Starting phenix.real_space_refine on Wed Apr 10 14:02:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/04_2024/6wbg_21589_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/04_2024/6wbg_21589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/04_2024/6wbg_21589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/04_2024/6wbg_21589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/04_2024/6wbg_21589_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/04_2024/6wbg_21589_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 50 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: 50 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: 50 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: 50 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: 50 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: 50 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: 50 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.75, per 1000 atoms: 0.55 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: 7.93 Conformation dependent library (CDL) restraints added in 3.5 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: 3.48 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: 5.600A 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: 5.147A 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: 4.276A 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: 4.014A 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: 5.601A 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: 4.014A 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: 5.148A 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: 4.014A 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: 5.602A pdb=" N GLU F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.277A 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: 4.013A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 341 removed outlier: 5.149A pdb=" N SER G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.276A 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: 5.32 Time building geometry restraints manager: 8.60 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: 2908 1.32 - 1.44: 5034 1.44 - 1.57: 12071 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 -0.035 1.17e-02 7.31e+03 9.16e+00 bond pdb=" N ASN B 369 " pdb=" CA ASN B 369 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.17e-02 7.31e+03 8.74e+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 8.65e+00 bond pdb=" N ASN D 369 " pdb=" CA ASN D 369 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.17e-02 7.31e+03 8.54e+00 bond pdb=" N ASN C 369 " pdb=" CA ASN C 369 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.17e-02 7.31e+03 8.49e+00 ... (remaining 20141 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.73: 462 105.73 - 112.81: 11159 112.81 - 119.89: 6733 119.89 - 126.96: 8786 126.96 - 134.04: 188 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 122.77 118.81 3.96 1.05e+00 9.07e-01 1.42e+01 angle pdb=" C TYR F 10 " pdb=" N VAL F 11 " pdb=" CA VAL F 11 " ideal model delta sigma weight residual 122.77 118.88 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 122.77 118.89 3.88 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C TYR A 10 " pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 122.77 118.91 3.86 1.05e+00 9.07e-01 1.35e+01 angle pdb=" C TYR B 10 " pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 122.77 118.92 3.85 1.05e+00 9.07e-01 1.35e+01 ... (remaining 27323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.68: 12375 29.68 - 59.37: 626 59.37 - 89.05: 32 89.05 - 118.73: 1 118.73 - 148.41: 14 Dihedral angle restraints: 13048 sinusoidal: 5873 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 -83.08 148.41 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N1 PTY E 401 " pdb=" C2 PTY E 401 " pdb=" C3 PTY E 401 " pdb=" O11 PTY E 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.07 148.40 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 -83.06 148.39 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 13045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2266 0.039 - 0.077: 709 0.077 - 0.116: 223 0.116 - 0.154: 43 0.154 - 0.193: 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 2.63 -0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA ILE C 373 " pdb=" N ILE C 373 " pdb=" C ILE C 373 " pdb=" CB ILE C 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 3252 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 407 " 0.090 2.00e-02 2.50e+03 7.42e-02 6.88e+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 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 407 " -0.090 2.00e-02 2.50e+03 7.39e-02 6.83e+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 B 407 " -0.090 2.00e-02 2.50e+03 7.38e-02 6.81e+01 pdb=" C7 NAG B 407 " 0.026 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: 1413 2.73 - 3.27: 21015 3.27 - 3.81: 33326 3.81 - 4.36: 39915 4.36 - 4.90: 68945 Nonbonded interactions: 164614 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.183 2.440 nonbonded pdb=" O LEU A 52 " pdb=" OH TYR G 111 " 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 164609 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 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: 0.590 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: 3.870 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 54.000 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.827 10.103 27328 Z= 0.458 Chirality : 0.043 0.193 3255 Planarity : 0.005 0.074 3178 Dihedral : 16.592 148.414 8344 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.38 % Allowed : 5.76 % Favored : 93.86 % 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: -1.48 (0.16), residues: 2380 helix: -0.10 (0.12), residues: 1603 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 104 HIS 0.002 0.001 HIS B 106 PHE 0.013 0.002 PHE B 54 TYR 0.015 0.001 TYR D 10 ARG 0.002 0.000 ARG E 152 *********************** 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 213 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 2.290 Fit side-chains REVERT: A 29 ARG cc_start: 0.8631 (mpt-90) cc_final: 0.8279 (mmt90) REVERT: A 242 ASP cc_start: 0.8957 (p0) cc_final: 0.8716 (p0) REVERT: B 352 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8706 (tp30) REVERT: D 29 ARG cc_start: 0.8571 (mpt-90) cc_final: 0.8326 (mmt90) REVERT: G 29 ARG cc_start: 0.8571 (mpt-90) cc_final: 0.8351 (mmt90) outliers start: 7 outliers final: 0 residues processed: 213 average time/residue: 1.7528 time to fit residues: 410.9247 Evaluate side-chains 156 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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: 1.9990 chunk 180 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 0.0570 chunk 216 optimal weight: 7.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 134 HIS B 76 GLN C 76 GLN D 76 GLN D 134 HIS E 76 GLN E 134 HIS F 76 GLN F 134 HIS G 76 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20146 Z= 0.175 Angle : 0.588 9.858 27328 Z= 0.280 Chirality : 0.040 0.156 3255 Planarity : 0.004 0.037 3178 Dihedral : 14.553 89.659 4522 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.74 % Allowed : 11.84 % Favored : 86.42 % 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: 0.16 (0.18), residues: 2380 helix: 1.27 (0.13), residues: 1582 sheet: None (None), residues: 0 loop : -2.39 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 104 HIS 0.004 0.002 HIS E 134 PHE 0.008 0.001 PHE C 54 TYR 0.014 0.001 TYR A 10 ARG 0.008 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 2 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 197 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 2.606 Fit side-chains REVERT: A 29 ARG cc_start: 0.8427 (mpt-90) cc_final: 0.8167 (mmt90) REVERT: A 337 GLU cc_start: 0.8566 (tp30) cc_final: 0.8342 (tm-30) REVERT: B 337 GLU cc_start: 0.8631 (tp30) cc_final: 0.8274 (tm-30) REVERT: B 352 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8543 (tm-30) REVERT: C 5 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 138 ASP cc_start: 0.8574 (m-30) cc_final: 0.8359 (m-30) REVERT: C 337 GLU cc_start: 0.8614 (tp30) cc_final: 0.8354 (tm-30) REVERT: D 29 ARG cc_start: 0.8427 (mpt-90) cc_final: 0.8127 (mmt90) REVERT: D 337 GLU cc_start: 0.8608 (tp30) cc_final: 0.8306 (tm-30) REVERT: E 337 GLU cc_start: 0.8618 (tp30) cc_final: 0.8366 (tm-30) REVERT: F 5 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7805 (tm-30) REVERT: F 29 ARG cc_start: 0.8571 (mmt90) cc_final: 0.7829 (mmt90) REVERT: F 337 GLU cc_start: 0.8627 (tp30) cc_final: 0.8202 (tm-30) REVERT: G 29 ARG cc_start: 0.8397 (mpt-90) cc_final: 0.7682 (mmt90) REVERT: G 337 GLU cc_start: 0.8596 (tp30) cc_final: 0.8200 (tm-30) outliers start: 32 outliers final: 1 residues processed: 191 average time/residue: 1.4873 time to fit residues: 318.5306 Evaluate side-chains 158 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 353 ASN B 134 HIS C 89 GLN C 134 HIS C 353 ASN E 353 ASN F 353 ASN G 89 GLN G 134 HIS G 353 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20146 Z= 0.318 Angle : 0.621 9.913 27328 Z= 0.296 Chirality : 0.041 0.144 3255 Planarity : 0.004 0.036 3178 Dihedral : 12.993 89.641 4522 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.28 % Allowed : 13.42 % Favored : 84.30 % 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: 0.57 (0.18), residues: 2380 helix: 1.62 (0.14), residues: 1582 sheet: None (None), residues: 0 loop : -2.31 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 104 HIS 0.002 0.001 HIS E 106 PHE 0.012 0.001 PHE G 67 TYR 0.009 0.001 TYR B 230 ARG 0.008 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 3 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 204 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 2.224 Fit side-chains REVERT: A 29 ARG cc_start: 0.8463 (mpt-90) cc_final: 0.7719 (mmt90) REVERT: A 337 GLU cc_start: 0.8514 (tp30) cc_final: 0.8211 (tm-30) REVERT: B 9 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: B 337 GLU cc_start: 0.8688 (tp30) cc_final: 0.8282 (tm-30) REVERT: B 352 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8598 (tm-30) REVERT: C 5 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7951 (tm-30) REVERT: C 9 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 337 GLU cc_start: 0.8605 (tp30) cc_final: 0.8069 (tm-30) REVERT: D 5 GLN cc_start: 0.8233 (tm-30) cc_final: 0.8018 (tm-30) REVERT: D 29 ARG cc_start: 0.8465 (mpt-90) cc_final: 0.7960 (mmt90) REVERT: D 337 GLU cc_start: 0.8535 (tp30) cc_final: 0.8021 (tm-30) REVERT: E 9 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7953 (tm-30) REVERT: E 337 GLU cc_start: 0.8599 (tp30) cc_final: 0.8042 (tm-30) REVERT: F 29 ARG cc_start: 0.8602 (mmt90) cc_final: 0.7999 (mmt90) REVERT: F 337 GLU cc_start: 0.8597 (tp30) cc_final: 0.8224 (tm-30) REVERT: G 5 GLN cc_start: 0.8245 (tm-30) cc_final: 0.8044 (tm-30) REVERT: G 9 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7920 (tm-30) REVERT: G 337 GLU cc_start: 0.8567 (tp30) cc_final: 0.8211 (tm-30) outliers start: 42 outliers final: 13 residues processed: 196 average time/residue: 1.5117 time to fit residues: 331.5780 Evaluate side-chains 170 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 145 optimal weight: 0.0050 chunk 217 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN E 89 GLN G 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20146 Z= 0.166 Angle : 0.553 11.462 27328 Z= 0.267 Chirality : 0.038 0.140 3255 Planarity : 0.004 0.039 3178 Dihedral : 12.073 76.536 4522 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.44 % Allowed : 14.23 % Favored : 83.32 % 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: 1.34 (0.18), residues: 2380 helix: 2.29 (0.14), residues: 1491 sheet: -0.21 (0.59), residues: 84 loop : -1.81 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 104 HIS 0.002 0.001 HIS D 106 PHE 0.009 0.001 PHE C 54 TYR 0.011 0.001 TYR F 10 ARG 0.008 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 4 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 216 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 171 time to evaluate : 2.259 Fit side-chains REVERT: A 9 GLU cc_start: 0.8265 (tm-30) cc_final: 0.8016 (tm-30) REVERT: A 337 GLU cc_start: 0.8458 (tp30) cc_final: 0.8152 (tm-30) REVERT: B 9 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: B 29 ARG cc_start: 0.8541 (mmt90) cc_final: 0.7718 (mmt90) REVERT: B 337 GLU cc_start: 0.8637 (tp30) cc_final: 0.8171 (tm-30) REVERT: B 352 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8613 (tm-30) REVERT: C 9 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7925 (tm-30) REVERT: C 29 ARG cc_start: 0.8485 (mmt90) cc_final: 0.8191 (mmm-85) REVERT: D 9 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8028 (tm-30) REVERT: D 29 ARG cc_start: 0.8410 (mpt-90) cc_final: 0.8196 (mmt90) REVERT: E 9 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8063 (tm-30) REVERT: E 29 ARG cc_start: 0.8481 (mmt90) cc_final: 0.7867 (mmt90) REVERT: E 337 GLU cc_start: 0.8570 (tp30) cc_final: 0.8044 (tm-30) REVERT: F 9 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7911 (tm-30) REVERT: F 29 ARG cc_start: 0.8444 (mmt90) cc_final: 0.7882 (mmt90) REVERT: F 254 ARG cc_start: 0.8435 (tpp80) cc_final: 0.8233 (tpp80) REVERT: F 337 GLU cc_start: 0.8584 (tp30) cc_final: 0.8139 (tm-30) REVERT: F 352 GLU cc_start: 0.8746 (tp30) cc_final: 0.8423 (tm-30) REVERT: G 9 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7934 (tm-30) REVERT: G 29 ARG cc_start: 0.8568 (mmt90) cc_final: 0.7857 (mmt90) REVERT: G 337 GLU cc_start: 0.8522 (tp30) cc_final: 0.8095 (tm-30) outliers start: 45 outliers final: 23 residues processed: 209 average time/residue: 1.4552 time to fit residues: 341.2233 Evaluate side-chains 187 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 353 ASN C 89 GLN E 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20146 Z= 0.195 Angle : 0.550 7.084 27328 Z= 0.267 Chirality : 0.038 0.137 3255 Planarity : 0.004 0.043 3178 Dihedral : 11.726 73.320 4522 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.39 % Allowed : 14.94 % Favored : 82.67 % 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: 1.29 (0.18), residues: 2380 helix: 2.21 (0.14), residues: 1533 sheet: -0.18 (0.59), residues: 84 loop : -1.99 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 104 HIS 0.001 0.001 HIS D 106 PHE 0.010 0.001 PHE C 54 TYR 0.010 0.001 TYR F 10 ARG 0.006 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 5 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 211 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 2.240 Fit side-chains REVERT: A 9 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 29 ARG cc_start: 0.8571 (mmt90) cc_final: 0.8138 (mmt90) REVERT: A 37 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8153 (ppp) REVERT: A 337 GLU cc_start: 0.8487 (tp30) cc_final: 0.7951 (tm-30) REVERT: B 9 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: B 29 ARG cc_start: 0.8546 (mmt90) cc_final: 0.7864 (mmt90) REVERT: B 337 GLU cc_start: 0.8619 (tp30) cc_final: 0.8254 (tm-30) REVERT: B 352 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8630 (tm-30) REVERT: C 9 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: C 29 ARG cc_start: 0.8506 (mmt90) cc_final: 0.7976 (mmm-85) REVERT: C 89 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8435 (mm-40) REVERT: C 337 GLU cc_start: 0.8572 (tp30) cc_final: 0.7973 (tm-30) REVERT: D 9 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 337 GLU cc_start: 0.8553 (tp30) cc_final: 0.8338 (tp30) REVERT: E 9 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 29 ARG cc_start: 0.8502 (mmt90) cc_final: 0.7865 (mmt90) REVERT: E 337 GLU cc_start: 0.8568 (tp30) cc_final: 0.8008 (tm-30) REVERT: F 9 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7962 (tm-30) REVERT: F 29 ARG cc_start: 0.8456 (mmt90) cc_final: 0.7920 (mmt90) REVERT: F 337 GLU cc_start: 0.8609 (tp30) cc_final: 0.8146 (tm-30) REVERT: F 352 GLU cc_start: 0.8771 (tp30) cc_final: 0.8483 (tm-30) REVERT: G 9 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7991 (tm-30) REVERT: G 29 ARG cc_start: 0.8576 (mmt90) cc_final: 0.7848 (mmt90) REVERT: G 337 GLU cc_start: 0.8530 (tp30) cc_final: 0.8088 (tm-30) outliers start: 44 outliers final: 23 residues processed: 203 average time/residue: 1.4613 time to fit residues: 333.2328 Evaluate side-chains 187 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 135 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 353 ASN C 89 GLN E 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20146 Z= 0.189 Angle : 0.553 9.906 27328 Z= 0.267 Chirality : 0.038 0.137 3255 Planarity : 0.004 0.045 3178 Dihedral : 11.534 76.698 4522 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.50 % Allowed : 14.77 % Favored : 82.73 % 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: 1.59 (0.19), residues: 2380 helix: 2.44 (0.14), residues: 1498 sheet: -0.27 (0.57), residues: 84 loop : -1.63 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.001 0.001 HIS B 134 PHE 0.010 0.001 PHE C 54 TYR 0.010 0.001 TYR F 10 ARG 0.008 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 6 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 213 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 3.953 Fit side-chains REVERT: A 9 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 29 ARG cc_start: 0.8524 (mmt90) cc_final: 0.8096 (mmt90) REVERT: A 37 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8124 (ppp) REVERT: A 337 GLU cc_start: 0.8490 (tp30) cc_final: 0.7933 (tm-30) REVERT: B 9 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: B 29 ARG cc_start: 0.8541 (mmt90) cc_final: 0.7922 (mmt90) REVERT: B 337 GLU cc_start: 0.8613 (tp30) cc_final: 0.8240 (tm-30) REVERT: B 352 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8656 (tm-30) REVERT: C 9 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: C 29 ARG cc_start: 0.8478 (mmt90) cc_final: 0.8129 (mmm-85) REVERT: C 352 GLU cc_start: 0.8664 (tp30) cc_final: 0.8367 (tm-30) REVERT: D 9 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8162 (tm-30) REVERT: D 337 GLU cc_start: 0.8534 (tp30) cc_final: 0.7829 (tm-30) REVERT: E 9 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8060 (tm-30) REVERT: E 29 ARG cc_start: 0.8532 (mmt90) cc_final: 0.7903 (mmt90) REVERT: E 337 GLU cc_start: 0.8562 (tp30) cc_final: 0.7992 (tm-30) REVERT: F 9 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7983 (tm-30) REVERT: F 29 ARG cc_start: 0.8431 (mmt90) cc_final: 0.7903 (mmt90) REVERT: F 337 GLU cc_start: 0.8620 (tp30) cc_final: 0.8152 (tm-30) REVERT: F 352 GLU cc_start: 0.8756 (tp30) cc_final: 0.8480 (tm-30) REVERT: G 9 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8024 (tm-30) REVERT: G 29 ARG cc_start: 0.8564 (mmt90) cc_final: 0.7842 (mmt90) REVERT: G 337 GLU cc_start: 0.8519 (tp30) cc_final: 0.8071 (tm-30) outliers start: 46 outliers final: 27 residues processed: 203 average time/residue: 1.4533 time to fit residues: 332.5532 Evaluate side-chains 193 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 353 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN F 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20146 Z= 0.278 Angle : 0.597 8.205 27328 Z= 0.287 Chirality : 0.039 0.147 3255 Planarity : 0.004 0.041 3178 Dihedral : 11.676 78.465 4522 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.39 % Allowed : 15.75 % Favored : 81.86 % 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: 1.08 (0.18), residues: 2380 helix: 1.97 (0.14), residues: 1589 sheet: None (None), residues: 0 loop : -2.04 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 104 HIS 0.001 0.001 HIS F 134 PHE 0.012 0.001 PHE G 67 TYR 0.011 0.001 TYR F 10 ARG 0.010 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 7 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 209 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 2.149 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 29 ARG cc_start: 0.8620 (mmt90) cc_final: 0.8140 (mmt90) REVERT: A 337 GLU cc_start: 0.8512 (tp30) cc_final: 0.7926 (tm-30) REVERT: B 9 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: B 29 ARG cc_start: 0.8582 (mmt90) cc_final: 0.7994 (mmt90) REVERT: B 337 GLU cc_start: 0.8581 (tp30) cc_final: 0.8257 (tm-30) REVERT: B 352 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8644 (tm-30) REVERT: C 9 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: C 29 ARG cc_start: 0.8529 (mmt90) cc_final: 0.7983 (mmm-85) REVERT: C 337 GLU cc_start: 0.8505 (tp30) cc_final: 0.7875 (tm-30) REVERT: D 9 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8179 (tm-30) REVERT: D 254 ARG cc_start: 0.8446 (tpp80) cc_final: 0.8233 (tpp80) REVERT: D 337 GLU cc_start: 0.8533 (tp30) cc_final: 0.7837 (tm-30) REVERT: E 9 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: E 337 GLU cc_start: 0.8587 (tp30) cc_final: 0.8032 (tm-30) REVERT: F 9 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8039 (tm-30) REVERT: F 29 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8189 (mmt90) REVERT: F 337 GLU cc_start: 0.8664 (tp30) cc_final: 0.8227 (tm-30) REVERT: G 9 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7981 (tm-30) outliers start: 44 outliers final: 27 residues processed: 203 average time/residue: 1.2510 time to fit residues: 286.1835 Evaluate side-chains 190 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.0050 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 89 GLN B 353 ASN C 89 GLN D 56 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20146 Z= 0.171 Angle : 0.560 10.416 27328 Z= 0.272 Chirality : 0.038 0.140 3255 Planarity : 0.004 0.043 3178 Dihedral : 11.311 83.318 4522 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.44 % Allowed : 16.57 % Favored : 80.99 % 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: 1.47 (0.19), residues: 2380 helix: 2.27 (0.14), residues: 1540 sheet: -0.27 (0.57), residues: 84 loop : -1.75 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.001 0.001 HIS D 106 PHE 0.012 0.001 PHE D 54 TYR 0.008 0.001 TYR D 10 ARG 0.009 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 8 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 211 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 2.472 Fit side-chains REVERT: A 9 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 29 ARG cc_start: 0.8511 (mmt90) cc_final: 0.8047 (mmt90) REVERT: A 337 GLU cc_start: 0.8497 (tp30) cc_final: 0.7908 (tm-30) REVERT: B 9 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: B 29 ARG cc_start: 0.8525 (mmt90) cc_final: 0.8012 (mmt90) REVERT: B 337 GLU cc_start: 0.8587 (tp30) cc_final: 0.8270 (tm-30) REVERT: B 352 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 9 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: C 29 ARG cc_start: 0.8400 (mmt90) cc_final: 0.8025 (mmm-85) REVERT: C 337 GLU cc_start: 0.8483 (tp30) cc_final: 0.7949 (tm-30) REVERT: C 352 GLU cc_start: 0.8719 (tp30) cc_final: 0.8434 (tm-30) REVERT: D 9 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8145 (tm-30) REVERT: D 254 ARG cc_start: 0.8445 (tpp80) cc_final: 0.8237 (tpp80) REVERT: D 337 GLU cc_start: 0.8503 (tp30) cc_final: 0.7805 (tm-30) REVERT: E 9 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: E 29 ARG cc_start: 0.8489 (mmt90) cc_final: 0.7871 (mmt90) REVERT: E 337 GLU cc_start: 0.8546 (tp30) cc_final: 0.8041 (tm-30) REVERT: F 9 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8054 (tm-30) REVERT: F 29 ARG cc_start: 0.8422 (mmt90) cc_final: 0.7872 (mmt90) REVERT: F 254 ARG cc_start: 0.8341 (tpp80) cc_final: 0.8121 (tpp80) REVERT: F 336 GLU cc_start: 0.8698 (tt0) cc_final: 0.8485 (pt0) REVERT: F 337 GLU cc_start: 0.8630 (tp30) cc_final: 0.8099 (tm-30) REVERT: G 9 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8016 (tm-30) REVERT: G 337 GLU cc_start: 0.8485 (tp30) cc_final: 0.8040 (tm-30) outliers start: 45 outliers final: 27 residues processed: 202 average time/residue: 1.4433 time to fit residues: 327.8691 Evaluate side-chains 192 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN E 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20146 Z= 0.177 Angle : 0.559 7.347 27328 Z= 0.274 Chirality : 0.038 0.150 3255 Planarity : 0.004 0.042 3178 Dihedral : 11.077 89.746 4522 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.50 % Allowed : 16.78 % Favored : 80.72 % 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: 1.81 (0.19), residues: 2380 helix: 2.54 (0.14), residues: 1505 sheet: -0.36 (0.56), residues: 84 loop : -1.39 (0.24), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 104 HIS 0.001 0.000 HIS D 106 PHE 0.011 0.001 PHE D 54 TYR 0.008 0.001 TYR D 10 ARG 0.009 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 9 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 213 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 2.230 Fit side-chains REVERT: A 9 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 29 ARG cc_start: 0.8481 (mmt90) cc_final: 0.8054 (mmt90) REVERT: A 37 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8147 (ppp) REVERT: A 337 GLU cc_start: 0.8503 (tp30) cc_final: 0.7888 (tm-30) REVERT: B 9 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: B 29 ARG cc_start: 0.8500 (mmt90) cc_final: 0.7959 (mmt90) REVERT: B 337 GLU cc_start: 0.8571 (tp30) cc_final: 0.8252 (tm-30) REVERT: B 352 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8686 (tm-30) REVERT: C 9 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: C 29 ARG cc_start: 0.8380 (mmt90) cc_final: 0.8011 (mmm-85) REVERT: C 337 GLU cc_start: 0.8507 (tp30) cc_final: 0.7957 (tm-30) REVERT: D 9 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8184 (tm-30) REVERT: D 337 GLU cc_start: 0.8498 (tp30) cc_final: 0.7816 (tm-30) REVERT: E 9 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: E 29 ARG cc_start: 0.8484 (mmt90) cc_final: 0.7891 (mmt90) REVERT: E 337 GLU cc_start: 0.8539 (tp30) cc_final: 0.8018 (tm-30) REVERT: F 9 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: F 29 ARG cc_start: 0.8409 (mmt90) cc_final: 0.7988 (mmt90) REVERT: F 337 GLU cc_start: 0.8624 (tp30) cc_final: 0.8130 (tm-30) REVERT: G 9 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8001 (tm-30) REVERT: G 337 GLU cc_start: 0.8477 (tp30) cc_final: 0.8049 (tm-30) outliers start: 46 outliers final: 30 residues processed: 205 average time/residue: 1.4428 time to fit residues: 332.5722 Evaluate side-chains 195 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 237 optimal weight: 0.0670 chunk 218 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 2.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 353 ASN E 89 GLN F 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20146 Z= 0.254 Angle : 0.590 8.000 27328 Z= 0.287 Chirality : 0.039 0.154 3255 Planarity : 0.004 0.042 3178 Dihedral : 11.231 88.163 4522 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.28 % Allowed : 17.16 % Favored : 80.55 % 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: 1.80 (0.19), residues: 2380 helix: 2.53 (0.14), residues: 1498 sheet: -0.30 (0.57), residues: 84 loop : -1.37 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.001 0.000 HIS D 106 PHE 0.012 0.001 PHE D 54 TYR 0.009 0.001 TYR D 10 ARG 0.009 0.001 ARG G 29 ********************** REFINEMENT MACRO_CYCLE 10 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 204 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 2.339 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 29 ARG cc_start: 0.8546 (mmt90) cc_final: 0.8071 (mmt90) REVERT: A 337 GLU cc_start: 0.8477 (tp30) cc_final: 0.7877 (tm-30) REVERT: B 9 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: B 29 ARG cc_start: 0.8568 (mmt90) cc_final: 0.8081 (mmt90) REVERT: B 337 GLU cc_start: 0.8578 (tp30) cc_final: 0.8291 (tm-30) REVERT: B 352 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8672 (tm-30) REVERT: C 9 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: C 29 ARG cc_start: 0.8492 (mmt90) cc_final: 0.8171 (mmm-85) REVERT: D 9 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8213 (tm-30) REVERT: D 254 ARG cc_start: 0.8420 (tpp80) cc_final: 0.8211 (tpp80) REVERT: D 337 GLU cc_start: 0.8497 (tp30) cc_final: 0.7820 (tm-30) REVERT: E 9 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: E 29 ARG cc_start: 0.8532 (mmt90) cc_final: 0.7907 (mmt90) REVERT: E 337 GLU cc_start: 0.8566 (tp30) cc_final: 0.8031 (tm-30) REVERT: F 9 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: F 29 ARG cc_start: 0.8495 (mmt90) cc_final: 0.8164 (mmt90) REVERT: F 337 GLU cc_start: 0.8672 (tp30) cc_final: 0.8207 (tm-30) REVERT: G 9 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8031 (tm-30) REVERT: G 337 GLU cc_start: 0.8494 (tp30) cc_final: 0.8030 (tm-30) outliers start: 42 outliers final: 29 residues processed: 195 average time/residue: 1.4575 time to fit residues: 319.3850 Evaluate side-chains 192 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 166 optimal weight: 0.0060 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 353 ASN E 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.084755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.065431 restraints weight = 46845.716| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.48 r_work: 0.2947 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20146 Z= 0.162 Angle : 0.556 7.359 27328 Z= 0.273 Chirality : 0.038 0.139 3255 Planarity : 0.004 0.045 3178 Dihedral : 10.814 82.952 4522 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.17 % Allowed : 17.38 % Favored : 80.45 % 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: 1.64 (0.19), residues: 2380 helix: 2.36 (0.14), residues: 1547 sheet: -0.44 (0.56), residues: 84 loop : -1.60 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 104 HIS 0.001 0.001 HIS B 134 PHE 0.012 0.001 PHE D 54 TYR 0.009 0.001 TYR E 309 ARG 0.010 0.001 ARG F 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5731.98 seconds wall clock time: 106 minutes 52.16 seconds (6412.16 seconds total)