Starting phenix.real_space_refine on Sat Mar 16 01:38:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6q_23207/03_2024/7l6q_23207_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6q_23207/03_2024/7l6q_23207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6q_23207/03_2024/7l6q_23207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6q_23207/03_2024/7l6q_23207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6q_23207/03_2024/7l6q_23207_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6q_23207/03_2024/7l6q_23207_updated.pdb" } resolution = 2.5 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= 0.013 sd= 0.225 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 30 5.16 5 C 8760 2.51 5 N 2115 2.21 5 O 2410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 13330 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 182 Unusual residues: {'CDL': 1, 'PGW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 131 Unusual residues: {'CDL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 131 Unusual residues: {'CDL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 131 Unusual residues: {'CDL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 80 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Time building chain proxies: 7.54, per 1000 atoms: 0.57 Number of scatterers: 13330 At special positions: 0 Unit cell: (90.132, 90.132, 120.176, 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 30 16.00 P 15 15.00 O 2410 8.00 N 2115 7.00 C 8760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.2 seconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 36.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.575A pdb=" N ILE A 63 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 64 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 67 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A 68 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 203 through 206 No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 209 through 224 removed outlier: 3.597A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP A 224 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 250 removed outlier: 3.646A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 295 through 320 removed outlier: 4.033A pdb=" N LEU A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.997A pdb=" N ILE A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.576A pdb=" N ILE B 63 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 64 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 68 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 203 through 206 No H-bonds generated for 'chain 'B' and resid 203 through 206' Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.597A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP B 224 " --> pdb=" O TRP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 250 removed outlier: 3.645A pdb=" N PHE B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 285 Processing helix chain 'B' and resid 295 through 320 removed outlier: 4.032A pdb=" N LEU B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.997A pdb=" N ILE B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 60 through 68 removed outlier: 3.576A pdb=" N ILE C 63 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 64 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 68 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 203 through 206 No H-bonds generated for 'chain 'C' and resid 203 through 206' Processing helix chain 'C' and resid 209 through 224 removed outlier: 3.597A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP C 224 " --> pdb=" O TRP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 250 removed outlier: 3.646A pdb=" N PHE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 285 Processing helix chain 'C' and resid 295 through 320 removed outlier: 4.031A pdb=" N LEU C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.997A pdb=" N ILE C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 60 through 68 removed outlier: 3.575A pdb=" N ILE D 63 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 64 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 67 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 68 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 203 through 206 No H-bonds generated for 'chain 'D' and resid 203 through 206' Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.597A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP D 224 " --> pdb=" O TRP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 250 removed outlier: 3.645A pdb=" N PHE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 285 Processing helix chain 'D' and resid 295 through 320 removed outlier: 4.033A pdb=" N LEU D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.997A pdb=" N ILE D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 60 through 68 removed outlier: 3.576A pdb=" N ILE E 63 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU E 64 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 67 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN E 68 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 155 through 157 No H-bonds generated for 'chain 'E' and resid 155 through 157' Processing helix chain 'E' and resid 203 through 206 No H-bonds generated for 'chain 'E' and resid 203 through 206' Processing helix chain 'E' and resid 209 through 224 removed outlier: 3.597A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER E 221 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP E 224 " --> pdb=" O TRP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 250 removed outlier: 3.647A pdb=" N PHE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR E 237 " --> pdb=" O GLN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 285 Processing helix chain 'E' and resid 295 through 320 removed outlier: 4.033A pdb=" N LEU E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.998A pdb=" N ILE E 320 " --> pdb=" O VAL E 316 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 143 through 146 removed outlier: 6.817A pdb=" N VAL A 16 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLN A 146 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 18 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 78 removed outlier: 4.207A pdb=" N ASP A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 167 through 174 Processing sheet with id= E, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'B' and resid 143 through 146 removed outlier: 6.816A pdb=" N VAL B 16 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLN B 146 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 18 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 76 through 78 removed outlier: 4.207A pdb=" N ASP B 196 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 167 through 174 Processing sheet with id= I, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.816A pdb=" N VAL C 16 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLN C 146 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 18 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.206A pdb=" N ASP C 196 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 167 through 174 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'D' and resid 143 through 146 removed outlier: 6.816A pdb=" N VAL D 16 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLN D 146 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 18 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 76 through 78 removed outlier: 4.206A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 167 through 174 Processing sheet with id= Q, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= R, first strand: chain 'E' and resid 143 through 146 removed outlier: 6.816A pdb=" N VAL E 16 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLN E 146 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 18 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 76 through 78 removed outlier: 4.207A pdb=" N ASP E 196 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 167 through 174 570 hydrogen bonds defined for protein. 1635 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: 4.07 Time building geometry restraints manager: 5.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3638 1.33 - 1.45: 2372 1.45 - 1.57: 7364 1.57 - 1.68: 211 1.68 - 1.80: 75 Bond restraints: 13660 Sorted by residual: bond pdb=" CB2 CDL B 402 " pdb=" C1 CDL B 402 " ideal model delta sigma weight residual 1.510 1.332 0.178 1.40e-02 5.10e+03 1.62e+02 bond pdb=" CB2 CDL C 402 " pdb=" C1 CDL C 402 " ideal model delta sigma weight residual 1.510 1.332 0.178 1.40e-02 5.10e+03 1.61e+02 bond pdb=" CB2 CDL A 402 " pdb=" C1 CDL A 402 " ideal model delta sigma weight residual 1.510 1.332 0.178 1.40e-02 5.10e+03 1.61e+02 bond pdb=" CB2 CDL E 401 " pdb=" C1 CDL E 401 " ideal model delta sigma weight residual 1.510 1.332 0.178 1.40e-02 5.10e+03 1.61e+02 bond pdb=" CB2 CDL D 402 " pdb=" C1 CDL D 402 " ideal model delta sigma weight residual 1.510 1.333 0.177 1.40e-02 5.10e+03 1.61e+02 ... (remaining 13655 not shown) Histogram of bond angle deviations from ideal: 92.08 - 100.46: 50 100.46 - 108.84: 984 108.84 - 117.22: 8647 117.22 - 125.60: 8529 125.60 - 133.97: 260 Bond angle restraints: 18470 Sorted by residual: angle pdb=" C51 CDL B 402 " pdb=" CB5 CDL B 402 " pdb=" OB6 CDL B 402 " ideal model delta sigma weight residual 111.33 124.44 -13.11 1.32e+00 5.72e-01 9.84e+01 angle pdb=" C51 CDL C 402 " pdb=" CB5 CDL C 402 " pdb=" OB6 CDL C 402 " ideal model delta sigma weight residual 111.33 124.40 -13.07 1.32e+00 5.72e-01 9.78e+01 angle pdb=" C51 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 111.33 124.39 -13.06 1.32e+00 5.72e-01 9.75e+01 angle pdb=" C51 CDL D 402 " pdb=" CB5 CDL D 402 " pdb=" OB6 CDL D 402 " ideal model delta sigma weight residual 111.33 124.38 -13.05 1.32e+00 5.72e-01 9.75e+01 angle pdb=" C51 CDL E 401 " pdb=" CB5 CDL E 401 " pdb=" OB6 CDL E 401 " ideal model delta sigma weight residual 111.33 124.35 -13.02 1.32e+00 5.72e-01 9.69e+01 ... (remaining 18465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 7809 35.70 - 71.40: 351 71.40 - 107.10: 35 107.10 - 142.80: 20 142.80 - 178.50: 5 Dihedral angle restraints: 8220 sinusoidal: 3665 harmonic: 4555 Sorted by residual: dihedral pdb=" CA ILE B 79 " pdb=" C ILE B 79 " pdb=" N ASN B 80 " pdb=" CA ASN B 80 " ideal model delta harmonic sigma weight residual 180.00 150.70 29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ILE A 79 " pdb=" C ILE A 79 " pdb=" N ASN A 80 " pdb=" CA ASN A 80 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE C 79 " pdb=" C ILE C 79 " pdb=" N ASN C 80 " pdb=" CA ASN C 80 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 8217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1954 0.126 - 0.251: 21 0.251 - 0.377: 5 0.377 - 0.503: 5 0.503 - 0.628: 10 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA4 CDL E 401 " pdb=" CA3 CDL E 401 " pdb=" CA6 CDL E 401 " pdb=" OA6 CDL E 401 " both_signs ideal model delta sigma weight residual False -2.57 -3.20 0.63 2.00e-01 2.50e+01 9.86e+00 chirality pdb=" CA4 CDL B 402 " pdb=" CA3 CDL B 402 " pdb=" CA6 CDL B 402 " pdb=" OA6 CDL B 402 " both_signs ideal model delta sigma weight residual False -2.57 -3.20 0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" CA4 CDL D 402 " pdb=" CA3 CDL D 402 " pdb=" CA6 CDL D 402 " pdb=" OA6 CDL D 402 " both_signs ideal model delta sigma weight residual False -2.57 -3.20 0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 1992 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 137 " -0.006 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASN A 137 " 0.023 2.00e-02 2.50e+03 pdb=" O ASN A 137 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN A 138 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 137 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ASN C 137 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN C 137 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN C 138 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 137 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C ASN D 137 " -0.022 2.00e-02 2.50e+03 pdb=" O ASN D 137 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN D 138 " 0.007 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2425 2.76 - 3.30: 11674 3.30 - 3.83: 21107 3.83 - 4.37: 25635 4.37 - 4.90: 45162 Nonbonded interactions: 106003 Sorted by model distance: nonbonded pdb=" OB2 CDL D 402 " pdb=" O1 CDL D 402 " model vdw 2.227 2.432 nonbonded pdb=" OB2 CDL A 402 " pdb=" O1 CDL A 402 " model vdw 2.227 2.432 nonbonded pdb=" OB2 CDL E 401 " pdb=" O1 CDL E 401 " model vdw 2.227 2.432 nonbonded pdb=" OB2 CDL B 402 " pdb=" O1 CDL B 402 " model vdw 2.227 2.432 nonbonded pdb=" OB2 CDL C 402 " pdb=" O1 CDL C 402 " model vdw 2.227 2.432 ... (remaining 105998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 321) selection = (chain 'B' and resid 11 through 321) selection = (chain 'C' and resid 11 through 321) selection = (chain 'D' and resid 11 through 321) selection = (chain 'E' and resid 11 through 321) } 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.090 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 37.980 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.016 0.207 13660 Z= 1.031 Angle : 1.210 18.574 18470 Z= 0.580 Chirality : 0.068 0.628 1995 Planarity : 0.003 0.029 2295 Dihedral : 19.806 178.499 5280 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.96 % Allowed : 8.27 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1545 helix: -1.30 (0.20), residues: 535 sheet: 0.32 (0.26), residues: 450 loop : -2.57 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 43 HIS 0.004 0.001 HIS D 177 PHE 0.009 0.001 PHE B 78 TYR 0.013 0.002 TYR D 270 ARG 0.004 0.001 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 269 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8189 (m-30) cc_final: 0.7835 (m-30) REVERT: A 87 THR cc_start: 0.9278 (t) cc_final: 0.8978 (m) REVERT: A 114 MET cc_start: 0.8987 (mtm) cc_final: 0.8607 (mtp) REVERT: A 156 GLU cc_start: 0.7956 (pm20) cc_final: 0.7699 (pm20) REVERT: A 187 GLU cc_start: 0.8050 (mt-10) cc_final: 0.6741 (pp20) REVERT: B 13 ASP cc_start: 0.8243 (m-30) cc_final: 0.7918 (m-30) REVERT: B 150 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: B 172 ASP cc_start: 0.8475 (m-30) cc_final: 0.8180 (m-30) REVERT: B 187 GLU cc_start: 0.7923 (mt-10) cc_final: 0.6629 (pp20) REVERT: C 86 ASP cc_start: 0.7952 (t70) cc_final: 0.7751 (t0) REVERT: C 114 MET cc_start: 0.9193 (mtm) cc_final: 0.8984 (mtm) REVERT: C 138 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7815 (pp30) REVERT: C 139 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: C 146 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: C 150 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6258 (mm-30) REVERT: C 172 ASP cc_start: 0.8567 (m-30) cc_final: 0.8285 (m-30) REVERT: C 185 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7429 (mp10) REVERT: C 187 GLU cc_start: 0.7752 (mt-10) cc_final: 0.6508 (pp20) REVERT: C 219 SER cc_start: 0.8664 (t) cc_final: 0.8268 (p) REVERT: D 39 ILE cc_start: 0.8585 (mt) cc_final: 0.8356 (tt) REVERT: D 150 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6378 (mm-30) REVERT: D 158 ASP cc_start: 0.7938 (m-30) cc_final: 0.7592 (m-30) REVERT: D 238 LEU cc_start: 0.8211 (mt) cc_final: 0.8008 (mt) REVERT: E 13 ASP cc_start: 0.8075 (m-30) cc_final: 0.7837 (m-30) REVERT: E 39 ILE cc_start: 0.8631 (mt) cc_final: 0.8422 (tt) REVERT: E 138 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7836 (pp30) REVERT: E 146 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: E 156 GLU cc_start: 0.7827 (pm20) cc_final: 0.7602 (pm20) REVERT: E 163 ARG cc_start: 0.8835 (mmt-90) cc_final: 0.8462 (mmp80) REVERT: E 187 GLU cc_start: 0.7900 (mt-10) cc_final: 0.6944 (pp20) REVERT: E 219 SER cc_start: 0.8664 (t) cc_final: 0.8417 (p) REVERT: E 298 GLN cc_start: 0.8031 (mt0) cc_final: 0.7774 (mt0) outliers start: 55 outliers final: 21 residues processed: 315 average time/residue: 1.3500 time to fit residues: 460.4766 Evaluate side-chains 218 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN D 27 ASN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN E 89 ASN E 137 ASN E 139 GLN E 184 ASN E 185 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13660 Z= 0.235 Angle : 0.595 5.628 18470 Z= 0.300 Chirality : 0.047 0.150 1995 Planarity : 0.004 0.028 2295 Dihedral : 19.595 133.028 2379 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.46 % Allowed : 13.24 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.65 (0.21), residues: 1545 helix: 0.55 (0.21), residues: 515 sheet: 0.83 (0.25), residues: 450 loop : -2.46 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 43 HIS 0.004 0.001 HIS A 285 PHE 0.010 0.001 PHE E 78 TYR 0.018 0.001 TYR A 270 ARG 0.007 0.001 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 195 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8996 (mtm) cc_final: 0.8565 (mtp) REVERT: A 172 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: A 187 GLU cc_start: 0.8052 (mt-10) cc_final: 0.6820 (pp20) REVERT: A 304 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: B 146 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.6710 (mt0) REVERT: B 187 GLU cc_start: 0.7994 (mt-10) cc_final: 0.6705 (pp20) REVERT: C 150 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6103 (mm-30) REVERT: C 185 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7362 (mp10) REVERT: C 219 SER cc_start: 0.8599 (t) cc_final: 0.8225 (p) REVERT: C 255 ARG cc_start: 0.7912 (tpp80) cc_final: 0.7689 (tpp-160) REVERT: C 304 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: D 158 ASP cc_start: 0.7922 (m-30) cc_final: 0.7602 (m-30) REVERT: D 187 GLU cc_start: 0.8115 (mt-10) cc_final: 0.6797 (pp20) REVERT: D 245 TYR cc_start: 0.8277 (t80) cc_final: 0.7617 (t80) REVERT: D 304 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: E 156 GLU cc_start: 0.7813 (pm20) cc_final: 0.7581 (pm20) REVERT: E 245 TYR cc_start: 0.8174 (t80) cc_final: 0.7487 (t80) REVERT: E 298 GLN cc_start: 0.7923 (mt0) cc_final: 0.7686 (mt0) REVERT: E 304 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8130 (m-80) outliers start: 62 outliers final: 25 residues processed: 242 average time/residue: 1.4205 time to fit residues: 370.6332 Evaluate side-chains 187 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 141 optimal weight: 0.0270 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 284 HIS C 89 ASN C 233 GLN D 89 ASN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 284 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 ASN E 185 GLN E 284 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13660 Z= 0.366 Angle : 0.610 7.557 18470 Z= 0.309 Chirality : 0.047 0.137 1995 Planarity : 0.004 0.056 2295 Dihedral : 17.831 137.155 2339 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.89 % Allowed : 14.53 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.29 (0.21), residues: 1545 helix: 1.13 (0.22), residues: 520 sheet: 0.86 (0.25), residues: 450 loop : -2.41 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 43 HIS 0.006 0.001 HIS C 177 PHE 0.041 0.002 PHE D 247 TYR 0.016 0.002 TYR C 270 ARG 0.010 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 173 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9015 (mtm) cc_final: 0.8780 (mtp) REVERT: A 172 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: A 187 GLU cc_start: 0.8079 (mt-10) cc_final: 0.6826 (pp20) REVERT: A 255 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7720 (tpp-160) REVERT: A 304 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: B 146 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.6740 (mt0) REVERT: B 178 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6985 (mp) REVERT: B 187 GLU cc_start: 0.8014 (mt-10) cc_final: 0.6703 (pp20) REVERT: C 185 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7401 (mp10) REVERT: C 219 SER cc_start: 0.8595 (t) cc_final: 0.8210 (p) REVERT: D 64 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6665 (tm-30) REVERT: D 146 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6822 (mt0) REVERT: D 158 ASP cc_start: 0.7921 (m-30) cc_final: 0.7577 (m-30) REVERT: D 187 GLU cc_start: 0.8150 (mt-10) cc_final: 0.6823 (pp20) REVERT: D 245 TYR cc_start: 0.8254 (t80) cc_final: 0.7588 (t80) REVERT: E 156 GLU cc_start: 0.7816 (pm20) cc_final: 0.7567 (pm20) REVERT: E 163 ARG cc_start: 0.8507 (mmt-90) cc_final: 0.8260 (mmp80) REVERT: E 245 TYR cc_start: 0.8130 (t80) cc_final: 0.7626 (t80) REVERT: E 298 GLN cc_start: 0.7954 (mt0) cc_final: 0.7728 (mt0) outliers start: 68 outliers final: 38 residues processed: 222 average time/residue: 1.4048 time to fit residues: 337.1350 Evaluate side-chains 212 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.9980 chunk 106 optimal weight: 0.0570 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 0.0870 chunk 149 optimal weight: 0.0870 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN E 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13660 Z= 0.147 Angle : 0.532 5.866 18470 Z= 0.270 Chirality : 0.044 0.134 1995 Planarity : 0.003 0.034 2295 Dihedral : 15.458 118.491 2328 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.88 % Allowed : 17.12 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.20 (0.22), residues: 1545 helix: 1.75 (0.22), residues: 520 sheet: 0.89 (0.24), residues: 460 loop : -2.20 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 43 HIS 0.003 0.001 HIS A 177 PHE 0.018 0.001 PHE D 247 TYR 0.011 0.001 TYR A 245 ARG 0.008 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8002 (mt-10) cc_final: 0.6788 (pp20) REVERT: A 304 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: B 146 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.6652 (mt0) REVERT: B 187 GLU cc_start: 0.7993 (mt-10) cc_final: 0.6685 (pp20) REVERT: B 309 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6973 (mp) REVERT: C 185 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7131 (mp-120) REVERT: C 219 SER cc_start: 0.8571 (t) cc_final: 0.8184 (p) REVERT: C 304 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: D 64 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6620 (tm-30) REVERT: D 158 ASP cc_start: 0.7918 (m-30) cc_final: 0.7602 (m-30) REVERT: D 245 TYR cc_start: 0.8249 (t80) cc_final: 0.7621 (t80) REVERT: E 270 TYR cc_start: 0.7941 (m-80) cc_final: 0.7095 (m-80) REVERT: E 279 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7866 (tp) REVERT: E 298 GLN cc_start: 0.7936 (mt0) cc_final: 0.7724 (mt0) REVERT: E 304 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8111 (m-80) outliers start: 40 outliers final: 11 residues processed: 227 average time/residue: 1.2958 time to fit residues: 319.7435 Evaluate side-chains 191 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 0.0060 chunk 103 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN E 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13660 Z= 0.230 Angle : 0.557 5.482 18470 Z= 0.283 Chirality : 0.045 0.131 1995 Planarity : 0.004 0.057 2295 Dihedral : 15.203 127.466 2325 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.53 % Allowed : 16.33 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1545 helix: 1.85 (0.23), residues: 520 sheet: 1.03 (0.25), residues: 460 loop : -2.19 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.004 0.001 HIS A 177 PHE 0.034 0.001 PHE D 247 TYR 0.012 0.001 TYR C 245 ARG 0.011 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 184 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8082 (mt-10) cc_final: 0.6856 (pp20) REVERT: A 255 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7678 (tpp-160) REVERT: A 304 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: B 142 PHE cc_start: 0.6286 (t80) cc_final: 0.6066 (t80) REVERT: B 146 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.6702 (mt0) REVERT: B 187 GLU cc_start: 0.7929 (mt-10) cc_final: 0.6710 (pp20) REVERT: C 185 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7117 (mp-120) REVERT: C 219 SER cc_start: 0.8615 (t) cc_final: 0.8212 (p) REVERT: C 304 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: D 64 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6617 (tm-30) REVERT: D 146 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.6006 (mp10) REVERT: D 158 ASP cc_start: 0.7906 (m-30) cc_final: 0.7604 (m-30) REVERT: D 245 TYR cc_start: 0.8250 (t80) cc_final: 0.7516 (t80) REVERT: E 245 TYR cc_start: 0.8126 (t80) cc_final: 0.6882 (t80) REVERT: E 270 TYR cc_start: 0.8028 (m-80) cc_final: 0.7076 (m-80) REVERT: E 304 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8141 (m-80) outliers start: 63 outliers final: 28 residues processed: 229 average time/residue: 1.2641 time to fit residues: 314.9774 Evaluate side-chains 204 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 89 ASN B 89 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13660 Z= 0.341 Angle : 0.597 5.622 18470 Z= 0.303 Chirality : 0.047 0.136 1995 Planarity : 0.004 0.060 2295 Dihedral : 15.399 142.826 2325 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.17 % Allowed : 16.91 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1545 helix: 1.75 (0.23), residues: 520 sheet: 1.09 (0.25), residues: 460 loop : -2.22 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 43 HIS 0.007 0.001 HIS D 177 PHE 0.020 0.002 PHE E 247 TYR 0.016 0.001 TYR E 248 ARG 0.013 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 172 time to evaluate : 1.460 Fit side-chains REVERT: A 187 GLU cc_start: 0.8056 (mt-10) cc_final: 0.6536 (pp20) REVERT: A 255 ARG cc_start: 0.7968 (tpp80) cc_final: 0.7662 (tpp-160) REVERT: A 279 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7506 (mm) REVERT: A 304 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 142 PHE cc_start: 0.6321 (t80) cc_final: 0.6105 (t80) REVERT: B 146 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.6836 (mt0) REVERT: B 187 GLU cc_start: 0.7952 (mt-10) cc_final: 0.6697 (pp20) REVERT: C 146 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.6872 (mt0) REVERT: C 185 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7118 (mp-120) REVERT: C 219 SER cc_start: 0.8604 (t) cc_final: 0.8214 (p) REVERT: C 251 ASN cc_start: 0.8826 (t0) cc_final: 0.8608 (t160) REVERT: D 64 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6641 (tm-30) REVERT: D 146 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.6847 (mt0) REVERT: D 245 TYR cc_start: 0.8204 (t80) cc_final: 0.7492 (t80) REVERT: E 245 TYR cc_start: 0.8127 (t80) cc_final: 0.7563 (t80) REVERT: E 304 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8200 (m-80) outliers start: 58 outliers final: 29 residues processed: 212 average time/residue: 1.3993 time to fit residues: 320.8581 Evaluate side-chains 205 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN E 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13660 Z= 0.270 Angle : 0.577 5.945 18470 Z= 0.294 Chirality : 0.046 0.138 1995 Planarity : 0.004 0.051 2295 Dihedral : 14.979 142.150 2323 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.24 % Allowed : 17.41 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1545 helix: 1.82 (0.22), residues: 520 sheet: 1.16 (0.25), residues: 460 loop : -2.19 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 43 HIS 0.006 0.001 HIS D 177 PHE 0.031 0.001 PHE D 247 TYR 0.013 0.001 TYR E 248 ARG 0.011 0.001 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 177 time to evaluate : 1.428 Fit side-chains REVERT: A 187 GLU cc_start: 0.8037 (mt-10) cc_final: 0.6544 (pp20) REVERT: A 255 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7669 (tpp-160) REVERT: B 142 PHE cc_start: 0.6274 (t80) cc_final: 0.6068 (t80) REVERT: B 146 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.6761 (mt0) REVERT: B 187 GLU cc_start: 0.7941 (mt-10) cc_final: 0.6705 (pp20) REVERT: B 247 PHE cc_start: 0.7654 (t80) cc_final: 0.6913 (t80) REVERT: B 309 LEU cc_start: 0.7546 (tt) cc_final: 0.7097 (mp) REVERT: C 146 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6896 (mt0) REVERT: C 185 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7164 (mp-120) REVERT: C 219 SER cc_start: 0.8576 (t) cc_final: 0.8188 (p) REVERT: D 64 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6605 (tm-30) REVERT: D 187 GLU cc_start: 0.8147 (mt-10) cc_final: 0.6839 (pp20) REVERT: D 230 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7602 (mt-10) REVERT: D 245 TYR cc_start: 0.8211 (t80) cc_final: 0.7445 (t80) REVERT: E 245 TYR cc_start: 0.8126 (t80) cc_final: 0.7131 (t80) REVERT: E 247 PHE cc_start: 0.7764 (t80) cc_final: 0.7538 (t80) outliers start: 59 outliers final: 31 residues processed: 220 average time/residue: 1.4198 time to fit residues: 337.3587 Evaluate side-chains 203 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.0770 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.0060 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 94 optimal weight: 0.3980 chunk 101 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13660 Z= 0.149 Angle : 0.548 7.573 18470 Z= 0.279 Chirality : 0.044 0.150 1995 Planarity : 0.004 0.049 2295 Dihedral : 14.115 132.392 2319 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.81 % Allowed : 18.71 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1545 helix: 1.92 (0.23), residues: 530 sheet: 1.23 (0.25), residues: 460 loop : -2.16 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 43 HIS 0.005 0.001 HIS D 177 PHE 0.029 0.001 PHE D 247 TYR 0.018 0.001 TYR E 248 ARG 0.013 0.001 ARG E 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 1.489 Fit side-chains REVERT: A 187 GLU cc_start: 0.8008 (mt-10) cc_final: 0.6571 (pp20) REVERT: A 208 PHE cc_start: 0.8388 (m-80) cc_final: 0.7905 (m-10) REVERT: B 146 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.6724 (mt0) REVERT: B 187 GLU cc_start: 0.7918 (mt-10) cc_final: 0.6667 (pp20) REVERT: B 309 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7140 (mp) REVERT: C 185 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7025 (mp-120) REVERT: C 219 SER cc_start: 0.8578 (t) cc_final: 0.8185 (p) REVERT: C 255 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7638 (tpp-160) REVERT: D 64 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6572 (tm-30) REVERT: D 158 ASP cc_start: 0.8062 (m-30) cc_final: 0.7551 (m-30) REVERT: D 187 GLU cc_start: 0.8113 (mt-10) cc_final: 0.6898 (pp20) REVERT: E 270 TYR cc_start: 0.7958 (m-80) cc_final: 0.7082 (m-80) REVERT: E 304 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8073 (m-80) outliers start: 39 outliers final: 19 residues processed: 213 average time/residue: 1.4042 time to fit residues: 323.5877 Evaluate side-chains 196 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 139 optimal weight: 0.0030 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS C 298 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13660 Z= 0.214 Angle : 0.569 7.944 18470 Z= 0.289 Chirality : 0.045 0.147 1995 Planarity : 0.004 0.055 2295 Dihedral : 13.984 133.006 2319 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.37 % Allowed : 19.86 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1545 helix: 1.89 (0.23), residues: 530 sheet: 1.29 (0.25), residues: 460 loop : -2.16 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 43 HIS 0.005 0.001 HIS D 177 PHE 0.036 0.001 PHE D 247 TYR 0.016 0.001 TYR E 248 ARG 0.013 0.001 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.550 Fit side-chains REVERT: A 187 GLU cc_start: 0.8002 (mt-10) cc_final: 0.6555 (pp20) REVERT: B 146 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.6720 (mt0) REVERT: B 187 GLU cc_start: 0.7945 (mt-10) cc_final: 0.6720 (pp20) REVERT: B 309 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7129 (mp) REVERT: C 185 GLN cc_start: 0.7554 (mm-40) cc_final: 0.6958 (mp-120) REVERT: C 219 SER cc_start: 0.8599 (t) cc_final: 0.8220 (p) REVERT: D 64 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6609 (tm-30) REVERT: D 187 GLU cc_start: 0.8044 (mt-10) cc_final: 0.6875 (pp20) REVERT: D 255 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: E 245 TYR cc_start: 0.8057 (t80) cc_final: 0.7124 (t80) REVERT: E 270 TYR cc_start: 0.8032 (m-80) cc_final: 0.7076 (m-80) REVERT: E 304 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8095 (m-80) outliers start: 33 outliers final: 23 residues processed: 200 average time/residue: 1.4424 time to fit residues: 311.1889 Evaluate side-chains 198 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 122 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.0000 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS C 298 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13660 Z= 0.182 Angle : 0.563 8.617 18470 Z= 0.286 Chirality : 0.045 0.149 1995 Planarity : 0.004 0.053 2295 Dihedral : 13.542 129.752 2319 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.45 % Allowed : 19.78 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1545 helix: 1.95 (0.23), residues: 530 sheet: 1.32 (0.25), residues: 460 loop : -2.12 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.005 0.001 HIS D 177 PHE 0.036 0.001 PHE D 247 TYR 0.016 0.001 TYR E 248 ARG 0.012 0.001 ARG B 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: B 146 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.6666 (mt0) REVERT: B 187 GLU cc_start: 0.7939 (mt-10) cc_final: 0.6675 (pp20) REVERT: B 309 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7165 (mp) REVERT: C 219 SER cc_start: 0.8606 (t) cc_final: 0.8224 (p) REVERT: C 299 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7733 (ttm110) REVERT: D 64 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6595 (tm-30) REVERT: D 187 GLU cc_start: 0.7994 (mt-10) cc_final: 0.6901 (pp20) REVERT: E 270 TYR cc_start: 0.8002 (m-80) cc_final: 0.7035 (m-80) REVERT: E 304 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.8050 (m-80) outliers start: 34 outliers final: 24 residues processed: 193 average time/residue: 1.3997 time to fit residues: 292.4566 Evaluate side-chains 202 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.0770 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.110514 restraints weight = 18097.015| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.91 r_work: 0.3436 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13660 Z= 0.246 Angle : 0.582 8.451 18470 Z= 0.296 Chirality : 0.046 0.156 1995 Planarity : 0.004 0.054 2295 Dihedral : 13.686 134.120 2319 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.52 % Allowed : 19.93 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1545 helix: 1.94 (0.23), residues: 525 sheet: 1.34 (0.25), residues: 460 loop : -2.21 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.006 0.001 HIS D 177 PHE 0.039 0.001 PHE D 247 TYR 0.016 0.001 TYR E 248 ARG 0.011 0.001 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5571.60 seconds wall clock time: 100 minutes 18.33 seconds (6018.33 seconds total)