: 1230 sheet: -1.38 (0.25), residues: 391 loop : -0.73 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.011 0.001 HIS E 40 PHE 0.011 0.001 PHE P 176 TYR 0.012 0.001 TYR C 143 ARG 0.009 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: E 299 MET cc_start: 0.6799 (ppp) cc_final: 0.6383 (ppp) outliers start: 39 outliers final: 31 residues processed: 159 average time/residue: 0.2671 time to fit residues: 73.4127 Evaluate side-chains 151 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 159 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 157 optimal weight: 0.0000 chunk 122 optimal weight: 0.0270 chunk 178 optimal weight: 10.0000 chunk 269 optimal weight: 50.0000 chunk 248 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 166 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 overall best weight: 0.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21468 Z= 0.146 Angle : 0.591 12.922 29000 Z= 0.287 Chirality : 0.043 0.228 3087 Planarity : 0.003 0.038 3810 Dihedral : 7.019 103.402 3078 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.43 % Allowed : 12.02 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % 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: 0.24 (0.17), residues: 2738 helix: 1.54 (0.16), residues: 1196 sheet: -1.23 (0.25), residues: 396 loop : -0.76 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 6 HIS 0.014 0.001 HIS A 40 PHE 0.014 0.001 PHE P 263 TYR 0.011 0.001 TYR P 389 ARG 0.005 0.000 ARG E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6718 (p-80) REVERT: C 107 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: E 299 MET cc_start: 0.6765 (ppp) cc_final: 0.6336 (ppp) outliers start: 31 outliers final: 27 residues processed: 158 average time/residue: 0.2726 time to fit residues: 73.9641 Evaluate side-chains 153 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 170 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.045429 restraints weight = 80299.675| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.18 r_work: 0.2719 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21468 Z= 0.237 Angle : 0.601 11.614 29000 Z= 0.296 Chirality : 0.044 0.239 3087 Planarity : 0.003 0.034 3810 Dihedral : 7.001 102.697 3078 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.57 % Allowed : 12.11 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2738 helix: 1.58 (0.16), residues: 1196 sheet: -1.24 (0.25), residues: 396 loop : -0.74 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 6 HIS 0.006 0.001 HIS B 40 PHE 0.010 0.001 PHE P 176 TYR 0.021 0.001 TYR E 279 ARG 0.008 0.000 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3956.09 seconds wall clock time: 73 minutes 7.02 seconds (4387.02 seconds total)