Starting phenix.real_space_refine (version: dev) on Fri Mar 17 14:26:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2023/6wbf_21588_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2023/6wbf_21588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2023/6wbf_21588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2023/6wbf_21588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2023/6wbf_21588_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbf_21588/03_2023/6wbf_21588_updated.pdb" } resolution = 2.83 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= 0.001 sd= 0.008 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 217": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G GLU 336": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "F" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.09, per 1000 atoms: 0.61 Number of scatterers: 19712 At special positions: 0 Unit cell: (107.73, 108.756, 121.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 21 15.00 O 3381 8.00 N 2912 7.00 C 13321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 407 " - " ASN A 255 " " NAG B 407 " - " ASN B 255 " " NAG C 407 " - " ASN C 255 " " NAG D 407 " - " ASN D 255 " " NAG E 407 " - " ASN E 255 " " NAG F 407 " - " ASN F 255 " " NAG G 407 " - " ASN G 255 " Time building additional restraints: 8.50 Conformation dependent library (CDL) restraints added in 3.0 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 7 sheets defined 63.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 33 through 53 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 109 through 130 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 132 through 161 Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 208 through 235 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 270 through 295 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 305 through 311 removed outlier: 4.013A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 removed outlier: 5.148A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.276A pdb=" N SER A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 33 through 53 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 109 through 130 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 132 through 161 Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 208 through 235 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 270 through 295 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 305 through 311 removed outlier: 4.014A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 341 removed outlier: 5.148A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.277A pdb=" N SER B 357 " --> pdb=" O ASN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 33 through 53 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 109 through 130 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 132 through 161 Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 208 through 235 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 270 through 295 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 305 through 311 removed outlier: 4.013A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 removed outlier: 5.149A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.277A pdb=" N SER C 357 " --> pdb=" O ASN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'D' and resid 3 through 10 Processing helix chain 'D' and resid 33 through 53 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 109 through 130 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 195 through 203 Processing helix chain 'D' and resid 208 through 235 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 270 through 295 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 297 through 300 No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 305 through 311 removed outlier: 4.013A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 341 removed outlier: 5.149A pdb=" N SER D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.276A pdb=" N SER D 357 " --> pdb=" O ASN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'E' and resid 3 through 10 Processing helix chain 'E' and resid 33 through 53 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 100 through 107 Processing helix chain 'E' and resid 109 through 130 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 132 through 161 Processing helix chain 'E' and resid 195 through 203 Processing helix chain 'E' and resid 208 through 235 Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 270 through 295 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 297 through 300 No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 305 through 311 removed outlier: 4.012A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 removed outlier: 5.147A pdb=" N SER E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.276A pdb=" N SER E 357 " --> pdb=" O ASN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 33 through 53 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 130 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 161 Processing helix chain 'F' and resid 195 through 203 Processing helix chain 'F' and resid 208 through 235 Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 270 through 295 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 297 through 300 No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 305 through 311 removed outlier: 4.013A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 removed outlier: 5.148A pdb=" N SER F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.276A pdb=" N SER F 357 " --> pdb=" O ASN F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 369 Processing helix chain 'G' and resid 3 through 10 Processing helix chain 'G' and resid 33 through 53 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 100 through 107 Processing helix chain 'G' and resid 109 through 130 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 132 through 161 Processing helix chain 'G' and resid 195 through 203 Processing helix chain 'G' and resid 208 through 235 Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 270 through 295 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 297 through 300 No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 305 through 311 removed outlier: 4.012A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 341 removed outlier: 5.148A pdb=" N SER G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLU G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.275A pdb=" N SER G 357 " --> pdb=" O ASN G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 369 Processing sheet with id= A, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= B, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= C, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= D, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= E, first strand: chain 'E' and resid 243 through 246 Processing sheet with id= F, first strand: chain 'F' and resid 243 through 246 Processing sheet with id= G, first strand: chain 'G' and resid 243 through 246 1064 hydrogen bonds defined for protein. 3108 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: 6.04 Time building geometry restraints manager: 9.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2895 1.32 - 1.44: 5035 1.44 - 1.57: 12083 1.57 - 1.69: 42 1.69 - 1.81: 91 Bond restraints: 20146 Sorted by residual: bond pdb=" N ASN A 369 " pdb=" CA ASN A 369 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.17e-02 7.31e+03 9.38e+00 bond pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.17e-02 7.31e+03 8.66e+00 bond pdb=" N ASN C 369 " pdb=" CA ASN C 369 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.17e-02 7.31e+03 8.62e+00 bond pdb=" N ASN D 369 " pdb=" CA ASN D 369 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.44e+00 bond pdb=" N ASN G 369 " pdb=" CA ASN G 369 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.11e+00 ... (remaining 20141 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.77: 462 105.77 - 112.83: 11162 112.83 - 119.90: 6767 119.90 - 126.96: 8750 126.96 - 134.03: 187 Bond angle restraints: 27328 Sorted by residual: angle pdb=" C TYR E 10 " pdb=" N VAL E 11 " pdb=" CA VAL E 11 " ideal model delta sigma weight residual 122.77 118.80 3.97 1.05e+00 9.07e-01 1.43e+01 angle pdb=" C TYR B 10 " pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 122.77 118.88 3.89 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C TYR D 10 " pdb=" N VAL D 11 " pdb=" CA VAL D 11 " ideal model delta sigma weight residual 122.77 118.91 3.86 1.05e+00 9.07e-01 1.35e+01 angle pdb=" C TYR F 10 " pdb=" N VAL F 11 " pdb=" CA VAL F 11 " ideal model delta sigma weight residual 122.77 118.91 3.86 1.05e+00 9.07e-01 1.35e+01 angle pdb=" C TYR A 10 " pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 122.77 118.92 3.85 1.05e+00 9.07e-01 1.34e+01 ... (remaining 27323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.69: 11289 29.69 - 59.39: 543 59.39 - 89.08: 32 89.08 - 118.77: 1 118.77 - 148.47: 14 Dihedral angle restraints: 11879 sinusoidal: 4704 harmonic: 7175 Sorted by residual: dihedral pdb=" N1 PTY A 401 " pdb=" C2 PTY A 401 " pdb=" C3 PTY A 401 " pdb=" O11 PTY A 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.14 148.47 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N1 PTY D 401 " pdb=" C2 PTY D 401 " pdb=" C3 PTY D 401 " pdb=" O11 PTY D 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.11 148.44 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N1 PTY B 401 " pdb=" C2 PTY B 401 " pdb=" C3 PTY B 401 " pdb=" O11 PTY B 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.09 148.42 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 11876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2253 0.038 - 0.076: 719 0.076 - 0.114: 228 0.114 - 0.152: 41 0.152 - 0.191: 14 Chirality restraints: 3255 Sorted by residual: chirality pdb=" CA ILE E 373 " pdb=" N ILE E 373 " pdb=" C ILE E 373 " pdb=" CB ILE E 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ILE D 373 " pdb=" N ILE D 373 " pdb=" C ILE D 373 " pdb=" CB ILE D 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA ILE A 373 " pdb=" N ILE A 373 " pdb=" C ILE A 373 " pdb=" CB ILE A 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 3252 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 407 " -0.090 2.00e-02 2.50e+03 7.40e-02 6.84e+01 pdb=" C7 NAG G 407 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG G 407 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG G 407 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG G 407 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 407 " 0.090 2.00e-02 2.50e+03 7.39e-02 6.84e+01 pdb=" C7 NAG F 407 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG F 407 " 0.069 2.00e-02 2.50e+03 pdb=" N2 NAG F 407 " -0.117 2.00e-02 2.50e+03 pdb=" O7 NAG F 407 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 407 " -0.090 2.00e-02 2.50e+03 7.39e-02 6.82e+01 pdb=" C7 NAG B 407 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG B 407 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG B 407 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG B 407 " 0.016 2.00e-02 2.50e+03 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1404 2.73 - 3.27: 20995 3.27 - 3.81: 33355 3.81 - 4.36: 39895 4.36 - 4.90: 68982 Nonbonded interactions: 164631 Sorted by model distance: nonbonded pdb=" O LEU A 52 " pdb=" OH TYR G 111 " model vdw 2.183 2.440 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.184 2.440 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.190 2.440 nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.193 2.440 ... (remaining 164626 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' selection = chain 'F' selection = chain 'G' } 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: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 77 5.16 5 C 13321 2.51 5 N 2912 2.21 5 O 3381 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.680 Check model and map are aligned: 0.250 Process input model: 51.970 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 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 : 0.007 0.049 20146 Z= 0.440 Angle : 0.826 10.089 27328 Z= 0.455 Chirality : 0.043 0.191 3255 Planarity : 0.005 0.074 3178 Dihedral : 17.101 148.466 7175 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.38 % 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: -1.45 (0.16), residues: 2380 helix: -0.08 (0.12), residues: 1603 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 777 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 517 time to evaluate : 2.197 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 521 average time/residue: 0.9530 time to fit residues: 564.8606 Evaluate side-chains 324 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 138 optimal weight: 8.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 89 GLN A 90 GLN A 92 ASN A 353 ASN B 76 GLN B 89 GLN C 76 GLN C 89 GLN C 90 GLN C 92 ASN C 134 HIS D 76 GLN D 89 GLN D 90 GLN D 92 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN E 76 GLN E 89 GLN E 100 ASN E 326 ASN F 76 GLN F 90 GLN F 326 ASN F 353 ASN G 76 GLN G 89 GLN G 90 GLN G 134 HIS G 326 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2775 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: