Starting phenix.real_space_refine on Sat Mar 23 23:57:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu6_26127/03_2024/7tu6_26127_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu6_26127/03_2024/7tu6_26127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu6_26127/03_2024/7tu6_26127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu6_26127/03_2024/7tu6_26127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu6_26127/03_2024/7tu6_26127_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu6_26127/03_2024/7tu6_26127_updated.pdb" } resolution = 2.7 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= 0.004 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19278 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 48 5.16 5 C 12756 2.51 5 N 3444 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 36": "OD1" <-> "OD2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 254": "OD1" <-> "OD2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20028 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 129 Chain: "C" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 129 Chain: "D" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 129 Chain: "E" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 129 Chain: "F" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.65, per 1000 atoms: 0.53 Number of scatterers: 20028 At special positions: 0 Unit cell: (130.48, 137.004, 97.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 36 15.00 Mg 6 11.99 O 3738 8.00 N 3444 7.00 C 12756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.08 Conformation dependent library (CDL) restraints added in 3.5 seconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 61.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 7 No H-bonds generated for 'chain 'A' and resid 4 through 7' Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.550A pdb=" N LEU A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 90 removed outlier: 3.508A pdb=" N SER A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.629A pdb=" N GLY A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.824A pdb=" N GLU A 128 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 244 through 267 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 299 through 324 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 363 through 388 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'B' and resid 4 through 7 No H-bonds generated for 'chain 'B' and resid 4 through 7' Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.550A pdb=" N LEU B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 removed outlier: 3.509A pdb=" N SER B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 102 through 114 removed outlier: 3.628A pdb=" N GLY B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 removed outlier: 3.823A pdb=" N GLU B 128 " --> pdb=" O HIS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 149 through 157 Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 217 through 227 Processing helix chain 'B' and resid 244 through 267 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 299 through 324 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 363 through 388 Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 412 through 425 Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'C' and resid 4 through 7 No H-bonds generated for 'chain 'C' and resid 4 through 7' Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.551A pdb=" N LEU C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 90 removed outlier: 3.509A pdb=" N SER C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.629A pdb=" N GLY C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.823A pdb=" N GLU C 128 " --> pdb=" O HIS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 149 through 157 Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 217 through 227 Processing helix chain 'C' and resid 244 through 267 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 299 through 324 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 346 through 358 Processing helix chain 'C' and resid 363 through 388 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 412 through 425 Processing helix chain 'C' and resid 428 through 438 Processing helix chain 'D' and resid 4 through 7 No H-bonds generated for 'chain 'D' and resid 4 through 7' Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 30 through 39 Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.551A pdb=" N LEU D 47 " --> pdb=" O PRO D 43 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 90 removed outlier: 3.508A pdb=" N SER D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 102 through 114 removed outlier: 3.628A pdb=" N GLY D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.823A pdb=" N GLU D 128 " --> pdb=" O HIS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 149 through 157 Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 183 through 189 Processing helix chain 'D' and resid 217 through 227 Processing helix chain 'D' and resid 244 through 267 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 299 through 324 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 346 through 358 Processing helix chain 'D' and resid 363 through 388 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 412 through 425 Processing helix chain 'D' and resid 428 through 438 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.551A pdb=" N LEU E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN E 48 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP E 49 " --> pdb=" O ARG E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 90 removed outlier: 3.509A pdb=" N SER E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.629A pdb=" N GLY E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 134 removed outlier: 3.823A pdb=" N GLU E 128 " --> pdb=" O HIS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 183 through 189 Processing helix chain 'E' and resid 217 through 227 Processing helix chain 'E' and resid 244 through 267 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 299 through 324 Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 346 through 358 Processing helix chain 'E' and resid 363 through 388 Processing helix chain 'E' and resid 393 through 402 Processing helix chain 'E' and resid 412 through 425 Processing helix chain 'E' and resid 428 through 438 Processing helix chain 'F' and resid 4 through 7 No H-bonds generated for 'chain 'F' and resid 4 through 7' Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 30 through 39 Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.550A pdb=" N LEU F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN F 48 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP F 49 " --> pdb=" O ARG F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 90 removed outlier: 3.508A pdb=" N SER F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.629A pdb=" N GLY F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 removed outlier: 3.824A pdb=" N GLU F 128 " --> pdb=" O HIS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 149 through 157 Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 183 through 189 Processing helix chain 'F' and resid 217 through 227 Processing helix chain 'F' and resid 244 through 267 Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 299 through 324 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 346 through 358 Processing helix chain 'F' and resid 363 through 388 Processing helix chain 'F' and resid 393 through 402 Processing helix chain 'F' and resid 412 through 425 Processing helix chain 'F' and resid 428 through 438 1008 hydrogen bonds defined for protein. 2862 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: 5.42 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3216 1.31 - 1.43: 5461 1.43 - 1.56: 11603 1.56 - 1.68: 66 1.68 - 1.81: 78 Bond restraints: 20424 Sorted by residual: bond pdb=" CA GLN E 52 " pdb=" C GLN E 52 " ideal model delta sigma weight residual 1.526 1.569 -0.043 9.20e-03 1.18e+04 2.14e+01 bond pdb=" CA GLN C 52 " pdb=" C GLN C 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.12e+01 bond pdb=" CA GLN F 52 " pdb=" C GLN F 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.10e+01 bond pdb=" CA GLN A 52 " pdb=" C GLN A 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.10e+01 bond pdb=" CA GLN D 52 " pdb=" C GLN D 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.06e+01 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 100.86 - 108.71: 949 108.71 - 116.56: 12781 116.56 - 124.41: 13603 124.41 - 132.26: 351 132.26 - 140.11: 48 Bond angle restraints: 27732 Sorted by residual: angle pdb=" N LEU B 412 " pdb=" CA LEU B 412 " pdb=" C LEU B 412 " ideal model delta sigma weight residual 111.71 118.90 -7.19 1.15e+00 7.56e-01 3.91e+01 angle pdb=" N LEU C 412 " pdb=" CA LEU C 412 " pdb=" C LEU C 412 " ideal model delta sigma weight residual 111.71 118.89 -7.18 1.15e+00 7.56e-01 3.89e+01 angle pdb=" N LEU F 412 " pdb=" CA LEU F 412 " pdb=" C LEU F 412 " ideal model delta sigma weight residual 111.71 118.88 -7.17 1.15e+00 7.56e-01 3.89e+01 angle pdb=" N LEU A 412 " pdb=" CA LEU A 412 " pdb=" C LEU A 412 " ideal model delta sigma weight residual 111.71 118.87 -7.16 1.15e+00 7.56e-01 3.88e+01 angle pdb=" N LEU D 412 " pdb=" CA LEU D 412 " pdb=" C LEU D 412 " ideal model delta sigma weight residual 111.71 118.86 -7.15 1.15e+00 7.56e-01 3.87e+01 ... (remaining 27727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 11180 17.72 - 35.44: 764 35.44 - 53.16: 260 53.16 - 70.88: 24 70.88 - 88.61: 60 Dihedral angle restraints: 12288 sinusoidal: 4782 harmonic: 7506 Sorted by residual: dihedral pdb=" C TYR B 257 " pdb=" N TYR B 257 " pdb=" CA TYR B 257 " pdb=" CB TYR B 257 " ideal model delta harmonic sigma weight residual -122.60 -132.57 9.97 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C TYR F 257 " pdb=" N TYR F 257 " pdb=" CA TYR F 257 " pdb=" CB TYR F 257 " ideal model delta harmonic sigma weight residual -122.60 -132.56 9.96 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C TYR C 257 " pdb=" N TYR C 257 " pdb=" CA TYR C 257 " pdb=" CB TYR C 257 " ideal model delta harmonic sigma weight residual -122.60 -132.55 9.95 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 12285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2885 0.085 - 0.169: 163 0.169 - 0.254: 54 0.254 - 0.339: 12 0.339 - 0.423: 12 Chirality restraints: 3126 Sorted by residual: chirality pdb=" CA TYR B 257 " pdb=" N TYR B 257 " pdb=" C TYR B 257 " pdb=" CB TYR B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA TYR E 257 " pdb=" N TYR E 257 " pdb=" C TYR E 257 " pdb=" CB TYR E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA TYR C 257 " pdb=" N TYR C 257 " pdb=" C TYR C 257 " pdb=" CB TYR C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 3123 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 269 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C GLY B 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY B 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 270 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 269 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C GLY A 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY A 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 270 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 269 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C GLY F 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY F 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU F 270 " -0.013 2.00e-02 2.50e+03 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 48 2.49 - 3.10: 13868 3.10 - 3.70: 29303 3.70 - 4.30: 43739 4.30 - 4.90: 73358 Nonbonded interactions: 160316 Sorted by model distance: nonbonded pdb=" NE2 HIS F 116 " pdb="MG MG F 503 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS C 116 " pdb="MG MG C 502 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS A 116 " pdb="MG MG A 503 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS D 116 " pdb="MG MG D 503 " model vdw 1.893 2.250 nonbonded pdb=" NE2 HIS E 116 " pdb="MG MG E 502 " model vdw 1.893 2.250 ... (remaining 160311 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' and (resid 3 through 441 or resid 501)) selection = (chain 'B' and (resid 3 through 441 or resid 501)) selection = (chain 'C' and (resid 3 through 441 or resid 501)) selection = (chain 'D' and (resid 3 through 441 or resid 501)) selection = (chain 'E' and (resid 3 through 441 or resid 501)) selection = (chain 'F' and (resid 3 through 441 or resid 501)) } 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.010 Extract box with map and model: 3.740 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 51.730 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 0.061 20424 Z= 0.456 Angle : 0.790 7.332 27732 Z= 0.532 Chirality : 0.058 0.423 3126 Planarity : 0.005 0.078 3474 Dihedral : 15.187 88.605 7476 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.90 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 8.33 % 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: 0.38 (0.17), residues: 2532 helix: 1.23 (0.13), residues: 1674 sheet: None (None), residues: 0 loop : -1.75 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 4 HIS 0.007 0.002 HIS C 6 PHE 0.006 0.001 PHE C 61 TYR 0.014 0.002 TYR C 305 ARG 0.007 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 523 time to evaluate : 2.051 Fit side-chains REVERT: A 102 PHE cc_start: 0.8226 (p90) cc_final: 0.7942 (p90) REVERT: A 253 ASP cc_start: 0.7549 (t70) cc_final: 0.7157 (t0) REVERT: B 28 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7866 (mmm160) REVERT: B 65 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7240 (tpt170) REVERT: B 117 ASP cc_start: 0.6763 (m-30) cc_final: 0.6531 (m-30) REVERT: B 153 GLN cc_start: 0.8322 (tp40) cc_final: 0.8082 (mm-40) REVERT: B 226 GLU cc_start: 0.6998 (tp30) cc_final: 0.6782 (tp30) REVERT: B 270 LEU cc_start: 0.8442 (mt) cc_final: 0.8214 (mt) REVERT: B 354 LEU cc_start: 0.7965 (tp) cc_final: 0.7749 (tt) REVERT: C 28 ARG cc_start: 0.8145 (ttt-90) cc_final: 0.7927 (mmm160) REVERT: C 65 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7263 (tpt170) REVERT: C 253 ASP cc_start: 0.7473 (t70) cc_final: 0.7227 (t70) REVERT: C 270 LEU cc_start: 0.8229 (mt) cc_final: 0.8014 (mt) REVERT: D 253 ASP cc_start: 0.7660 (t70) cc_final: 0.7207 (t0) REVERT: D 270 LEU cc_start: 0.8634 (mt) cc_final: 0.8393 (mt) REVERT: D 326 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 20 LEU cc_start: 0.8548 (mt) cc_final: 0.8276 (mt) REVERT: E 45 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8184 (ttp80) REVERT: E 86 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7895 (mtmt) REVERT: E 207 ASP cc_start: 0.7376 (p0) cc_final: 0.7086 (p0) REVERT: E 214 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8305 (mm-40) REVERT: E 326 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7406 (tm-30) REVERT: F 20 LEU cc_start: 0.8727 (mt) cc_final: 0.8450 (mt) REVERT: F 45 ARG cc_start: 0.8410 (ttm170) cc_final: 0.8123 (ttp80) REVERT: F 270 LEU cc_start: 0.8460 (mt) cc_final: 0.8248 (mp) REVERT: F 326 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7512 (tm-30) outliers start: 12 outliers final: 1 residues processed: 532 average time/residue: 1.5645 time to fit residues: 919.3193 Evaluate side-chains 435 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 432 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain E residue 411 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 234 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 48 GLN A 153 GLN A 343 ASN A 389 ASN A 395 ASN B 3 ASN B 24 GLN B 48 GLN B 52 GLN B 120 ASN B 199 HIS B 343 ASN B 345 GLN B 389 ASN B 395 ASN C 24 GLN C 48 GLN C 52 GLN C 199 HIS C 345 GLN C 389 ASN C 395 ASN D 13 GLN D 24 GLN D 48 GLN D 153 GLN D 389 ASN D 395 ASN E 52 GLN E 120 ASN E 153 GLN E 389 ASN E 395 ASN F 13 GLN F 48 GLN F 52 GLN F 120 ASN F 137 ASN F 343 ASN F 389 ASN F 395 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.215 Angle : 0.484 5.851 27732 Z= 0.263 Chirality : 0.037 0.139 3126 Planarity : 0.004 0.035 3474 Dihedral : 11.500 81.027 3183 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.53 % Allowed : 11.87 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.89 (0.17), residues: 2532 helix: 1.67 (0.13), residues: 1686 sheet: None (None), residues: 0 loop : -1.71 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.008 0.002 HIS A 243 PHE 0.015 0.002 PHE C 213 TYR 0.032 0.002 TYR B 257 ARG 0.005 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 522 time to evaluate : 2.317 Fit side-chains REVERT: A 52 GLN cc_start: 0.7685 (tp40) cc_final: 0.6889 (tp40) REVERT: A 86 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7968 (mtmt) REVERT: A 102 PHE cc_start: 0.8430 (p90) cc_final: 0.8143 (p90) REVERT: A 253 ASP cc_start: 0.7378 (t70) cc_final: 0.7162 (t0) REVERT: B 214 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8279 (mm110) REVERT: B 216 GLU cc_start: 0.7109 (mp0) cc_final: 0.6368 (mp0) REVERT: B 226 GLU cc_start: 0.7047 (tp30) cc_final: 0.6830 (tp30) REVERT: B 270 LEU cc_start: 0.8462 (mt) cc_final: 0.8249 (mt) REVERT: C 214 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8371 (mm110) REVERT: C 270 LEU cc_start: 0.8287 (mt) cc_final: 0.8042 (mt) REVERT: D 151 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7166 (mp0) REVERT: D 253 ASP cc_start: 0.7514 (t70) cc_final: 0.7243 (t0) REVERT: D 270 LEU cc_start: 0.8517 (mt) cc_final: 0.8294 (mt) REVERT: D 326 GLU cc_start: 0.7677 (tm-30) cc_final: 0.6792 (tm-30) REVERT: E 45 ARG cc_start: 0.8458 (ttm170) cc_final: 0.8207 (ttp80) REVERT: E 65 ARG cc_start: 0.7738 (tpt170) cc_final: 0.7480 (mmt-90) REVERT: E 161 ASN cc_start: 0.7964 (m110) cc_final: 0.7723 (m110) REVERT: E 270 LEU cc_start: 0.8331 (mt) cc_final: 0.8083 (mp) REVERT: E 415 ASN cc_start: 0.7966 (m-40) cc_final: 0.7681 (m-40) REVERT: F 45 ARG cc_start: 0.8441 (ttm170) cc_final: 0.8210 (ttp80) REVERT: F 52 GLN cc_start: 0.7592 (tp40) cc_final: 0.7058 (tp-100) REVERT: F 65 ARG cc_start: 0.7572 (tpt170) cc_final: 0.7208 (mmt-90) REVERT: F 81 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7500 (ttp-170) REVERT: F 155 LEU cc_start: 0.8528 (mt) cc_final: 0.8302 (mm) REVERT: F 270 LEU cc_start: 0.8389 (mt) cc_final: 0.8179 (mp) REVERT: F 326 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7361 (tm-30) REVERT: F 415 ASN cc_start: 0.8072 (m-40) cc_final: 0.7788 (m-40) outliers start: 49 outliers final: 17 residues processed: 539 average time/residue: 1.4508 time to fit residues: 868.9343 Evaluate side-chains 493 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 475 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 234 optimal weight: 0.4980 chunk 253 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 24 GLN A 48 GLN B 3 ASN B 13 GLN B 52 GLN B 343 ASN B 345 GLN C 24 GLN C 345 GLN D 13 GLN D 24 GLN D 343 ASN E 24 GLN E 52 GLN E 137 ASN E 161 ASN E 267 ASN F 24 GLN F 137 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20424 Z= 0.355 Angle : 0.544 5.462 27732 Z= 0.295 Chirality : 0.041 0.150 3126 Planarity : 0.004 0.032 3474 Dihedral : 11.082 89.521 3174 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.92 % Allowed : 14.34 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.59 (0.16), residues: 2532 helix: 1.39 (0.12), residues: 1686 sheet: None (None), residues: 0 loop : -1.70 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 240 HIS 0.010 0.002 HIS A 243 PHE 0.021 0.002 PHE F 220 TYR 0.020 0.002 TYR C 257 ARG 0.004 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 524 time to evaluate : 2.269 Fit side-chains REVERT: A 52 GLN cc_start: 0.7764 (tp40) cc_final: 0.6945 (tp40) REVERT: A 85 LYS cc_start: 0.8308 (ttmp) cc_final: 0.8052 (tttm) REVERT: A 102 PHE cc_start: 0.8560 (p90) cc_final: 0.8271 (p90) REVERT: A 324 LYS cc_start: 0.8122 (tttt) cc_final: 0.7900 (ttpt) REVERT: B 214 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8332 (mm110) REVERT: B 216 GLU cc_start: 0.7094 (mp0) cc_final: 0.6322 (mp0) REVERT: B 226 GLU cc_start: 0.7076 (tp30) cc_final: 0.6858 (tp30) REVERT: B 354 LEU cc_start: 0.8320 (tp) cc_final: 0.8084 (tt) REVERT: B 373 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7169 (t80) REVERT: C 24 GLN cc_start: 0.7972 (mt0) cc_final: 0.7674 (tt0) REVERT: C 214 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8369 (mm110) REVERT: C 216 GLU cc_start: 0.7211 (mp0) cc_final: 0.6345 (mp0) REVERT: C 280 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7146 (mtp) REVERT: C 373 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.6884 (t80) REVERT: C 425 THR cc_start: 0.8564 (t) cc_final: 0.8313 (t) REVERT: D 270 LEU cc_start: 0.8489 (mt) cc_final: 0.8249 (mt) REVERT: D 326 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6808 (tm-30) REVERT: E 11 LYS cc_start: 0.8047 (ptmt) cc_final: 0.7781 (tttt) REVERT: E 24 GLN cc_start: 0.7766 (mt0) cc_final: 0.7443 (tt0) REVERT: F 45 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8102 (ttp80) REVERT: F 91 TYR cc_start: 0.7894 (m-10) cc_final: 0.7664 (m-80) REVERT: F 155 LEU cc_start: 0.8575 (mt) cc_final: 0.8325 (mm) REVERT: F 415 ASN cc_start: 0.8024 (m-40) cc_final: 0.7778 (m-40) outliers start: 76 outliers final: 36 residues processed: 549 average time/residue: 1.3424 time to fit residues: 824.7093 Evaluate side-chains 554 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 515 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 249 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 3 ASN B 52 GLN B 345 GLN B 415 ASN B 434 ASN C 52 GLN C 434 ASN D 24 GLN D 343 ASN E 13 GLN E 48 GLN E 137 ASN F 52 GLN F 137 ASN F 267 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.222 Angle : 0.462 5.184 27732 Z= 0.253 Chirality : 0.037 0.136 3126 Planarity : 0.003 0.036 3474 Dihedral : 10.427 88.658 3174 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.30 % Allowed : 17.03 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.78 (0.17), residues: 2532 helix: 1.57 (0.13), residues: 1686 sheet: None (None), residues: 0 loop : -1.70 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.007 0.001 HIS A 243 PHE 0.014 0.001 PHE F 220 TYR 0.019 0.002 TYR A 257 ARG 0.003 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 506 time to evaluate : 2.386 Fit side-chains REVERT: A 102 PHE cc_start: 0.8484 (p90) cc_final: 0.8193 (p90) REVERT: A 324 LYS cc_start: 0.7991 (tttt) cc_final: 0.7750 (ttpt) REVERT: B 45 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7855 (ttp80) REVERT: B 65 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7062 (tpt170) REVERT: B 214 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8299 (mm110) REVERT: B 216 GLU cc_start: 0.7182 (mp0) cc_final: 0.6348 (mp0) REVERT: B 226 GLU cc_start: 0.7070 (tp30) cc_final: 0.6804 (tp30) REVERT: B 354 LEU cc_start: 0.8226 (tp) cc_final: 0.8021 (tt) REVERT: B 373 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.6943 (t80) REVERT: C 12 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7573 (mtt-85) REVERT: C 24 GLN cc_start: 0.7990 (mt0) cc_final: 0.7710 (tt0) REVERT: C 216 GLU cc_start: 0.7193 (mp0) cc_final: 0.6303 (mp0) REVERT: C 226 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6361 (tt0) REVERT: C 280 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6975 (mtp) REVERT: C 296 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8013 (mt) REVERT: C 354 LEU cc_start: 0.8222 (tp) cc_final: 0.8007 (tt) REVERT: C 373 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6719 (t80) REVERT: C 425 THR cc_start: 0.8526 (t) cc_final: 0.8266 (t) REVERT: D 151 GLU cc_start: 0.7498 (mp0) cc_final: 0.6580 (mp0) REVERT: D 326 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6818 (tm-30) REVERT: E 11 LYS cc_start: 0.8036 (ptmt) cc_final: 0.7753 (tttt) REVERT: E 24 GLN cc_start: 0.7748 (mt0) cc_final: 0.7473 (tt0) REVERT: E 45 ARG cc_start: 0.8432 (ttm110) cc_final: 0.8197 (ttp80) REVERT: E 415 ASN cc_start: 0.7888 (m-40) cc_final: 0.7636 (m-40) REVERT: F 45 ARG cc_start: 0.8405 (ttm170) cc_final: 0.7986 (ttp80) REVERT: F 52 GLN cc_start: 0.7691 (tp40) cc_final: 0.6649 (tp-100) REVERT: F 65 ARG cc_start: 0.7467 (mmt90) cc_final: 0.7067 (mmt-90) REVERT: F 91 TYR cc_start: 0.7804 (m-10) cc_final: 0.7601 (m-80) REVERT: F 415 ASN cc_start: 0.7954 (m-40) cc_final: 0.7696 (m-40) outliers start: 64 outliers final: 36 residues processed: 530 average time/residue: 1.3935 time to fit residues: 824.4034 Evaluate side-chains 552 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 508 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 185 optimal weight: 0.0010 chunk 102 optimal weight: 0.6980 chunk 212 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 62 optimal weight: 0.0370 overall best weight: 0.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 3 ASN B 52 GLN B 345 GLN C 52 GLN D 24 GLN D 343 ASN D 434 ASN E 13 GLN E 137 ASN F 137 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20424 Z= 0.124 Angle : 0.407 5.974 27732 Z= 0.222 Chirality : 0.034 0.141 3126 Planarity : 0.003 0.031 3474 Dihedral : 9.346 73.770 3174 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.30 % Allowed : 17.18 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.13 (0.17), residues: 2532 helix: 1.87 (0.13), residues: 1686 sheet: None (None), residues: 0 loop : -1.65 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 240 HIS 0.004 0.001 HIS F 204 PHE 0.009 0.001 PHE F 61 TYR 0.016 0.001 TYR B 257 ARG 0.002 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 504 time to evaluate : 2.449 Fit side-chains REVERT: A 52 GLN cc_start: 0.7767 (tp40) cc_final: 0.6976 (tp40) REVERT: A 102 PHE cc_start: 0.8406 (p90) cc_final: 0.8112 (p90) REVERT: A 151 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6911 (mt-10) REVERT: A 266 ILE cc_start: 0.7120 (mt) cc_final: 0.6858 (tt) REVERT: B 45 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7764 (ttp80) REVERT: B 226 GLU cc_start: 0.7062 (tp30) cc_final: 0.6792 (tp30) REVERT: B 373 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6597 (t80) REVERT: C 12 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7464 (mtt-85) REVERT: C 24 GLN cc_start: 0.7946 (mt0) cc_final: 0.7684 (tt0) REVERT: C 216 GLU cc_start: 0.7273 (mp0) cc_final: 0.6435 (mp0) REVERT: C 296 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7977 (mp) REVERT: C 373 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6450 (t80) REVERT: C 425 THR cc_start: 0.8495 (t) cc_final: 0.8259 (t) REVERT: D 151 GLU cc_start: 0.7557 (mp0) cc_final: 0.6543 (mp0) REVERT: D 326 GLU cc_start: 0.7615 (tm-30) cc_final: 0.6833 (tm-30) REVERT: E 24 GLN cc_start: 0.7746 (mt0) cc_final: 0.7487 (tt0) REVERT: E 330 LEU cc_start: 0.8470 (tp) cc_final: 0.8236 (mt) REVERT: E 415 ASN cc_start: 0.7824 (m-40) cc_final: 0.7582 (m-40) REVERT: F 45 ARG cc_start: 0.8395 (ttm170) cc_final: 0.8182 (ttp80) REVERT: F 91 TYR cc_start: 0.7623 (m-10) cc_final: 0.7416 (m-80) outliers start: 64 outliers final: 33 residues processed: 528 average time/residue: 1.3770 time to fit residues: 813.7167 Evaluate side-chains 532 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 494 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 257 TYR Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.1980 chunk 224 optimal weight: 0.0470 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 0.0370 chunk 131 optimal weight: 8.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 343 ASN A 434 ASN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 52 GLN C 343 ASN C 345 GLN D 24 GLN D 343 ASN E 13 GLN E 137 ASN F 52 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20424 Z= 0.114 Angle : 0.398 6.261 27732 Z= 0.214 Chirality : 0.034 0.142 3126 Planarity : 0.003 0.029 3474 Dihedral : 8.694 60.692 3174 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.94 % Allowed : 19.20 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.22 (0.17), residues: 2532 helix: 1.93 (0.13), residues: 1698 sheet: None (None), residues: 0 loop : -1.66 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 240 HIS 0.004 0.001 HIS C 204 PHE 0.010 0.001 PHE F 102 TYR 0.015 0.001 TYR D 257 ARG 0.002 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 491 time to evaluate : 2.397 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7811 (tp40) cc_final: 0.6987 (tp40) REVERT: A 102 PHE cc_start: 0.8378 (p90) cc_final: 0.8125 (p90) REVERT: B 45 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7762 (ttp80) REVERT: B 139 TYR cc_start: 0.6881 (t80) cc_final: 0.6499 (t80) REVERT: B 226 GLU cc_start: 0.7050 (tp30) cc_final: 0.6788 (tp30) REVERT: B 336 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: B 373 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6548 (t80) REVERT: C 24 GLN cc_start: 0.7942 (mt0) cc_final: 0.7669 (tt0) REVERT: C 216 GLU cc_start: 0.7277 (mp0) cc_final: 0.6471 (mp0) REVERT: C 373 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6423 (t80) REVERT: C 425 THR cc_start: 0.8483 (t) cc_final: 0.8263 (t) REVERT: D 209 LYS cc_start: 0.8260 (mttp) cc_final: 0.8034 (mttt) REVERT: D 358 ARG cc_start: 0.7719 (mmm-85) cc_final: 0.7433 (mtt-85) REVERT: E 24 GLN cc_start: 0.7719 (mt0) cc_final: 0.7468 (tt0) REVERT: E 207 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7222 (p0) REVERT: E 323 MET cc_start: 0.7340 (tpt) cc_final: 0.7078 (mmm) REVERT: E 330 LEU cc_start: 0.8454 (tp) cc_final: 0.8219 (mt) REVERT: E 415 ASN cc_start: 0.7800 (m-40) cc_final: 0.7581 (m-40) REVERT: F 45 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8064 (ttp80) REVERT: F 207 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7095 (p0) REVERT: F 263 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6122 (pt0) REVERT: F 323 MET cc_start: 0.7383 (tpt) cc_final: 0.7014 (mmm) outliers start: 57 outliers final: 24 residues processed: 514 average time/residue: 1.4060 time to fit residues: 806.5432 Evaluate side-chains 509 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 478 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 24 GLN A 48 GLN A 267 ASN B 3 ASN B 52 GLN B 343 ASN C 52 GLN C 343 ASN C 415 ASN D 24 GLN D 267 ASN D 343 ASN D 415 ASN E 52 GLN E 137 ASN F 24 GLN F 52 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20424 Z= 0.449 Angle : 0.573 6.346 27732 Z= 0.309 Chirality : 0.045 0.166 3126 Planarity : 0.004 0.033 3474 Dihedral : 9.796 79.509 3174 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.35 % Allowed : 19.76 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.66 (0.16), residues: 2532 helix: 1.43 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -1.62 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 240 HIS 0.013 0.002 HIS A 243 PHE 0.023 0.003 PHE F 220 TYR 0.027 0.002 TYR B 257 ARG 0.005 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 551 time to evaluate : 2.318 Fit side-chains REVERT: A 52 GLN cc_start: 0.7836 (tp40) cc_final: 0.6974 (tp40) REVERT: A 102 PHE cc_start: 0.8612 (p90) cc_final: 0.8336 (p90) REVERT: B 45 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: B 216 GLU cc_start: 0.7183 (mp0) cc_final: 0.6434 (mp0) REVERT: B 226 GLU cc_start: 0.7091 (tp30) cc_final: 0.6819 (tp30) REVERT: B 373 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7250 (t80) REVERT: C 24 GLN cc_start: 0.8050 (mt0) cc_final: 0.7826 (tt0) REVERT: C 45 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7833 (ttp80) REVERT: C 74 VAL cc_start: 0.7622 (t) cc_final: 0.7259 (m) REVERT: C 81 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7360 (mtt180) REVERT: C 202 SER cc_start: 0.8667 (m) cc_final: 0.8301 (t) REVERT: C 214 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8312 (mm110) REVERT: C 216 GLU cc_start: 0.7284 (mp0) cc_final: 0.6379 (mp0) REVERT: C 296 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8020 (mt) REVERT: C 354 LEU cc_start: 0.8252 (tp) cc_final: 0.8009 (tt) REVERT: C 373 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6967 (t80) REVERT: C 425 THR cc_start: 0.8573 (t) cc_final: 0.8315 (t) REVERT: D 151 GLU cc_start: 0.7548 (mp0) cc_final: 0.6563 (mp0) REVERT: D 326 GLU cc_start: 0.7710 (tm-30) cc_final: 0.6792 (tm-30) REVERT: E 11 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7755 (tttt) REVERT: E 24 GLN cc_start: 0.7820 (mt0) cc_final: 0.7552 (tt0) REVERT: E 354 LEU cc_start: 0.8215 (tp) cc_final: 0.7888 (tp) REVERT: E 415 ASN cc_start: 0.7967 (m-40) cc_final: 0.7636 (m-40) REVERT: F 45 ARG cc_start: 0.8463 (ttm170) cc_final: 0.8041 (ttp80) REVERT: F 129 LYS cc_start: 0.7885 (mmpt) cc_final: 0.7623 (mttm) REVERT: F 260 ILE cc_start: 0.8069 (mm) cc_final: 0.7809 (mt) REVERT: F 358 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7458 (mmm-85) outliers start: 65 outliers final: 38 residues processed: 567 average time/residue: 1.3749 time to fit residues: 872.8367 Evaluate side-chains 581 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 537 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 24 GLN B 3 ASN C 52 GLN C 343 ASN D 24 GLN D 343 ASN E 137 ASN E 434 ASN F 24 GLN F 52 GLN F 137 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20424 Z= 0.174 Angle : 0.444 5.541 27732 Z= 0.242 Chirality : 0.036 0.145 3126 Planarity : 0.003 0.033 3474 Dihedral : 9.206 71.503 3174 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.73 % Allowed : 21.16 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.94 (0.17), residues: 2532 helix: 1.71 (0.13), residues: 1686 sheet: None (None), residues: 0 loop : -1.68 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS A 243 PHE 0.010 0.001 PHE E 220 TYR 0.018 0.001 TYR B 257 ARG 0.002 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 506 time to evaluate : 2.264 Fit side-chains REVERT: A 52 GLN cc_start: 0.7818 (tp40) cc_final: 0.7141 (tp40) REVERT: A 65 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.6911 (mmt-90) REVERT: A 102 PHE cc_start: 0.8502 (p90) cc_final: 0.8209 (p90) REVERT: B 45 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7820 (ttp80) REVERT: B 226 GLU cc_start: 0.7061 (tp30) cc_final: 0.6768 (tp30) REVERT: B 330 LEU cc_start: 0.8320 (tp) cc_final: 0.8119 (mt) REVERT: B 354 LEU cc_start: 0.8298 (tp) cc_final: 0.8043 (tt) REVERT: B 373 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6839 (t80) REVERT: C 45 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7722 (ttp80) REVERT: C 81 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7290 (mtt180) REVERT: C 136 LYS cc_start: 0.7857 (ttmm) cc_final: 0.7656 (ttmm) REVERT: C 216 GLU cc_start: 0.7281 (mp0) cc_final: 0.6419 (mp0) REVERT: C 296 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7974 (mt) REVERT: C 373 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6614 (t80) REVERT: C 425 THR cc_start: 0.8520 (t) cc_final: 0.8284 (t) REVERT: D 151 GLU cc_start: 0.7549 (mp0) cc_final: 0.6547 (mp0) REVERT: D 209 LYS cc_start: 0.8258 (mttp) cc_final: 0.8026 (mttt) REVERT: D 266 ILE cc_start: 0.7409 (mt) cc_final: 0.7057 (tt) REVERT: D 326 GLU cc_start: 0.7640 (tm-30) cc_final: 0.6823 (tm-30) REVERT: E 11 LYS cc_start: 0.8022 (ptmt) cc_final: 0.7816 (tttt) REVERT: E 24 GLN cc_start: 0.7759 (mt0) cc_final: 0.7523 (tt0) REVERT: E 330 LEU cc_start: 0.8480 (tp) cc_final: 0.8266 (mt) REVERT: E 354 LEU cc_start: 0.8197 (tp) cc_final: 0.7847 (tp) REVERT: E 415 ASN cc_start: 0.7856 (m-40) cc_final: 0.7564 (m-40) REVERT: F 45 ARG cc_start: 0.8419 (ttm110) cc_final: 0.8170 (ttp80) REVERT: F 52 GLN cc_start: 0.7668 (tp40) cc_final: 0.6924 (tp-100) REVERT: F 65 ARG cc_start: 0.7385 (mmt90) cc_final: 0.7128 (mmt180) outliers start: 53 outliers final: 36 residues processed: 521 average time/residue: 1.3428 time to fit residues: 781.6089 Evaluate side-chains 545 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 503 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 3 ASN B 52 GLN B 343 ASN C 24 GLN C 52 GLN C 343 ASN D 343 ASN E 137 ASN F 24 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20424 Z= 0.231 Angle : 0.471 5.459 27732 Z= 0.255 Chirality : 0.038 0.154 3126 Planarity : 0.003 0.035 3474 Dihedral : 9.149 70.716 3174 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.84 % Allowed : 21.31 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.90 (0.17), residues: 2532 helix: 1.66 (0.13), residues: 1686 sheet: None (None), residues: 0 loop : -1.66 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.007 0.001 HIS A 243 PHE 0.013 0.001 PHE E 220 TYR 0.019 0.001 TYR C 257 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 516 time to evaluate : 1.961 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7836 (tp40) cc_final: 0.7137 (tp40) REVERT: A 65 ARG cc_start: 0.7516 (mmt-90) cc_final: 0.7018 (mmt-90) REVERT: B 45 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7855 (ttp80) REVERT: B 226 GLU cc_start: 0.7051 (tp30) cc_final: 0.6757 (tp30) REVERT: B 354 LEU cc_start: 0.8296 (tp) cc_final: 0.8054 (tt) REVERT: B 373 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6956 (t80) REVERT: C 45 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7799 (ttp80) REVERT: C 71 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6932 (mt-10) REVERT: C 81 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7325 (mtt180) REVERT: C 202 SER cc_start: 0.8503 (m) cc_final: 0.8187 (t) REVERT: C 214 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8298 (mm110) REVERT: C 216 GLU cc_start: 0.7238 (mp0) cc_final: 0.6368 (mp0) REVERT: C 280 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6581 (mtp) REVERT: C 296 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7970 (mp) REVERT: C 373 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6719 (t80) REVERT: C 425 THR cc_start: 0.8537 (t) cc_final: 0.8295 (t) REVERT: D 151 GLU cc_start: 0.7542 (mp0) cc_final: 0.6535 (mp0) REVERT: D 209 LYS cc_start: 0.8263 (mttp) cc_final: 0.8025 (mttt) REVERT: D 280 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6890 (mtp) REVERT: D 296 LEU cc_start: 0.8001 (mt) cc_final: 0.7763 (mt) REVERT: D 326 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6814 (tm-30) REVERT: E 11 LYS cc_start: 0.8026 (ptmt) cc_final: 0.7723 (tttt) REVERT: E 24 GLN cc_start: 0.7779 (mt0) cc_final: 0.7520 (tt0) REVERT: E 330 LEU cc_start: 0.8488 (tp) cc_final: 0.8271 (mt) REVERT: E 354 LEU cc_start: 0.8197 (tp) cc_final: 0.7844 (tp) REVERT: E 415 ASN cc_start: 0.7878 (m-40) cc_final: 0.7585 (m-40) REVERT: F 45 ARG cc_start: 0.8437 (ttm110) cc_final: 0.8172 (ttp80) REVERT: F 231 LYS cc_start: 0.7986 (mttt) cc_final: 0.7777 (mtpm) outliers start: 55 outliers final: 42 residues processed: 531 average time/residue: 1.4157 time to fit residues: 839.5622 Evaluate side-chains 557 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 507 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 257 optimal weight: 0.3980 chunk 236 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN B 52 GLN B 343 ASN C 52 GLN C 343 ASN D 343 ASN E 137 ASN F 24 GLN F 52 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20424 Z= 0.154 Angle : 0.434 6.514 27732 Z= 0.235 Chirality : 0.036 0.154 3126 Planarity : 0.003 0.034 3474 Dihedral : 8.762 63.856 3174 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.58 % Allowed : 21.26 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.12 (0.17), residues: 2532 helix: 1.83 (0.13), residues: 1668 sheet: None (None), residues: 0 loop : -1.50 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.004 0.001 HIS C 243 PHE 0.010 0.001 PHE E 220 TYR 0.016 0.001 TYR C 257 ARG 0.003 0.000 ARG F 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 507 time to evaluate : 3.055 Fit side-chains REVERT: A 52 GLN cc_start: 0.7844 (tp40) cc_final: 0.7146 (tp40) REVERT: A 65 ARG cc_start: 0.7491 (mmt-90) cc_final: 0.7029 (mmt-90) REVERT: A 102 PHE cc_start: 0.8512 (p90) cc_final: 0.8240 (p90) REVERT: A 266 ILE cc_start: 0.7252 (mt) cc_final: 0.6967 (tt) REVERT: B 45 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7806 (ttp80) REVERT: B 220 PHE cc_start: 0.7635 (t80) cc_final: 0.7085 (t80) REVERT: B 226 GLU cc_start: 0.7047 (tp30) cc_final: 0.6742 (tp30) REVERT: B 330 LEU cc_start: 0.8330 (tp) cc_final: 0.8125 (mt) REVERT: B 354 LEU cc_start: 0.8275 (tp) cc_final: 0.8064 (tt) REVERT: B 373 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6680 (t80) REVERT: C 45 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7675 (ttp80) REVERT: C 71 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6826 (mt-10) REVERT: C 81 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7310 (mtt180) REVERT: C 216 GLU cc_start: 0.7286 (mp0) cc_final: 0.6436 (mp0) REVERT: C 280 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6494 (mtp) REVERT: C 296 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (mp) REVERT: C 354 LEU cc_start: 0.8197 (tp) cc_final: 0.7959 (tt) REVERT: C 373 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6504 (t80) REVERT: C 425 THR cc_start: 0.8492 (t) cc_final: 0.8262 (t) REVERT: D 280 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6766 (mtp) REVERT: D 296 LEU cc_start: 0.7962 (mt) cc_final: 0.7736 (mt) REVERT: E 24 GLN cc_start: 0.7748 (mt0) cc_final: 0.7524 (tt0) REVERT: E 330 LEU cc_start: 0.8462 (tp) cc_final: 0.8246 (mt) REVERT: E 354 LEU cc_start: 0.8190 (tp) cc_final: 0.7843 (tp) REVERT: E 415 ASN cc_start: 0.7830 (m-40) cc_final: 0.7552 (m-40) REVERT: F 45 ARG cc_start: 0.8426 (ttm110) cc_final: 0.8173 (ttp80) REVERT: F 52 GLN cc_start: 0.7714 (tp40) cc_final: 0.6921 (tp-100) REVERT: F 207 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7123 (p0) REVERT: F 226 GLU cc_start: 0.6934 (tp30) cc_final: 0.6703 (tt0) REVERT: F 231 LYS cc_start: 0.7964 (mttt) cc_final: 0.7754 (mtpm) outliers start: 50 outliers final: 39 residues processed: 523 average time/residue: 1.3885 time to fit residues: 811.4734 Evaluate side-chains 548 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 500 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 188 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN B 52 GLN B 343 ASN C 52 GLN C 343 ASN D 343 ASN E 137 ASN F 137 ASN F 343 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117939 restraints weight = 25396.759| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.70 r_work: 0.3353 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20424 Z= 0.200 Angle : 0.457 5.318 27732 Z= 0.248 Chirality : 0.037 0.157 3126 Planarity : 0.003 0.036 3474 Dihedral : 8.782 64.770 3174 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.48 % Allowed : 21.52 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.06 (0.17), residues: 2532 helix: 1.77 (0.13), residues: 1668 sheet: None (None), residues: 0 loop : -1.50 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.006 0.001 HIS A 243 PHE 0.012 0.001 PHE E 220 TYR 0.019 0.001 TYR B 257 ARG 0.008 0.000 ARG F 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10792.84 seconds wall clock time: 189 minutes 15.83 seconds (11355.83 seconds total)