Starting phenix.real_space_refine on Sun Feb 18 06:06:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1h_7331/02_2024/6c1h_7331_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1h_7331/02_2024/6c1h_7331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1h_7331/02_2024/6c1h_7331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1h_7331/02_2024/6c1h_7331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1h_7331/02_2024/6c1h_7331_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1h_7331/02_2024/6c1h_7331_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 126 5.16 5 C 13105 2.51 5 N 3625 2.21 5 O 4095 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 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 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 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 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 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 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 389": "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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20966 Number of models: 1 Model: "" Number of chains: 12 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': 8, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 697} 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: "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} Time building chain proxies: 10.78, per 1000 atoms: 0.51 Number of scatterers: 20966 At special positions: 0 Unit cell: (202.8, 109.2, 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 126 16.00 P 10 15.00 Mg 5 11.99 O 4095 8.00 N 3625 7.00 C 13105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.32 Conformation dependent library (CDL) restraints added in 4.0 seconds 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 26 sheets defined 43.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 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: 3.972A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.926A 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 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.811A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.720A 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: 3.800A 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: 5.496A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.029A 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: 3.972A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.927A 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 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.811A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.720A 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: 3.801A 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: 5.497A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.029A 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: 3.973A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.928A 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 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.811A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.719A 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: 3.801A 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: 5.497A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.029A 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: 3.973A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.927A 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 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.811A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.720A 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: 3.801A 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: 5.496A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.029A 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: 3.973A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.927A 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 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.811A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 320 removed outlier: 3.720A 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: 3.801A 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: 5.497A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 22 No H-bonds generated for 'chain 'P' and resid 20 through 22' Processing helix chain 'P' and resid 28 through 40 removed outlier: 3.542A pdb=" N ASP P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'P' and resid 66 through 72 removed outlier: 3.713A pdb=" N GLU P 70 " --> pdb=" O PRO P 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 96 removed outlier: 3.759A pdb=" N ARG P 93 " --> pdb=" O ASP P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 128 Processing helix chain 'P' and resid 132 through 153 removed outlier: 3.513A pdb=" N GLN P 141 " --> pdb=" O GLN P 137 " (cutoff:3.500A) Proline residue: P 147 - end of helix removed outlier: 3.631A pdb=" N PHE P 152 " --> pdb=" O VAL P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 196 removed outlier: 3.772A pdb=" N VAL P 196 " --> pdb=" O SER P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 214 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 247 through 261 removed outlier: 3.645A pdb=" N ARG P 252 " --> pdb=" O ALA P 248 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 283 removed outlier: 4.263A pdb=" N GLY P 282 " --> pdb=" O VAL P 278 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN P 283 " --> pdb=" O LEU P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 313 Processing helix chain 'P' and resid 317 through 325 removed outlier: 3.835A pdb=" N SER P 325 " --> pdb=" O GLU P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 342 through 372 removed outlier: 3.803A pdb=" N GLU P 370 " --> pdb=" O ASN P 366 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER P 371 " --> pdb=" O ARG P 367 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE P 372 " --> pdb=" O ILE P 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 399 through 429 Processing helix chain 'P' and resid 443 through 450 Processing helix chain 'P' and resid 456 through 465 Processing helix chain 'P' and resid 472 through 482 Processing helix chain 'P' and resid 526 through 530 Processing helix chain 'P' and resid 536 through 544 Processing helix chain 'P' and resid 548 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 570 through 586 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 644 Processing helix chain 'P' and resid 646 through 648 No H-bonds generated for 'chain 'P' and resid 646 through 648' Processing helix chain 'P' and resid 660 through 671 Processing helix chain 'P' and resid 675 through 677 No H-bonds generated for 'chain 'P' and resid 675 through 677' Processing helix chain 'P' and resid 690 through 730 removed outlier: 4.178A pdb=" N GLU P 705 " --> pdb=" O LYS P 701 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP P 706 " --> pdb=" O GLN P 702 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 18 removed outlier: 4.047A pdb=" N GLU R 11 " --> pdb=" O GLU R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 38 removed outlier: 3.715A pdb=" N MET R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 55 removed outlier: 3.961A pdb=" N VAL R 55 " --> pdb=" O MET R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 78 removed outlier: 4.796A pdb=" N LYS R 77 " --> pdb=" O ALA R 73 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASP R 78 " --> pdb=" O ARG R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 92 removed outlier: 3.675A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 111 Processing helix chain 'R' and resid 118 through 128 Processing helix chain 'R' and resid 141 through 145 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 48 removed outlier: 9.799A pdb=" N VAL P 52 " --> pdb=" O PRO P 590 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR P 592 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER P 54 " --> pdb=" O TYR P 592 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG P 594 " --> pdb=" O SER P 54 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY P 108 " --> pdb=" O ILE P 388 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP P 175 " --> pdb=" O PRO P 180 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 286 through 289 removed outlier: 4.691A pdb=" N GLU P 297 " --> pdb=" O GLU P 289 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 326 through 330 Processing sheet with id= X, first strand: chain 'P' and resid 509 through 514 Processing sheet with id= Y, first strand: chain 'P' and resid 634 through 637 Processing sheet with id= Z, first strand: chain 'R' and resid 99 through 101 825 hydrogen bonds defined for protein. 2262 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: 6.45 Time building geometry restraints manager: 8.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5555 1.33 - 1.45: 3841 1.45 - 1.57: 11755 1.57 - 1.69: 15 1.69 - 1.81: 216 Bond restraints: 21382 Sorted by residual: bond pdb=" CA PRO P 568 " pdb=" C PRO P 568 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.44e+00 bond pdb=" C SER P 81 " pdb=" N PRO P 82 " ideal model delta sigma weight residual 1.331 1.359 -0.028 1.20e-02 6.94e+03 5.43e+00 bond pdb=" N LYS P 495 " pdb=" CA LYS P 495 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.31e+00 bond pdb=" C PRO P 568 " pdb=" N THR P 569 " ideal model delta sigma weight residual 1.329 1.359 -0.030 1.40e-02 5.10e+03 4.64e+00 bond pdb=" CA ARG D 95 " pdb=" CB ARG D 95 " ideal model delta sigma weight residual 1.533 1.506 0.028 1.37e-02 5.33e+03 4.10e+00 ... (remaining 21377 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.95: 542 105.95 - 113.47: 11434 113.47 - 120.99: 10655 120.99 - 128.51: 6102 128.51 - 136.03: 142 Bond angle restraints: 28875 Sorted by residual: angle pdb=" C SER P 494 " pdb=" N LYS P 495 " pdb=" CA LYS P 495 " ideal model delta sigma weight residual 121.70 133.98 -12.28 1.80e+00 3.09e-01 4.65e+01 angle pdb=" N ILE B 289 " pdb=" CA ILE B 289 " pdb=" C ILE B 289 " ideal model delta sigma weight residual 113.53 107.52 6.01 9.80e-01 1.04e+00 3.77e+01 angle pdb=" N ILE D 289 " pdb=" CA ILE D 289 " pdb=" C ILE D 289 " ideal model delta sigma weight residual 113.53 107.54 5.99 9.80e-01 1.04e+00 3.74e+01 angle pdb=" N ILE C 289 " pdb=" CA ILE C 289 " pdb=" C ILE C 289 " ideal model delta sigma weight residual 113.53 107.54 5.99 9.80e-01 1.04e+00 3.73e+01 angle pdb=" N ILE E 289 " pdb=" CA ILE E 289 " pdb=" C ILE E 289 " ideal model delta sigma weight residual 113.53 107.55 5.98 9.80e-01 1.04e+00 3.73e+01 ... (remaining 28870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.67: 12381 25.67 - 51.33: 207 51.33 - 77.00: 13 77.00 - 102.66: 1 102.66 - 128.33: 5 Dihedral angle restraints: 12607 sinusoidal: 5042 harmonic: 7565 Sorted by residual: dihedral pdb=" CA ASN P 563 " pdb=" C ASN P 563 " pdb=" N LEU P 564 " pdb=" CA LEU P 564 " ideal model delta harmonic sigma weight residual 180.00 133.51 46.49 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA ARG P 629 " pdb=" C ARG P 629 " pdb=" N ALA P 630 " pdb=" CA ALA P 630 " ideal model delta harmonic sigma weight residual -180.00 -137.41 -42.59 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA LEU P 564 " pdb=" C LEU P 564 " pdb=" N LYS P 565 " pdb=" CA LYS P 565 " ideal model delta harmonic sigma weight residual 180.00 143.63 36.37 0 5.00e+00 4.00e-02 5.29e+01 ... (remaining 12604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2099 0.051 - 0.101: 740 0.101 - 0.152: 173 0.152 - 0.203: 50 0.203 - 0.253: 11 Chirality restraints: 3073 Sorted by residual: chirality pdb=" CB ILE P 404 " pdb=" CA ILE P 404 " pdb=" CG1 ILE P 404 " pdb=" CG2 ILE P 404 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE C 71 " pdb=" CA ILE C 71 " pdb=" CG1 ILE C 71 " pdb=" CG2 ILE C 71 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 71 " pdb=" CA ILE A 71 " pdb=" CG1 ILE A 71 " pdb=" CG2 ILE A 71 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3070 not shown) Planarity restraints: 3802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG P 466 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO P 467 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO P 467 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO P 467 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 629 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C ARG P 629 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG P 629 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA P 630 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN P 689 " 0.051 5.00e-02 4.00e+02 7.70e-02 9.49e+00 pdb=" N PRO P 690 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO P 690 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO P 690 " 0.042 5.00e-02 4.00e+02 ... (remaining 3799 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 7 2.27 - 2.93: 8366 2.93 - 3.58: 29563 3.58 - 4.24: 49649 4.24 - 4.90: 81278 Nonbonded interactions: 168863 Sorted by model distance: nonbonded pdb=" CD2 LEU P 142 " pdb=" CE MET P 170 " model vdw 1.611 3.880 nonbonded pdb=" O1A ADP A 401 " pdb="MG MG A 402 " model vdw 2.164 2.170 nonbonded pdb=" O1A ADP C 401 " pdb="MG MG C 402 " model vdw 2.167 2.170 nonbonded pdb=" O1A ADP E 401 " pdb="MG MG E 402 " model vdw 2.185 2.170 nonbonded pdb=" O1A ADP D 401 " pdb="MG MG D 402 " model vdw 2.194 2.170 ... (remaining 168858 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.500 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 56.660 Find NCS groups from input model: 1.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21382 Z= 0.315 Angle : 0.925 12.278 28875 Z= 0.535 Chirality : 0.057 0.253 3073 Planarity : 0.007 0.080 3802 Dihedral : 10.022 128.330 7893 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.15 (0.12), residues: 2738 helix: -2.87 (0.10), residues: 1185 sheet: -2.19 (0.24), residues: 360 loop : -2.66 (0.14), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 340 HIS 0.009 0.001 HIS B 161 PHE 0.020 0.002 PHE P 324 TYR 0.027 0.002 TYR P 47 ARG 0.012 0.001 ARG P 466 *********************** 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 250 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 4.070 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: symmetry clash REVERT: E 190 MET cc_start: 0.8011 (ttp) cc_final: 0.7805 (tmm) REVERT: E 212 ILE cc_start: 0.8868 (mt) cc_final: 0.8640 (tp) REVERT: P 171 ASP cc_start: 0.7756 (m-30) cc_final: 0.7058 (m-30) REVERT: P 211 LEU cc_start: 0.9238 (tp) cc_final: 0.8922 (pp) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.4060 time to fit residues: 152.4588 Evaluate side-chains 143 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 70 optimal weight: 0.3980 chunk 138 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 73 HIS A 128 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 73 HIS B 128 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS C 40 HIS C 73 HIS C 128 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 12 ASN D 40 HIS D 73 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS E 12 ASN E 40 HIS E 73 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS P 83 HIS P 102 GLN P 136 ASN P 144 GLN ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 ASN P 317 GLN P 355 ASN P 366 ASN P 408 ASN P 442 ASN P 486 HIS P 507 HIS P 563 ASN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 624 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 21382 Z= 0.389 Angle : 0.766 9.110 28875 Z= 0.391 Chirality : 0.045 0.149 3073 Planarity : 0.005 0.057 3802 Dihedral : 7.410 117.461 3039 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.66 % Allowed : 6.73 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % 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: -2.04 (0.15), residues: 2738 helix: -0.53 (0.14), residues: 1262 sheet: -1.79 (0.26), residues: 395 loop : -2.06 (0.17), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 86 HIS 0.010 0.002 HIS E 161 PHE 0.021 0.002 PHE P 31 TYR 0.017 0.002 TYR P 347 ARG 0.005 0.001 ARG P 628 *********************** 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 168 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.7326 (t0) cc_final: 0.7107 (t0) REVERT: B 132 MET cc_start: 0.8136 (tmm) cc_final: 0.7740 (tmm) REVERT: C 132 MET cc_start: 0.8476 (tmm) cc_final: 0.7977 (tmm) REVERT: C 305 MET cc_start: 0.7831 (mpp) cc_final: 0.7164 (mpp) REVERT: E 227 MET cc_start: 0.8803 (mmm) cc_final: 0.8594 (mmm) REVERT: P 493 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7253 (mmp) outliers start: 36 outliers final: 12 residues processed: 163 average time/residue: 0.3328 time to fit residues: 84.9445 Evaluate side-chains 136 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 493 MET Chi-restraints excluded: chain P residue 499 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 67 optimal weight: 0.0980 chunk 246 optimal weight: 10.0000 chunk 266 optimal weight: 50.0000 chunk 219 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 136 ASN ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21382 Z= 0.276 Angle : 0.676 10.903 28875 Z= 0.337 Chirality : 0.043 0.145 3073 Planarity : 0.004 0.073 3802 Dihedral : 6.944 114.571 3039 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 1.43 % Allowed : 7.83 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.13 (0.16), residues: 2738 helix: 0.40 (0.14), residues: 1238 sheet: -1.67 (0.26), residues: 388 loop : -1.66 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.007 0.001 HIS B 161 PHE 0.016 0.001 PHE A 375 TYR 0.016 0.001 TYR P 47 ARG 0.006 0.000 ARG C 335 *********************** 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 150 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.5315 (pmm) cc_final: 0.4946 (pmm) REVERT: C 227 MET cc_start: 0.9066 (mmm) cc_final: 0.8796 (mmm) REVERT: E 47 MET cc_start: 0.7201 (mmm) cc_final: 0.6148 (mmm) REVERT: E 132 MET cc_start: 0.8684 (tmm) cc_final: 0.8065 (tmm) outliers start: 31 outliers final: 10 residues processed: 146 average time/residue: 0.3620 time to fit residues: 81.8009 Evaluate side-chains 125 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain P residue 499 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 243 optimal weight: 6.9990 chunk 185 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 261 optimal weight: 50.0000 chunk 129 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 280 ASN C 280 ASN D 263 GLN D 280 ASN E 128 ASN E 353 GLN ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 21382 Z= 0.362 Angle : 0.716 8.649 28875 Z= 0.361 Chirality : 0.043 0.142 3073 Planarity : 0.004 0.073 3802 Dihedral : 6.721 110.655 3039 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 0.97 % Allowed : 9.44 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % 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: -0.85 (0.16), residues: 2738 helix: 0.66 (0.15), residues: 1238 sheet: -1.79 (0.25), residues: 388 loop : -1.45 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 363 HIS 0.010 0.002 HIS B 161 PHE 0.015 0.002 PHE D 266 TYR 0.024 0.002 TYR P 169 ARG 0.009 0.001 ARG P 566 *********************** 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 138 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.7992 (mpp) cc_final: 0.7482 (mpp) REVERT: C 227 MET cc_start: 0.8968 (mmm) cc_final: 0.8708 (mmm) REVERT: C 261 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9008 (tt) outliers start: 21 outliers final: 9 residues processed: 134 average time/residue: 0.3380 time to fit residues: 71.8044 Evaluate side-chains 120 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 499 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 218 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 235 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** P 206 HIS ** 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: 0.8135 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21382 Z= 0.264 Angle : 0.655 13.306 28875 Z= 0.324 Chirality : 0.042 0.144 3073 Planarity : 0.004 0.082 3802 Dihedral : 6.489 105.980 3039 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.30 % Rotamer: Outliers : 1.11 % Allowed : 10.09 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % 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: -0.36 (0.17), residues: 2738 helix: 1.10 (0.15), residues: 1208 sheet: -1.79 (0.25), residues: 388 loop : -1.07 (0.20), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 79 HIS 0.008 0.001 HIS B 161 PHE 0.009 0.001 PHE E 90 TYR 0.016 0.001 TYR P 169 ARG 0.010 0.000 ARG P 566 *********************** 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 137 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.8092 (mpp) cc_final: 0.7615 (mpp) REVERT: C 227 MET cc_start: 0.8950 (mmm) cc_final: 0.8669 (mmm) REVERT: C 305 MET cc_start: 0.7558 (mpp) cc_final: 0.6923 (mpp) REVERT: E 123 MET cc_start: 0.7685 (mmp) cc_final: 0.7484 (mmp) REVERT: E 132 MET cc_start: 0.8667 (tmm) cc_final: 0.8114 (tmm) REVERT: P 533 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8419 (pt) outliers start: 24 outliers final: 9 residues processed: 133 average time/residue: 0.3028 time to fit residues: 66.6267 Evaluate side-chains 118 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 88 optimal weight: 0.6980 chunk 235 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 153 optimal weight: 0.0270 chunk 64 optimal weight: 0.1980 chunk 262 optimal weight: 0.0770 chunk 217 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 HIS P 250 ASN ** 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: 0.8045 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21382 Z= 0.140 Angle : 0.631 13.316 28875 Z= 0.306 Chirality : 0.042 0.158 3073 Planarity : 0.004 0.047 3802 Dihedral : 6.054 92.731 3039 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.83 % Allowed : 10.73 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % 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: 1.28 (0.15), residues: 1233 sheet: -1.68 (0.25), residues: 389 loop : -0.95 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 340 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE P 31 TYR 0.013 0.001 TYR P 47 ARG 0.008 0.000 ARG C 116 *********************** 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 133 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.4177 (pmm) cc_final: 0.3767 (pmm) REVERT: A 123 MET cc_start: 0.7747 (mmm) cc_final: 0.7466 (tpp) REVERT: C 227 MET cc_start: 0.8896 (mmm) cc_final: 0.8599 (mmm) REVERT: C 305 MET cc_start: 0.7674 (mpp) cc_final: 0.6970 (mpp) REVERT: E 47 MET cc_start: 0.6109 (mmm) cc_final: 0.5898 (mmm) REVERT: E 119 MET cc_start: 0.8760 (ptp) cc_final: 0.8234 (ptp) REVERT: E 132 MET cc_start: 0.8746 (tmm) cc_final: 0.8130 (tmm) REVERT: P 332 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8118 (ptpp) outliers start: 18 outliers final: 6 residues processed: 129 average time/residue: 0.3122 time to fit residues: 66.4818 Evaluate side-chains 118 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 332 LYS Chi-restraints excluded: chain P residue 499 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 252 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 149 optimal weight: 30.0000 chunk 191 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 163 optimal weight: 40.0000 chunk 159 optimal weight: 0.0870 chunk 120 optimal weight: 9.9990 overall best weight: 6.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 136 ASN ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 21382 Z= 0.435 Angle : 0.770 13.385 28875 Z= 0.383 Chirality : 0.044 0.185 3073 Planarity : 0.004 0.078 3802 Dihedral : 6.214 93.523 3039 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 1.15 % Allowed : 11.10 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2738 helix: 1.25 (0.15), residues: 1202 sheet: -1.62 (0.26), residues: 363 loop : -1.00 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 363 HIS 0.010 0.002 HIS C 161 PHE 0.015 0.002 PHE P 526 TYR 0.018 0.002 TYR P 169 ARG 0.012 0.001 ARG P 566 *********************** 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 130 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.4855 (pmm) cc_final: 0.4299 (ptt) REVERT: A 123 MET cc_start: 0.7862 (mmm) cc_final: 0.7557 (tpp) REVERT: B 305 MET cc_start: 0.8252 (mpp) cc_final: 0.7477 (mpp) REVERT: C 227 MET cc_start: 0.8950 (mmm) cc_final: 0.8695 (mmm) REVERT: E 132 MET cc_start: 0.8675 (tmm) cc_final: 0.8307 (tmm) REVERT: E 299 MET cc_start: 0.7394 (ppp) cc_final: 0.7177 (ppp) REVERT: P 533 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8542 (pt) outliers start: 25 outliers final: 15 residues processed: 126 average time/residue: 0.3011 time to fit residues: 63.2524 Evaluate side-chains 121 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 501 ASN Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 161 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 250 ASN ** P 531 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: 0.8155 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21382 Z= 0.251 Angle : 0.692 14.901 28875 Z= 0.336 Chirality : 0.043 0.168 3073 Planarity : 0.004 0.056 3802 Dihedral : 5.987 95.454 3039 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.59 % Favored : 94.38 % Rotamer: Outliers : 0.97 % Allowed : 11.15 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.00 (0.17), residues: 2738 helix: 1.39 (0.15), residues: 1209 sheet: -1.54 (0.26), residues: 359 loop : -0.93 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.010 0.001 HIS B 161 PHE 0.010 0.001 PHE D 262 TYR 0.015 0.001 TYR A 143 ARG 0.007 0.000 ARG P 566 *********************** 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 129 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7778 (mmm) cc_final: 0.7504 (tpp) REVERT: B 305 MET cc_start: 0.8231 (mpp) cc_final: 0.7572 (mpp) REVERT: C 227 MET cc_start: 0.8924 (mmm) cc_final: 0.8633 (mmm) REVERT: C 305 MET cc_start: 0.7744 (mpp) cc_final: 0.7119 (mpp) REVERT: E 132 MET cc_start: 0.8567 (tmm) cc_final: 0.8258 (tmm) REVERT: E 299 MET cc_start: 0.7420 (ppp) cc_final: 0.7078 (ppp) REVERT: P 533 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8546 (pt) outliers start: 21 outliers final: 13 residues processed: 123 average time/residue: 0.3024 time to fit residues: 61.8660 Evaluate side-chains 121 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 501 ASN Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 237 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 136 ASN ** P 154 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: 0.8088 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21382 Z= 0.155 Angle : 0.660 14.479 28875 Z= 0.315 Chirality : 0.043 0.180 3073 Planarity : 0.003 0.054 3802 Dihedral : 5.535 78.887 3039 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.64 % Allowed : 11.52 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2738 helix: 1.62 (0.15), residues: 1203 sheet: -1.38 (0.26), residues: 369 loop : -0.77 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 356 HIS 0.008 0.001 HIS C 161 PHE 0.009 0.001 PHE E 90 TYR 0.015 0.001 TYR A 143 ARG 0.004 0.000 ARG P 566 *********************** 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 125 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7639 (mmm) cc_final: 0.7348 (tpp) REVERT: B 51 ASP cc_start: 0.7998 (p0) cc_final: 0.7755 (p0) REVERT: B 283 MET cc_start: 0.8137 (mmm) cc_final: 0.7696 (mmp) REVERT: C 227 MET cc_start: 0.8891 (mmm) cc_final: 0.8582 (mmm) REVERT: C 305 MET cc_start: 0.7711 (mpp) cc_final: 0.7071 (mpp) REVERT: D 283 MET cc_start: 0.9192 (mmm) cc_final: 0.8945 (mmm) REVERT: E 132 MET cc_start: 0.8695 (tmm) cc_final: 0.8283 (tmm) REVERT: E 299 MET cc_start: 0.7447 (ppp) cc_final: 0.7027 (ppp) REVERT: P 533 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8495 (pt) outliers start: 14 outliers final: 10 residues processed: 119 average time/residue: 0.2963 time to fit residues: 57.9005 Evaluate side-chains 119 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 501 ASN Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 159 optimal weight: 0.4980 chunk 257 optimal weight: 50.0000 chunk 157 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 269 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 21382 Z= 0.411 Angle : 0.784 15.607 28875 Z= 0.386 Chirality : 0.044 0.173 3073 Planarity : 0.005 0.080 3802 Dihedral : 5.768 78.058 3039 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.57 % Favored : 93.39 % Rotamer: Outliers : 0.74 % Allowed : 11.38 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.06 (0.17), residues: 2738 helix: 1.30 (0.15), residues: 1205 sheet: -1.60 (0.25), residues: 364 loop : -0.88 (0.19), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 543 HIS 0.012 0.002 HIS B 161 PHE 0.015 0.002 PHE P 526 TYR 0.026 0.002 TYR A 143 ARG 0.012 0.001 ARG P 566 ********************** 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 123 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7852 (mmm) cc_final: 0.7478 (tpp) REVERT: B 305 MET cc_start: 0.8205 (mpp) cc_final: 0.7537 (mpp) REVERT: C 47 MET cc_start: 0.7626 (ppp) cc_final: 0.7090 (ppp) REVERT: D 355 MET cc_start: 0.8717 (pmm) cc_final: 0.8390 (pmm) REVERT: E 299 MET cc_start: 0.7482 (ppp) cc_final: 0.7027 (ppp) REVERT: P 533 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8350 (pt) outliers start: 16 outliers final: 14 residues processed: 119 average time/residue: 0.3042 time to fit residues: 60.0250 Evaluate side-chains 121 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 501 ASN Chi-restraints excluded: chain P residue 533 LEU 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: 0.8980 chunk 65 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 221 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.029793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.022731 restraints weight = 217534.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.023559 restraints weight = 125349.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.024132 restraints weight = 85126.934| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21382 Z= 0.189 Angle : 0.688 15.929 28875 Z= 0.331 Chirality : 0.043 0.176 3073 Planarity : 0.004 0.062 3802 Dihedral : 5.545 73.160 3039 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.60 % Allowed : 11.61 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % 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: 0.23 (0.17), residues: 2738 helix: 1.55 (0.15), residues: 1201 sheet: -1.42 (0.26), residues: 369 loop : -0.74 (0.20), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP P 543 HIS 0.010 0.001 HIS B 161 PHE 0.011 0.001 PHE E 21 TYR 0.016 0.001 TYR A 143 ARG 0.007 0.000 ARG E 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.30 seconds wall clock time: 60 minutes 24.42 seconds (3624.42 seconds total)