Starting phenix.real_space_refine (version: dev) on Tue Feb 21 08:34:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2023/6plz_20381_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2023/6plz_20381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2023/6plz_20381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2023/6plz_20381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2023/6plz_20381_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2023/6plz_20381_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.062 sd= 2.818 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 Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14210 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.15, per 1000 atoms: 0.57 Number of scatterers: 14210 At special positions: 0 Unit cell: (108.636, 104.521, 134.149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2570 8.00 N 2290 7.00 C 9250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 20 sheets defined 35.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 26 through 33 removed outlier: 3.840A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.653A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 108 " --> pdb=" O MET A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.510A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.780A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.622A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 4.138A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 removed outlier: 3.658A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 426 removed outlier: 3.803A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.834A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 removed outlier: 3.878A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.636A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.512A pdb=" N ILE B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.773A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 284 removed outlier: 3.714A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 324 removed outlier: 4.113A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 426 removed outlier: 3.851A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.757A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 33 removed outlier: 3.895A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.615A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.506A pdb=" N ILE C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.959A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 286 removed outlier: 3.611A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 313 removed outlier: 4.139A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.727A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.836A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.825A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.864A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.651A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.523A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.943A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.674A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 323 removed outlier: 4.092A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 315 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 426 removed outlier: 3.816A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.734A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 33 removed outlier: 3.867A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.670A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.516A pdb=" N ILE E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.858A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 256 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 284 removed outlier: 3.642A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 324 removed outlier: 4.032A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 315 " --> pdb=" O PHE E 311 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 426 removed outlier: 3.861A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.737A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.405A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.696A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= D, first strand: chain 'A' and resid 165 through 168 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.383A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.679A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= H, first strand: chain 'B' and resid 165 through 168 Processing sheet with id= I, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.395A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.697A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= L, first strand: chain 'C' and resid 165 through 168 Processing sheet with id= M, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.412A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.697A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= P, first strand: chain 'D' and resid 165 through 168 Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.367A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.655A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'E' and resid 209 through 213 443 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4315 1.34 - 1.46: 3384 1.46 - 1.58: 6691 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 14560 Sorted by residual: bond pdb=" C2 NAG J 2 " pdb=" C3 NAG J 2 " ideal model delta sigma weight residual 1.526 1.551 -0.025 1.50e-02 4.44e+03 2.74e+00 bond pdb=" C2 NAG H 2 " pdb=" C3 NAG H 2 " ideal model delta sigma weight residual 1.526 1.550 -0.024 1.50e-02 4.44e+03 2.48e+00 bond pdb=" C2 NAG I 2 " pdb=" C3 NAG I 2 " ideal model delta sigma weight residual 1.526 1.550 -0.024 1.50e-02 4.44e+03 2.46e+00 bond pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " ideal model delta sigma weight residual 1.526 1.549 -0.023 1.50e-02 4.44e+03 2.34e+00 bond pdb=" C2 NAG G 2 " pdb=" C3 NAG G 2 " ideal model delta sigma weight residual 1.526 1.549 -0.023 1.50e-02 4.44e+03 2.30e+00 ... (remaining 14555 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.62: 368 105.62 - 112.71: 7491 112.71 - 119.80: 4920 119.80 - 126.89: 6742 126.89 - 133.99: 219 Bond angle restraints: 19740 Sorted by residual: angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.27e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 132.38 -10.84 1.91e+00 2.74e-01 3.22e+01 ... (remaining 19735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 8398 18.10 - 36.20: 265 36.20 - 54.30: 22 54.30 - 72.40: 6 72.40 - 90.49: 19 Dihedral angle restraints: 8710 sinusoidal: 3610 harmonic: 5100 Sorted by residual: dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.49 90.49 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.31 90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " pdb=" SG CYS B 225 " pdb=" CB CYS B 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.23 90.23 1 1.00e+01 1.00e-02 9.64e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1837 0.066 - 0.132: 347 0.132 - 0.198: 51 0.198 - 0.264: 10 0.264 - 0.330: 10 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 54 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 54 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 54 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2252 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 151 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C VAL C 151 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL C 151 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU C 152 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " -0.040 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 411 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.56e+00 pdb=" N PRO D 411 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.033 5.00e-02 4.00e+02 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4611 2.85 - 3.36: 12514 3.36 - 3.88: 22554 3.88 - 4.39: 26593 4.39 - 4.90: 46400 Nonbonded interactions: 112672 Sorted by model distance: nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.338 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.359 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.365 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.369 2.440 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.377 2.440 ... (remaining 112667 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' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9250 2.51 5 N 2290 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.000 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: 8.050 Check model and map are aligned: 0.220 Process input model: 35.910 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 0.006 0.055 14560 Z= 0.357 Angle : 0.942 10.963 19740 Z= 0.518 Chirality : 0.059 0.330 2255 Planarity : 0.007 0.060 2445 Dihedral : 9.681 84.463 5370 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.15), residues: 1705 helix: -4.61 (0.08), residues: 580 sheet: -2.73 (0.20), residues: 425 loop : -2.66 (0.20), residues: 700 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 4 residues processed: 451 average time/residue: 1.2960 time to fit residues: 637.7942 Evaluate side-chains 251 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 247 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.2226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 231 HIS B 141 ASN B 171 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 82 GLN C 171 GLN C 231 HIS D 82 GLN D 141 ASN D 231 HIS E 231 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 14560 Z= 0.247 Angle : 0.714 12.313 19740 Z= 0.373 Chirality : 0.051 0.311 2255 Planarity : 0.005 0.047 2445 Dihedral : 8.496 87.686 2000 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.17), residues: 1705 helix: -3.16 (0.14), residues: 585 sheet: -1.92 (0.23), residues: 420 loop : -2.04 (0.21), residues: 700 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 285 time to evaluate : 1.887 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 13 residues processed: 318 average time/residue: 1.1702 time to fit residues: 411.1868 Evaluate side-chains 238 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 225 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1909 time to fit residues: 3.2016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.0010 chunk 47 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN B 62 ASN B 77 ASN B 82 GLN B 180 ASN C 77 ASN D 62 ASN D 77 ASN E 77 ASN E 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 14560 Z= 0.200 Angle : 0.657 10.199 19740 Z= 0.341 Chirality : 0.049 0.302 2255 Planarity : 0.004 0.030 2445 Dihedral : 8.376 89.904 2000 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.18), residues: 1705 helix: -2.15 (0.17), residues: 585 sheet: -1.52 (0.24), residues: 440 loop : -1.64 (0.23), residues: 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 244 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 17 residues processed: 279 average time/residue: 1.2696 time to fit residues: 390.2681 Evaluate side-chains 233 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 216 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.3649 time to fit residues: 4.5517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN C 62 ASN C 141 ASN E 62 ASN E 77 ASN E 141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 14560 Z= 0.229 Angle : 0.648 11.187 19740 Z= 0.335 Chirality : 0.048 0.297 2255 Planarity : 0.003 0.026 2445 Dihedral : 8.307 90.674 2000 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 4.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.19), residues: 1705 helix: -1.28 (0.20), residues: 590 sheet: -1.19 (0.25), residues: 420 loop : -1.47 (0.23), residues: 695 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 239 time to evaluate : 1.538 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 28 residues processed: 283 average time/residue: 1.1650 time to fit residues: 363.8771 Evaluate side-chains 237 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 7 average time/residue: 0.3164 time to fit residues: 5.1246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN D 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 14560 Z= 0.327 Angle : 0.661 10.031 19740 Z= 0.346 Chirality : 0.049 0.296 2255 Planarity : 0.003 0.033 2445 Dihedral : 8.395 90.685 2000 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 4.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1705 helix: -0.91 (0.20), residues: 595 sheet: -1.21 (0.25), residues: 425 loop : -1.34 (0.23), residues: 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 254 time to evaluate : 1.673 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 41 residues processed: 303 average time/residue: 1.2416 time to fit residues: 414.8022 Evaluate side-chains 271 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 230 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 30 residues processed: 12 average time/residue: 0.6602 time to fit residues: 11.5994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 14560 Z= 0.186 Angle : 0.612 9.068 19740 Z= 0.319 Chirality : 0.047 0.300 2255 Planarity : 0.003 0.026 2445 Dihedral : 8.347 91.253 2000 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 4.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.20), residues: 1705 helix: -0.52 (0.21), residues: 595 sheet: -1.15 (0.25), residues: 415 loop : -1.21 (0.23), residues: 695 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 time to evaluate : 1.596 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 36 residues processed: 281 average time/residue: 1.1795 time to fit residues: 366.4332 Evaluate side-chains 254 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 5 average time/residue: 0.4196 time to fit residues: 5.1277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 75 optimal weight: 0.0770 chunk 101 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 14560 Z= 0.175 Angle : 0.578 8.558 19740 Z= 0.303 Chirality : 0.046 0.294 2255 Planarity : 0.003 0.026 2445 Dihedral : 8.251 91.466 2000 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1705 helix: -0.24 (0.21), residues: 595 sheet: -1.05 (0.25), residues: 415 loop : -1.14 (0.23), residues: 695 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 232 time to evaluate : 1.726 Fit side-chains outliers start: 51 outliers final: 37 residues processed: 269 average time/residue: 1.1897 time to fit residues: 354.2467 Evaluate side-chains 258 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 7 average time/residue: 0.7863 time to fit residues: 8.4497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 0.0570 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 14560 Z= 0.192 Angle : 0.588 8.606 19740 Z= 0.307 Chirality : 0.046 0.295 2255 Planarity : 0.003 0.044 2445 Dihedral : 8.235 91.514 2000 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1705 helix: -0.06 (0.21), residues: 595 sheet: -0.90 (0.26), residues: 415 loop : -1.13 (0.23), residues: 695 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 232 time to evaluate : 1.771 Fit side-chains outliers start: 49 outliers final: 37 residues processed: 272 average time/residue: 1.1498 time to fit residues: 347.7522 Evaluate side-chains 254 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 0.4625 time to fit residues: 5.1025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 0.0370 chunk 144 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14560 Z= 0.163 Angle : 0.560 8.353 19740 Z= 0.294 Chirality : 0.046 0.298 2255 Planarity : 0.003 0.033 2445 Dihedral : 8.182 91.755 2000 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1705 helix: 0.23 (0.22), residues: 590 sheet: -0.75 (0.26), residues: 415 loop : -1.13 (0.23), residues: 700 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 1.704 Fit side-chains outliers start: 42 outliers final: 36 residues processed: 264 average time/residue: 1.2037 time to fit residues: 351.4893 Evaluate side-chains 259 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.3987 time to fit residues: 4.3852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14560 Z= 0.178 Angle : 0.582 13.276 19740 Z= 0.301 Chirality : 0.046 0.296 2255 Planarity : 0.003 0.027 2445 Dihedral : 8.158 91.826 2000 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1705 helix: 0.37 (0.22), residues: 590 sheet: -0.66 (0.26), residues: 415 loop : -1.10 (0.23), residues: 700 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.804 Fit side-chains outliers start: 38 outliers final: 32 residues processed: 259 average time/residue: 1.2272 time to fit residues: 350.3735 Evaluate side-chains 252 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 220 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 0.1823 time to fit residues: 2.6523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 5.9990 chunk 124 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096587 restraints weight = 19013.789| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.19 r_work: 0.2920 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14560 Z= 0.149 Angle : 0.558 12.896 19740 Z= 0.291 Chirality : 0.045 0.298 2255 Planarity : 0.003 0.051 2445 Dihedral : 8.131 92.051 2000 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1705 helix: 0.63 (0.22), residues: 585 sheet: -0.59 (0.26), residues: 415 loop : -1.11 (0.23), residues: 705 =============================================================================== Job complete usr+sys time: 5963.00 seconds wall clock time: 106 minutes 4.08 seconds (6364.08 seconds total)