Starting phenix.real_space_refine on Wed Mar 20 11:04:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhs_16068/03_2024/8bhs_16068_trim_updated.pdb" } resolution = 3.24 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 5 7.06 5 S 85 5.16 5 C 8900 2.51 5 N 2285 2.21 5 O 2470 1.98 5 F 10 1.80 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27170 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'QK9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'QK9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'QK9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'QK9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'QK9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.31, per 1000 atoms: 0.45 Number of scatterers: 27170 At special positions: 0 Unit cell: (93.45, 92.4, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 5 34.99 S 85 16.00 F 10 9.00 O 2470 8.00 N 2285 7.00 C 8900 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 20.90 Conformation dependent library (CDL) restraints added in 2.9 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 15 sheets defined 35.4% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.505A pdb=" N SER A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 279 removed outlier: 3.509A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 313 Processing helix chain 'A' and resid 318 through 417 removed outlier: 3.608A pdb=" N LYS A 393 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 16 through 26 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.506A pdb=" N SER B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 279 removed outlier: 3.509A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 313 Processing helix chain 'B' and resid 318 through 417 removed outlier: 3.608A pdb=" N LYS B 393 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 16 through 26 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 249 removed outlier: 3.505A pdb=" N SER C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 279 removed outlier: 3.508A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 313 Processing helix chain 'C' and resid 318 through 417 removed outlier: 3.608A pdb=" N LYS C 393 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 16 through 26 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 234 through 249 removed outlier: 3.506A pdb=" N SER D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 3.509A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 313 Processing helix chain 'D' and resid 318 through 417 removed outlier: 3.608A pdb=" N LYS D 393 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 249 removed outlier: 3.506A pdb=" N SER E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 279 removed outlier: 3.509A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 313 Processing helix chain 'E' and resid 318 through 417 removed outlier: 3.607A pdb=" N LYS E 393 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.789A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.521A pdb=" N MET A 48 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 137 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 153 through 160 removed outlier: 3.864A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.790A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.521A pdb=" N MET B 48 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 137 " --> pdb=" O PHE B 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 153 through 160 removed outlier: 3.864A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.789A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 182 through 184 removed outlier: 6.521A pdb=" N MET C 48 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 137 " --> pdb=" O PHE C 111 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 153 through 160 removed outlier: 3.865A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.790A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 182 through 184 removed outlier: 6.520A pdb=" N MET D 48 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 137 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 153 through 160 removed outlier: 3.865A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.790A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.521A pdb=" N MET E 48 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 137 " --> pdb=" O PHE E 111 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 153 through 160 removed outlier: 3.864A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1740 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: 9.27 Time building geometry restraints manager: 21.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 13415 1.05 - 1.26: 2100 1.26 - 1.47: 6080 1.47 - 1.69: 5795 1.69 - 1.90: 155 Bond restraints: 27545 Sorted by residual: bond pdb=" C QK9 C 502 " pdb=" N4 QK9 C 502 " ideal model delta sigma weight residual 1.000 1.466 -0.466 2.00e-02 2.50e+03 5.42e+02 bond pdb=" C QK9 E 502 " pdb=" N4 QK9 E 502 " ideal model delta sigma weight residual 1.000 1.465 -0.465 2.00e-02 2.50e+03 5.41e+02 bond pdb=" C QK9 A 502 " pdb=" N4 QK9 A 502 " ideal model delta sigma weight residual 1.000 1.465 -0.465 2.00e-02 2.50e+03 5.41e+02 bond pdb=" C QK9 D 502 " pdb=" N4 QK9 D 502 " ideal model delta sigma weight residual 1.000 1.464 -0.464 2.00e-02 2.50e+03 5.39e+02 bond pdb=" C QK9 B 502 " pdb=" N4 QK9 B 502 " ideal model delta sigma weight residual 1.000 1.464 -0.464 2.00e-02 2.50e+03 5.39e+02 ... (remaining 27540 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.12: 516 107.12 - 113.93: 32208 113.93 - 120.74: 9903 120.74 - 127.55: 6698 127.55 - 134.36: 190 Bond angle restraints: 49515 Sorted by residual: angle pdb=" C1 QK9 D 502 " pdb=" N1 QK9 D 502 " pdb=" C4 QK9 D 502 " ideal model delta sigma weight residual 112.05 126.85 -14.80 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C1 QK9 B 502 " pdb=" N1 QK9 B 502 " pdb=" C4 QK9 B 502 " ideal model delta sigma weight residual 112.05 126.84 -14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C1 QK9 A 502 " pdb=" N1 QK9 A 502 " pdb=" C4 QK9 A 502 " ideal model delta sigma weight residual 112.05 126.81 -14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C1 QK9 C 502 " pdb=" N1 QK9 C 502 " pdb=" C4 QK9 C 502 " ideal model delta sigma weight residual 112.05 126.80 -14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C1 QK9 E 502 " pdb=" N1 QK9 E 502 " pdb=" C4 QK9 E 502 " ideal model delta sigma weight residual 112.05 126.80 -14.75 3.00e+00 1.11e-01 2.42e+01 ... (remaining 49510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 12428 14.87 - 29.75: 442 29.75 - 44.62: 115 44.62 - 59.49: 110 59.49 - 74.36: 10 Dihedral angle restraints: 13105 sinusoidal: 6975 harmonic: 6130 Sorted by residual: dihedral pdb=" CA LEU A 93 " pdb=" CB LEU A 93 " pdb=" CG LEU A 93 " pdb=" CD1 LEU A 93 " ideal model delta sinusoidal sigma weight residual 180.00 137.02 42.98 3 1.50e+01 4.44e-03 7.72e+00 dihedral pdb=" CA LEU D 93 " pdb=" CB LEU D 93 " pdb=" CG LEU D 93 " pdb=" CD1 LEU D 93 " ideal model delta sinusoidal sigma weight residual 180.00 137.03 42.97 3 1.50e+01 4.44e-03 7.72e+00 dihedral pdb=" CA LEU C 93 " pdb=" CB LEU C 93 " pdb=" CG LEU C 93 " pdb=" CD1 LEU C 93 " ideal model delta sinusoidal sigma weight residual 180.00 137.04 42.96 3 1.50e+01 4.44e-03 7.72e+00 ... (remaining 13102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1203 0.024 - 0.048: 628 0.048 - 0.071: 164 0.071 - 0.095: 80 0.095 - 0.119: 85 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE E 65 " pdb=" N ILE E 65 " pdb=" C ILE E 65 " pdb=" CB ILE E 65 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 2157 not shown) Planarity restraints: 3995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 QK9 C 502 " -0.017 2.00e-02 2.50e+03 1.38e-02 4.28e+00 pdb=" C4 QK9 C 502 " -0.004 2.00e-02 2.50e+03 pdb=" C5 QK9 C 502 " 0.002 2.00e-02 2.50e+03 pdb=" C6 QK9 C 502 " 0.007 2.00e-02 2.50e+03 pdb=" C7 QK9 C 502 " 0.001 2.00e-02 2.50e+03 pdb=" C8 QK9 C 502 " -0.013 2.00e-02 2.50e+03 pdb=" C9 QK9 C 502 " -0.016 2.00e-02 2.50e+03 pdb=" N1 QK9 C 502 " 0.028 2.00e-02 2.50e+03 pdb="BR QK9 C 502 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 QK9 B 502 " 0.018 2.00e-02 2.50e+03 1.37e-02 4.25e+00 pdb=" C4 QK9 B 502 " 0.004 2.00e-02 2.50e+03 pdb=" C5 QK9 B 502 " -0.002 2.00e-02 2.50e+03 pdb=" C6 QK9 B 502 " -0.007 2.00e-02 2.50e+03 pdb=" C7 QK9 B 502 " -0.001 2.00e-02 2.50e+03 pdb=" C8 QK9 B 502 " 0.014 2.00e-02 2.50e+03 pdb=" C9 QK9 B 502 " 0.015 2.00e-02 2.50e+03 pdb=" N1 QK9 B 502 " -0.027 2.00e-02 2.50e+03 pdb="BR QK9 B 502 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 QK9 E 502 " 0.017 2.00e-02 2.50e+03 1.37e-02 4.24e+00 pdb=" C4 QK9 E 502 " 0.004 2.00e-02 2.50e+03 pdb=" C5 QK9 E 502 " -0.002 2.00e-02 2.50e+03 pdb=" C6 QK9 E 502 " -0.007 2.00e-02 2.50e+03 pdb=" C7 QK9 E 502 " -0.001 2.00e-02 2.50e+03 pdb=" C8 QK9 E 502 " 0.013 2.00e-02 2.50e+03 pdb=" C9 QK9 E 502 " 0.015 2.00e-02 2.50e+03 pdb=" N1 QK9 E 502 " -0.028 2.00e-02 2.50e+03 pdb="BR QK9 E 502 " -0.012 2.00e-02 2.50e+03 ... (remaining 3992 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.27: 3982 2.27 - 2.88: 64390 2.88 - 3.49: 72716 3.49 - 4.09: 107603 4.09 - 4.70: 166298 Nonbonded interactions: 414989 Sorted by model distance: nonbonded pdb=" O PHE B 229 " pdb=" H THR B 233 " model vdw 1.669 1.850 nonbonded pdb=" O PHE E 229 " pdb=" H THR E 233 " model vdw 1.669 1.850 nonbonded pdb=" O PHE D 229 " pdb=" H THR D 233 " model vdw 1.669 1.850 nonbonded pdb=" O PHE C 229 " pdb=" H THR C 233 " model vdw 1.669 1.850 nonbonded pdb=" O PHE A 229 " pdb=" H THR A 233 " model vdw 1.669 1.850 ... (remaining 414984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.980 Check model and map are aligned: 0.390 Set scattering table: 0.270 Process input model: 86.140 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.020 0.466 14130 Z= 1.219 Angle : 0.746 14.801 19240 Z= 0.296 Chirality : 0.037 0.119 2160 Planarity : 0.003 0.025 2390 Dihedral : 7.511 74.364 5095 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.23 (0.22), residues: 1670 helix: 2.66 (0.23), residues: 550 sheet: -0.15 (0.25), residues: 505 loop : 0.06 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 414 HIS 0.001 0.000 HIS B 105 PHE 0.005 0.001 PHE A 104 TYR 0.004 0.001 TYR A 172 ARG 0.001 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 GLN cc_start: 0.8878 (tp40) cc_final: 0.8525 (tp40) REVERT: B 289 MET cc_start: 0.8674 (ttp) cc_final: 0.8317 (ttp) REVERT: C 232 GLN cc_start: 0.8888 (tp40) cc_final: 0.8515 (tp40) REVERT: E 289 MET cc_start: 0.8733 (ttp) cc_final: 0.8509 (ttp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.5060 time to fit residues: 106.2417 Evaluate side-chains 97 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 105 HIS B 85 GLN B 105 HIS C 85 GLN C 105 HIS D 85 GLN D 105 HIS E 85 GLN E 105 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14130 Z= 0.195 Angle : 0.491 4.555 19240 Z= 0.250 Chirality : 0.040 0.144 2160 Planarity : 0.004 0.033 2390 Dihedral : 4.574 69.366 1960 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.27 % Allowed : 4.77 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.25 (0.22), residues: 1670 helix: 2.94 (0.22), residues: 545 sheet: -0.27 (0.24), residues: 510 loop : -0.05 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 73 HIS 0.002 0.001 HIS D 221 PHE 0.008 0.001 PHE C 409 TYR 0.008 0.001 TYR D 417 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 GLN cc_start: 0.9023 (tp40) cc_final: 0.8557 (tp40) REVERT: C 232 GLN cc_start: 0.9050 (tp40) cc_final: 0.8785 (tp40) outliers start: 4 outliers final: 4 residues processed: 110 average time/residue: 0.4517 time to fit residues: 80.0142 Evaluate side-chains 99 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 410 ASN B 155 ASN B 410 ASN C 155 ASN C 410 ASN D 106 ASN D 410 ASN E 410 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 14130 Z= 0.409 Angle : 0.578 5.606 19240 Z= 0.294 Chirality : 0.041 0.137 2160 Planarity : 0.004 0.036 2390 Dihedral : 3.937 31.896 1960 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.34 % Allowed : 4.70 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.80 (0.21), residues: 1670 helix: 2.61 (0.22), residues: 550 sheet: -0.70 (0.23), residues: 490 loop : -0.22 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 291 HIS 0.003 0.001 HIS D 221 PHE 0.016 0.001 PHE E 104 TYR 0.010 0.002 TYR D 163 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8485 (mtm) cc_final: 0.8122 (mtm) REVERT: D 289 MET cc_start: 0.8796 (ttp) cc_final: 0.8474 (ttp) REVERT: E 61 MET cc_start: 0.8787 (mmt) cc_final: 0.8582 (mmt) REVERT: E 115 MET cc_start: 0.8509 (mmt) cc_final: 0.8202 (mmt) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.5468 time to fit residues: 83.1021 Evaluate side-chains 100 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 114 TRP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 14130 Z= 0.169 Angle : 0.464 4.900 19240 Z= 0.230 Chirality : 0.039 0.131 2160 Planarity : 0.003 0.036 2390 Dihedral : 4.205 52.759 1960 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.34 % Allowed : 6.11 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 (0.21), residues: 1670 helix: 2.98 (0.22), residues: 545 sheet: -0.61 (0.24), residues: 480 loop : -0.14 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 73 HIS 0.001 0.000 HIS A 221 PHE 0.011 0.001 PHE D 104 TYR 0.009 0.001 TYR C 417 ARG 0.001 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 289 MET cc_start: 0.8792 (ttp) cc_final: 0.8368 (ttp) REVERT: E 115 MET cc_start: 0.8490 (mmp) cc_final: 0.8037 (mmt) outliers start: 5 outliers final: 5 residues processed: 96 average time/residue: 0.4983 time to fit residues: 75.6442 Evaluate side-chains 91 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14130 Z= 0.223 Angle : 0.474 5.056 19240 Z= 0.236 Chirality : 0.039 0.131 2160 Planarity : 0.003 0.036 2390 Dihedral : 4.167 51.166 1960 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.60 % Allowed : 6.11 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.04 (0.21), residues: 1670 helix: 3.01 (0.22), residues: 545 sheet: -0.67 (0.23), residues: 480 loop : -0.17 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 414 HIS 0.002 0.001 HIS C 221 PHE 0.011 0.001 PHE E 104 TYR 0.007 0.001 TYR A 132 ARG 0.001 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: B 115 MET cc_start: 0.8257 (mmt) cc_final: 0.8001 (mmp) REVERT: C 245 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7884 (mp10) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.4706 time to fit residues: 69.4269 Evaluate side-chains 95 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 39 optimal weight: 0.2980 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 14130 Z= 0.239 Angle : 0.475 5.159 19240 Z= 0.236 Chirality : 0.039 0.130 2160 Planarity : 0.003 0.036 2390 Dihedral : 4.156 49.548 1960 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.01 % Allowed : 6.11 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.00 (0.21), residues: 1670 helix: 3.05 (0.22), residues: 545 sheet: -0.78 (0.23), residues: 480 loop : -0.19 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 114 HIS 0.002 0.001 HIS C 221 PHE 0.012 0.001 PHE E 104 TYR 0.008 0.001 TYR A 132 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: B 115 MET cc_start: 0.8357 (mmt) cc_final: 0.8084 (mmp) REVERT: B 245 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: C 245 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: D 245 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7875 (mp10) outliers start: 15 outliers final: 11 residues processed: 95 average time/residue: 0.4757 time to fit residues: 72.4576 Evaluate side-chains 103 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 114 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14130 Z= 0.273 Angle : 0.490 5.125 19240 Z= 0.244 Chirality : 0.039 0.130 2160 Planarity : 0.004 0.037 2390 Dihedral : 4.130 46.623 1960 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.01 % Allowed : 6.38 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.91 (0.21), residues: 1670 helix: 3.00 (0.22), residues: 550 sheet: -0.92 (0.23), residues: 490 loop : -0.19 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 114 HIS 0.002 0.001 HIS E 113 PHE 0.013 0.001 PHE E 104 TYR 0.007 0.001 TYR D 163 ARG 0.001 0.000 ARG E 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: B 245 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: C 245 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: D 245 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7890 (mp10) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.4853 time to fit residues: 72.8092 Evaluate side-chains 103 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 114 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14130 Z= 0.149 Angle : 0.451 5.077 19240 Z= 0.220 Chirality : 0.038 0.126 2160 Planarity : 0.003 0.037 2390 Dihedral : 4.329 57.872 1960 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.67 % Allowed : 6.58 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.15 (0.22), residues: 1670 helix: 3.17 (0.22), residues: 550 sheet: -0.78 (0.23), residues: 480 loop : -0.04 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 114 HIS 0.001 0.000 HIS C 221 PHE 0.009 0.001 PHE E 104 TYR 0.008 0.001 TYR D 417 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: B 245 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: C 245 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8031 (mp10) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.4743 time to fit residues: 76.2061 Evaluate side-chains 104 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14130 Z= 0.162 Angle : 0.455 5.132 19240 Z= 0.221 Chirality : 0.038 0.126 2160 Planarity : 0.003 0.037 2390 Dihedral : 4.235 55.999 1960 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.94 % Allowed : 6.58 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.19 (0.22), residues: 1670 helix: 3.20 (0.22), residues: 550 sheet: -0.74 (0.23), residues: 480 loop : -0.04 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 414 HIS 0.001 0.000 HIS E 105 PHE 0.009 0.001 PHE E 104 TYR 0.008 0.001 TYR D 417 ARG 0.001 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8273 (mp10) REVERT: B 245 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: C 245 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: D 245 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7916 (mp10) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.4856 time to fit residues: 77.9416 Evaluate side-chains 108 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 114 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 14130 Z= 0.142 Angle : 0.446 5.169 19240 Z= 0.216 Chirality : 0.038 0.126 2160 Planarity : 0.003 0.037 2390 Dihedral : 4.258 58.141 1960 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.67 % Allowed : 6.64 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.26 (0.22), residues: 1670 helix: 3.27 (0.22), residues: 550 sheet: -0.70 (0.23), residues: 480 loop : -0.00 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 414 HIS 0.001 0.000 HIS B 221 PHE 0.008 0.001 PHE E 104 TYR 0.011 0.001 TYR D 297 ARG 0.001 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: C 245 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7988 (mp10) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.4726 time to fit residues: 76.1806 Evaluate side-chains 103 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 16 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061982 restraints weight = 95646.763| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.66 r_work: 0.2947 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 14130 Z= 0.133 Angle : 0.444 5.090 19240 Z= 0.215 Chirality : 0.038 0.124 2160 Planarity : 0.003 0.037 2390 Dihedral : 4.241 58.648 1960 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.60 % Allowed : 6.71 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.33 (0.22), residues: 1670 helix: 3.34 (0.22), residues: 550 sheet: -0.66 (0.23), residues: 480 loop : 0.02 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 414 HIS 0.001 0.000 HIS E 219 PHE 0.008 0.001 PHE D 261 TYR 0.010 0.001 TYR B 297 ARG 0.001 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4718.80 seconds wall clock time: 84 minutes 58.15 seconds (5098.15 seconds total)