Starting phenix.real_space_refine on Wed Mar 20 11:44:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/03_2024/8bho_16063_trim_updated.pdb" } resolution = 2.93 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8925 2.51 5 N 2275 2.21 5 O 2490 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 301": "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: 27190 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 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: 12.38, per 1000 atoms: 0.46 Number of scatterers: 27190 At special positions: 0 Unit cell: (92.4, 94.5, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 2490 8.00 N 2275 7.00 C 8925 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: 20.95 Conformation dependent library (CDL) restraints added in 2.6 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: 45 helices and 15 sheets defined 36.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 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 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 234 through 249 removed outlier: 4.152A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 279 removed outlier: 3.859A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.361A 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: 3.959A 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 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 234 through 249 removed outlier: 4.152A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 279 removed outlier: 3.858A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.361A 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: 3.958A 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 178 through 181 No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 249 removed outlier: 4.152A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 279 removed outlier: 3.859A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.361A 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: 3.958A 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 178 through 181 No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 234 through 249 removed outlier: 4.152A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 3.859A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.360A 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: 3.958A 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 178 through 181 No H-bonds generated for 'chain 'E' and resid 178 through 181' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 249 removed outlier: 4.152A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 279 removed outlier: 3.858A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.360A 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: 3.959A 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: 6.769A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.340A 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: 6.765A pdb=" N MET A 48 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.674A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.575A 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: 6.768A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.339A 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: 6.765A pdb=" N MET B 48 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.575A 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: 6.769A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.339A 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: 6.765A pdb=" N MET C 48 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.575A 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: 6.769A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.339A 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: 6.765A pdb=" N MET D 48 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.574A 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: 6.769A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.339A 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: 6.764A pdb=" N MET E 48 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.674A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1755 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: 10.03 Time building geometry restraints manager: 21.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 10 1.23 - 1.42: 6105 1.42 - 1.61: 7885 1.61 - 1.81: 150 Bond restraints: 27565 Sorted by residual: bond pdb=" C13 QMJ A 502 " pdb=" N2 QMJ A 502 " ideal model delta sigma weight residual 1.139 1.464 -0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C13 QMJ D 502 " pdb=" N2 QMJ D 502 " ideal model delta sigma weight residual 1.139 1.464 -0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C13 QMJ C 502 " pdb=" N2 QMJ C 502 " ideal model delta sigma weight residual 1.139 1.463 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" C13 QMJ E 502 " pdb=" N2 QMJ E 502 " ideal model delta sigma weight residual 1.139 1.463 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" C13 QMJ B 502 " pdb=" N2 QMJ B 502 " ideal model delta sigma weight residual 1.139 1.463 -0.324 2.00e-02 2.50e+03 2.63e+02 ... (remaining 27560 not shown) Histogram of bond angle deviations from ideal: 100.61 - 107.28: 626 107.28 - 113.96: 32078 113.96 - 120.63: 9635 120.63 - 127.31: 7006 127.31 - 133.99: 195 Bond angle restraints: 49540 Sorted by residual: angle pdb=" N QMJ A 502 " pdb=" C4 QMJ A 502 " pdb=" C13 QMJ A 502 " ideal model delta sigma weight residual 110.68 126.35 -15.67 3.00e+00 1.11e-01 2.73e+01 angle pdb=" N QMJ D 502 " pdb=" C4 QMJ D 502 " pdb=" C13 QMJ D 502 " ideal model delta sigma weight residual 110.68 126.34 -15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" N QMJ B 502 " pdb=" C4 QMJ B 502 " pdb=" C13 QMJ B 502 " ideal model delta sigma weight residual 110.68 126.33 -15.65 3.00e+00 1.11e-01 2.72e+01 angle pdb=" N QMJ C 502 " pdb=" C4 QMJ C 502 " pdb=" C13 QMJ C 502 " ideal model delta sigma weight residual 110.68 126.32 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" N QMJ E 502 " pdb=" C4 QMJ E 502 " pdb=" C13 QMJ E 502 " ideal model delta sigma weight residual 110.68 126.29 -15.61 3.00e+00 1.11e-01 2.71e+01 ... (remaining 49535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 12665 16.10 - 32.20: 245 32.20 - 48.29: 120 48.29 - 64.39: 100 64.39 - 80.49: 10 Dihedral angle restraints: 13140 sinusoidal: 7010 harmonic: 6130 Sorted by residual: dihedral pdb=" C12 QMJ A 502 " pdb=" C16 QMJ A 502 " pdb=" N2 QMJ A 502 " pdb=" C15 QMJ A 502 " ideal model delta sinusoidal sigma weight residual -98.17 -174.04 75.87 1 3.00e+01 1.11e-03 8.06e+00 dihedral pdb=" C12 QMJ D 502 " pdb=" C16 QMJ D 502 " pdb=" N2 QMJ D 502 " pdb=" C15 QMJ D 502 " ideal model delta sinusoidal sigma weight residual -98.17 -174.04 75.87 1 3.00e+01 1.11e-03 8.06e+00 dihedral pdb=" C12 QMJ B 502 " pdb=" C16 QMJ B 502 " pdb=" N2 QMJ B 502 " pdb=" C15 QMJ B 502 " ideal model delta sinusoidal sigma weight residual -98.17 -174.03 75.86 1 3.00e+01 1.11e-03 8.06e+00 ... (remaining 13137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1302 0.025 - 0.050: 571 0.050 - 0.075: 152 0.075 - 0.100: 56 0.100 - 0.125: 84 Chirality restraints: 2165 Sorted by residual: chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 205 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 205 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 205 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 2162 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 QMJ A 502 " 0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ A 502 " -0.032 2.00e-02 2.50e+03 pdb=" C13 QMJ A 502 " -0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ A 502 " 0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ A 502 " 0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ A 502 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QMJ E 502 " 0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ E 502 " -0.032 2.00e-02 2.50e+03 pdb=" C13 QMJ E 502 " -0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ E 502 " 0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ E 502 " 0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ E 502 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QMJ C 502 " -0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ C 502 " 0.031 2.00e-02 2.50e+03 pdb=" C13 QMJ C 502 " 0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ C 502 " -0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ C 502 " -0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ C 502 " 0.375 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 5541 2.31 - 2.88: 62234 2.88 - 3.45: 67898 3.45 - 4.03: 97283 4.03 - 4.60: 146747 Nonbonded interactions: 379703 Sorted by model distance: nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.735 1.850 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.735 1.850 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.735 1.850 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.735 1.850 nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.735 1.850 ... (remaining 379698 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: 1.210 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: 0.400 Extract box with map and model: 8.220 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 85.750 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.013 0.325 14150 Z= 0.836 Angle : 0.714 15.672 19265 Z= 0.268 Chirality : 0.037 0.125 2165 Planarity : 0.014 0.301 2395 Dihedral : 7.530 80.490 5130 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 2.52 (0.22), residues: 1670 helix: 3.34 (0.21), residues: 575 sheet: 0.79 (0.27), residues: 435 loop : 0.89 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 73 HIS 0.002 0.000 HIS E 195 PHE 0.004 0.000 PHE C 149 TYR 0.004 0.001 TYR C 285 ARG 0.001 0.000 ARG E 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 160 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.268 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 48 MET cc_start: 0.8782 (ttm) cc_final: 0.8433 (ttm) REVERT: B 48 MET cc_start: 0.8877 (ttm) cc_final: 0.8649 (mtp) REVERT: B 289 MET cc_start: 0.8636 (ttp) cc_final: 0.8315 (ttp) REVERT: D 289 MET cc_start: 0.8606 (ttp) cc_final: 0.8395 (ttp) REVERT: E 289 MET cc_start: 0.8619 (ttp) cc_final: 0.8387 (ttp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 2.9235 time to fit residues: 509.5457 Evaluate side-chains 106 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.271 ------------------------------------------------------------------------------- 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: 6.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.0050 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN D 71 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14150 Z= 0.193 Angle : 0.571 9.612 19265 Z= 0.271 Chirality : 0.039 0.139 2165 Planarity : 0.004 0.062 2395 Dihedral : 8.256 106.026 1995 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.60 % Allowed : 5.50 % Favored : 93.89 % 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: 2.20 (0.22), residues: 1670 helix: 3.20 (0.22), residues: 580 sheet: 0.63 (0.26), residues: 460 loop : 0.51 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 174 HIS 0.002 0.001 HIS B 221 PHE 0.010 0.001 PHE E 69 TYR 0.008 0.001 TYR E 413 ARG 0.005 0.000 ARG A 190 *********************** 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 127 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 2.281 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: A 239 MET cc_start: 0.8845 (mmm) cc_final: 0.8615 (mmm) REVERT: B 289 MET cc_start: 0.8549 (ttp) cc_final: 0.8316 (ttp) REVERT: C 115 MET cc_start: 0.7927 (mmp) cc_final: 0.7724 (mmp) REVERT: D 269 MET cc_start: 0.8907 (mmm) cc_final: 0.8504 (mmm) REVERT: D 397 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8257 (ttt) outliers start: 9 outliers final: 0 residues processed: 118 average time/residue: 2.6573 time to fit residues: 347.5877 Evaluate side-chains 93 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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: 4.9990 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14150 Z= 0.162 Angle : 0.559 11.460 19265 Z= 0.258 Chirality : 0.039 0.129 2165 Planarity : 0.004 0.040 2395 Dihedral : 7.654 92.851 1995 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.54 % Allowed : 7.05 % Favored : 92.42 % 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: 2.10 (0.21), residues: 1670 helix: 3.25 (0.22), residues: 580 sheet: 0.50 (0.26), residues: 455 loop : 0.37 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 114 HIS 0.003 0.001 HIS C 195 PHE 0.010 0.001 PHE E 69 TYR 0.007 0.001 TYR E 413 ARG 0.004 0.000 ARG A 190 *********************** 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 109 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 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: D 397 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8215 (ttt) outliers start: 8 outliers final: 1 residues processed: 101 average time/residue: 2.7635 time to fit residues: 307.1847 Evaluate side-chains 99 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain D 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: 0.4980 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14150 Z= 0.215 Angle : 0.566 11.202 19265 Z= 0.264 Chirality : 0.039 0.131 2165 Planarity : 0.004 0.056 2395 Dihedral : 7.534 94.056 1995 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.47 % Allowed : 6.38 % Favored : 93.15 % 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: 1.92 (0.21), residues: 1670 helix: 3.29 (0.22), residues: 580 sheet: 0.30 (0.25), residues: 460 loop : 0.17 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 114 HIS 0.002 0.001 HIS D 221 PHE 0.010 0.001 PHE B 69 TYR 0.009 0.001 TYR A 417 ARG 0.003 0.000 ARG C 123 *********************** 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 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 3.648 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: A 245 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: D 115 MET cc_start: 0.8085 (mmp) cc_final: 0.7846 (mmp) REVERT: D 216 MET cc_start: 0.9165 (mmm) cc_final: 0.8957 (mmm) REVERT: D 397 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8258 (ttt) REVERT: E 397 MET cc_start: 0.8522 (ttm) cc_final: 0.8066 (ttp) outliers start: 7 outliers final: 2 residues processed: 105 average time/residue: 2.7200 time to fit residues: 316.0978 Evaluate side-chains 104 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 114 TRP 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: 1.9990 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 14150 Z= 0.255 Angle : 0.576 11.449 19265 Z= 0.270 Chirality : 0.039 0.126 2165 Planarity : 0.004 0.050 2395 Dihedral : 7.239 95.607 1995 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.87 % Allowed : 6.31 % Favored : 92.82 % 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: 1.70 (0.21), residues: 1670 helix: 3.43 (0.21), residues: 550 sheet: 0.19 (0.24), residues: 485 loop : -0.14 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.002 0.001 HIS B 221 PHE 0.009 0.001 PHE B 104 TYR 0.011 0.001 TYR C 132 ARG 0.003 0.000 ARG A 190 *********************** 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 115 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: C 245 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: D 397 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8284 (ttt) REVERT: E 397 MET cc_start: 0.8536 (ttm) cc_final: 0.8077 (ttp) outliers start: 13 outliers final: 4 residues processed: 107 average time/residue: 2.6194 time to fit residues: 311.2467 Evaluate side-chains 106 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14150 Z= 0.265 Angle : 0.578 11.363 19265 Z= 0.271 Chirality : 0.040 0.129 2165 Planarity : 0.004 0.054 2395 Dihedral : 7.363 100.993 1995 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.74 % Allowed : 6.64 % 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: 1.74 (0.21), residues: 1670 helix: 3.46 (0.21), residues: 550 sheet: 0.09 (0.26), residues: 430 loop : -0.02 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 114 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.001 PHE D 104 TYR 0.011 0.001 TYR A 417 ARG 0.003 0.000 ARG A 190 *********************** 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 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: C 245 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: D 115 MET cc_start: 0.8152 (mmp) cc_final: 0.7849 (mmt) REVERT: D 397 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8302 (ttt) REVERT: E 397 MET cc_start: 0.8514 (ttm) cc_final: 0.8063 (ttp) outliers start: 11 outliers final: 4 residues processed: 105 average time/residue: 2.6245 time to fit residues: 305.4078 Evaluate side-chains 98 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 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: 4.9990 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14150 Z= 0.252 Angle : 0.574 11.397 19265 Z= 0.268 Chirality : 0.039 0.127 2165 Planarity : 0.004 0.049 2395 Dihedral : 7.523 108.763 1995 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.54 % Allowed : 7.72 % Favored : 91.74 % 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: 1.71 (0.21), residues: 1670 helix: 3.50 (0.21), residues: 550 sheet: 0.02 (0.25), residues: 430 loop : -0.04 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 114 HIS 0.002 0.000 HIS E 221 PHE 0.010 0.001 PHE D 104 TYR 0.010 0.001 TYR D 417 ARG 0.003 0.000 ARG B 190 *********************** 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: 8 poor density : 95 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: C 84 MET cc_start: 0.6889 (ttm) cc_final: 0.6643 (ttm) REVERT: C 144 MET cc_start: 0.8592 (mmt) cc_final: 0.8347 (mmt) REVERT: C 245 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: D 115 MET cc_start: 0.8173 (mmp) cc_final: 0.7881 (mmt) REVERT: D 397 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8277 (ttt) REVERT: E 397 MET cc_start: 0.8500 (ttm) cc_final: 0.8037 (ttp) outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 2.8076 time to fit residues: 305.2772 Evaluate side-chains 94 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14150 Z= 0.182 Angle : 0.550 10.953 19265 Z= 0.254 Chirality : 0.039 0.123 2165 Planarity : 0.004 0.052 2395 Dihedral : 7.504 107.843 1995 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.60 % Allowed : 7.38 % Favored : 92.01 % 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: 1.83 (0.21), residues: 1670 helix: 3.65 (0.21), residues: 550 sheet: 0.07 (0.25), residues: 430 loop : -0.01 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 114 HIS 0.002 0.000 HIS A 113 PHE 0.008 0.001 PHE D 104 TYR 0.008 0.001 TYR E 417 ARG 0.004 0.000 ARG D 190 *********************** 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 98 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 MET cc_start: 0.6872 (ttm) cc_final: 0.6642 (ttm) REVERT: C 144 MET cc_start: 0.8528 (mmt) cc_final: 0.8294 (mmt) REVERT: C 245 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: D 61 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8540 (mmm) REVERT: D 115 MET cc_start: 0.8149 (mmp) cc_final: 0.7891 (mmt) REVERT: D 397 MET cc_start: 0.8574 (ttm) cc_final: 0.8270 (ttt) REVERT: E 397 MET cc_start: 0.8479 (ttm) cc_final: 0.7996 (ttp) outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 2.6817 time to fit residues: 281.2033 Evaluate side-chains 94 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 133 THR 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: 0.3980 chunk 148 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 147 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14150 Z= 0.123 Angle : 0.527 10.483 19265 Z= 0.239 Chirality : 0.039 0.123 2165 Planarity : 0.004 0.038 2395 Dihedral : 7.332 100.943 1995 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.54 % Allowed : 7.72 % Favored : 91.74 % 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: 2.00 (0.21), residues: 1670 helix: 3.84 (0.21), residues: 550 sheet: 0.16 (0.25), residues: 430 loop : 0.05 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 114 HIS 0.002 0.001 HIS B 113 PHE 0.008 0.001 PHE E 261 TYR 0.006 0.001 TYR A 297 ARG 0.004 0.000 ARG B 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 102 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 2.315 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: B 27 ASP cc_start: 0.7667 (p0) cc_final: 0.7401 (p0) REVERT: C 84 MET cc_start: 0.7012 (ttm) cc_final: 0.6772 (ttm) REVERT: D 61 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8641 (tpt) REVERT: D 115 MET cc_start: 0.8150 (mmp) cc_final: 0.7849 (mmt) REVERT: D 151 MET cc_start: 0.7866 (mpt) cc_final: 0.7219 (mpt) REVERT: D 397 MET cc_start: 0.8532 (ttm) cc_final: 0.8230 (ttt) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 2.6723 time to fit residues: 291.9824 Evaluate side-chains 99 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14150 Z= 0.215 Angle : 0.558 11.017 19265 Z= 0.257 Chirality : 0.039 0.125 2165 Planarity : 0.004 0.059 2395 Dihedral : 7.329 107.270 1995 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.47 % Allowed : 7.99 % Favored : 91.54 % 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: 1.95 (0.21), residues: 1670 helix: 3.85 (0.21), residues: 550 sheet: 0.08 (0.25), residues: 430 loop : -0.01 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 114 HIS 0.002 0.001 HIS B 195 PHE 0.008 0.001 PHE B 104 TYR 0.009 0.001 TYR A 417 ARG 0.005 0.000 ARG D 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 99 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 2.169 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: A 245 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 245 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 84 MET cc_start: 0.7058 (ttm) cc_final: 0.6800 (ttm) REVERT: C 144 MET cc_start: 0.8332 (mmt) cc_final: 0.8032 (mmt) REVERT: D 61 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8612 (tpt) REVERT: D 115 MET cc_start: 0.8156 (mmp) cc_final: 0.7887 (mmt) REVERT: D 397 MET cc_start: 0.8559 (ttm) cc_final: 0.8257 (ttt) REVERT: E 397 MET cc_start: 0.8474 (ttm) cc_final: 0.8014 (ttp) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 2.5640 time to fit residues: 272.7320 Evaluate side-chains 97 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.079094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065738 restraints weight = 94496.779| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.09 r_work: 0.2992 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14150 Z= 0.141 Angle : 0.539 10.691 19265 Z= 0.245 Chirality : 0.039 0.121 2165 Planarity : 0.004 0.044 2395 Dihedral : 7.301 103.492 1995 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.47 % Allowed : 8.05 % Favored : 91.48 % 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: 1.99 (0.21), residues: 1670 helix: 3.87 (0.21), residues: 550 sheet: 0.13 (0.25), residues: 430 loop : 0.01 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 114 HIS 0.004 0.000 HIS C 113 PHE 0.007 0.001 PHE E 261 TYR 0.006 0.001 TYR D 413 ARG 0.004 0.000 ARG D 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7190.69 seconds wall clock time: 127 minutes 17.11 seconds (7637.11 seconds total)