Starting phenix.real_space_refine on Thu Jun 27 05:38:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/06_2024/8uvu_42629_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/06_2024/8uvu_42629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/06_2024/8uvu_42629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/06_2024/8uvu_42629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/06_2024/8uvu_42629_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/06_2024/8uvu_42629_updated.pdb" } resolution = 3.0 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= 0.003 sd= 0.102 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 7784 2.51 5 N 2000 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 423": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 ABDF A 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF A 501 " occ=0.75 residue: pdb=" C1 BFRU A 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU A 502 " occ=0.25 residue: pdb=" C1 ABDF B 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF B 501 " occ=0.75 residue: pdb=" C1 BFRU B 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU B 502 " occ=0.25 residue: pdb=" C1 ABDF C 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF C 501 " occ=0.75 residue: pdb=" C1 BFRU C 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU C 502 " occ=0.25 residue: pdb=" C1 ABDF D 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF D 501 " occ=0.75 residue: pdb=" C1 BFRU D 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU D 502 " occ=0.25 Time building chain proxies: 7.28, per 1000 atoms: 0.61 Number of scatterers: 11976 At special positions: 0 Unit cell: (110.004, 110.004, 93.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2072 8.00 N 2000 7.00 C 7784 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: 4.87 Conformation dependent library (CDL) restraints added in 2.1 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 79.7% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.526A pdb=" N ALA A 23 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 25 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 26 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 91 through 111 removed outlier: 3.767A pdb=" N VAL A 95 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 removed outlier: 3.916A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 175 removed outlier: 3.555A pdb=" N LEU A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 224 removed outlier: 5.260A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.645A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 340 Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 345 through 389 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 395 through 409 removed outlier: 3.691A pdb=" N ARG A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.716A pdb=" N VAL A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.526A pdb=" N ALA B 23 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 25 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU B 26 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 78 Processing helix chain 'B' and resid 91 through 111 removed outlier: 3.767A pdb=" N VAL B 95 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 133 removed outlier: 3.916A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 175 removed outlier: 3.554A pdb=" N LEU B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 224 removed outlier: 5.261A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 311 removed outlier: 3.645A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 340 Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 345 through 389 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.690A pdb=" N ARG B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.716A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.526A pdb=" N ALA C 23 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE C 25 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU C 26 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 78 Processing helix chain 'C' and resid 91 through 111 removed outlier: 3.767A pdb=" N VAL C 95 " --> pdb=" O MET C 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 133 removed outlier: 3.917A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 175 removed outlier: 3.554A pdb=" N LEU C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 224 removed outlier: 5.261A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 311 removed outlier: 3.646A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 340 Proline residue: C 331 - end of helix Processing helix chain 'C' and resid 345 through 389 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 395 through 409 removed outlier: 3.690A pdb=" N ARG C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.716A pdb=" N VAL C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.527A pdb=" N ALA D 23 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE D 25 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU D 26 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 29 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 78 Processing helix chain 'D' and resid 91 through 111 removed outlier: 3.767A pdb=" N VAL D 95 " --> pdb=" O MET D 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 133 removed outlier: 3.916A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 175 removed outlier: 3.555A pdb=" N LEU D 147 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 224 removed outlier: 5.260A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 311 removed outlier: 3.646A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 340 Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 345 through 389 Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 395 through 409 removed outlier: 3.691A pdb=" N ARG D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.716A pdb=" N VAL D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 16 through 18 removed outlier: 4.267A pdb=" N CYS A 16 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 49 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 16 through 18 removed outlier: 4.268A pdb=" N CYS B 16 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 49 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 16 through 18 removed outlier: 4.268A pdb=" N CYS C 16 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 49 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 16 through 18 removed outlier: 4.269A pdb=" N CYS D 16 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 49 " --> pdb=" O ARG D 38 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2712 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: 3.26 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3716 1.34 - 1.46: 2834 1.46 - 1.58: 5478 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 12208 Sorted by residual: bond pdb=" C2 BFRU B 502 " pdb=" O2 BFRU B 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C2 BFRU A 502 " pdb=" O2 BFRU A 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C2 BFRU C 502 " pdb=" O2 BFRU C 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C2 BFRU D 502 " pdb=" O2 BFRU D 502 " ideal model delta sigma weight residual 1.388 1.425 -0.037 2.00e-02 2.50e+03 3.49e+00 bond pdb=" C2 ABDF A 501 " pdb=" O2 ABDF A 501 " ideal model delta sigma weight residual 1.390 1.425 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 12203 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.35: 292 106.35 - 113.29: 7041 113.29 - 120.23: 4263 120.23 - 127.17: 4872 127.17 - 134.10: 116 Bond angle restraints: 16584 Sorted by residual: angle pdb=" N ALA B 23 " pdb=" CA ALA B 23 " pdb=" C ALA B 23 " ideal model delta sigma weight residual 114.62 108.80 5.82 1.14e+00 7.69e-01 2.61e+01 angle pdb=" N ALA A 23 " pdb=" CA ALA A 23 " pdb=" C ALA A 23 " ideal model delta sigma weight residual 114.62 108.83 5.79 1.14e+00 7.69e-01 2.58e+01 angle pdb=" N ALA D 23 " pdb=" CA ALA D 23 " pdb=" C ALA D 23 " ideal model delta sigma weight residual 114.62 108.83 5.79 1.14e+00 7.69e-01 2.58e+01 angle pdb=" N ALA C 23 " pdb=" CA ALA C 23 " pdb=" C ALA C 23 " ideal model delta sigma weight residual 114.62 108.86 5.76 1.14e+00 7.69e-01 2.55e+01 angle pdb=" CA ALA A 23 " pdb=" C ALA A 23 " pdb=" N PHE A 24 " ideal model delta sigma weight residual 119.71 116.12 3.59 1.17e+00 7.31e-01 9.41e+00 ... (remaining 16579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6640 17.96 - 35.91: 599 35.91 - 53.87: 145 53.87 - 71.82: 32 71.82 - 89.78: 8 Dihedral angle restraints: 7424 sinusoidal: 3000 harmonic: 4424 Sorted by residual: dihedral pdb=" CA LYS D 52 " pdb=" C LYS D 52 " pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LYS A 52 " pdb=" C LYS A 52 " pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LYS C 52 " pdb=" C LYS C 52 " pdb=" N GLY C 53 " pdb=" CA GLY C 53 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 7421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1846 0.062 - 0.124: 186 0.124 - 0.186: 8 0.186 - 0.248: 8 0.248 - 0.309: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C3 BFRU A 502 " pdb=" C2 BFRU A 502 " pdb=" C4 BFRU A 502 " pdb=" O3 BFRU A 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3 BFRU C 502 " pdb=" C2 BFRU C 502 " pdb=" C4 BFRU C 502 " pdb=" O3 BFRU C 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3 BFRU B 502 " pdb=" C2 BFRU B 502 " pdb=" C4 BFRU B 502 " pdb=" O3 BFRU B 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2049 not shown) Planarity restraints: 1992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 285 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO D 286 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 285 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 286 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 285 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO C 286 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 286 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 286 " -0.019 5.00e-02 4.00e+02 ... (remaining 1989 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2393 2.78 - 3.31: 12395 3.31 - 3.84: 20696 3.84 - 4.37: 23863 4.37 - 4.90: 42038 Nonbonded interactions: 101385 Sorted by model distance: nonbonded pdb=" OD1 ASN A 218 " pdb=" OG1 THR A 379 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN B 218 " pdb=" OG1 THR B 379 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN D 218 " pdb=" OG1 THR D 379 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN C 218 " pdb=" OG1 THR C 379 " model vdw 2.246 2.440 nonbonded pdb=" N GLN B 179 " pdb=" OE1 GLN B 179 " model vdw 2.256 2.520 ... (remaining 101380 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 14 through 446) selection = (chain 'B' and resid 14 through 446) selection = (chain 'C' and resid 14 through 446) selection = (chain 'D' and resid 14 through 446) } 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=0.25 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: 3.690 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: 12.140 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.500 Find NCS groups from input model: 0.750 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: 0.000 Load rotamer database and sin/cos tables:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.003 0.038 12208 Z= 0.210 Angle : 0.601 9.182 16584 Z= 0.304 Chirality : 0.041 0.309 2052 Planarity : 0.004 0.035 1992 Dihedral : 14.700 89.777 4568 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.70 (0.22), residues: 1500 helix: 2.06 (0.14), residues: 1224 sheet: -4.55 (0.58), residues: 44 loop : -2.92 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.002 0.000 HIS D 307 PHE 0.014 0.001 PHE C 189 TYR 0.019 0.001 TYR D 124 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.344 Fit side-chains REVERT: A 389 LEU cc_start: 0.8293 (mt) cc_final: 0.8018 (mt) REVERT: B 121 MET cc_start: 0.8756 (tmm) cc_final: 0.8540 (tmt) REVERT: B 389 LEU cc_start: 0.8310 (mt) cc_final: 0.8022 (mt) REVERT: C 389 LEU cc_start: 0.8322 (mt) cc_final: 0.8045 (mt) REVERT: D 389 LEU cc_start: 0.8328 (mt) cc_final: 0.8062 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 1.3198 time to fit residues: 315.5576 Evaluate side-chains 178 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12208 Z= 0.241 Angle : 0.535 6.448 16584 Z= 0.275 Chirality : 0.037 0.131 2052 Planarity : 0.004 0.036 1992 Dihedral : 3.945 15.406 1856 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.59 % Allowed : 8.26 % Favored : 90.15 % 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: 1.97 (0.22), residues: 1500 helix: 2.30 (0.14), residues: 1224 sheet: -4.42 (0.56), residues: 44 loop : -3.22 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 193 HIS 0.003 0.001 HIS C 22 PHE 0.013 0.001 PHE B 203 TYR 0.018 0.001 TYR C 124 ARG 0.003 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.314 Fit side-chains REVERT: A 389 LEU cc_start: 0.8517 (mt) cc_final: 0.8244 (mt) REVERT: B 121 MET cc_start: 0.8796 (tmm) cc_final: 0.8563 (tmt) REVERT: B 389 LEU cc_start: 0.8519 (mt) cc_final: 0.8248 (mt) REVERT: C 389 LEU cc_start: 0.8525 (mt) cc_final: 0.8254 (mt) REVERT: D 389 LEU cc_start: 0.8526 (mt) cc_final: 0.8252 (mt) outliers start: 21 outliers final: 12 residues processed: 196 average time/residue: 1.3210 time to fit residues: 279.9310 Evaluate side-chains 188 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 392 HIS B 222 ASN B 392 HIS C 222 ASN C 392 HIS D 222 ASN D 392 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12208 Z= 0.367 Angle : 0.612 7.089 16584 Z= 0.310 Chirality : 0.041 0.166 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.184 16.667 1856 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.95 % Allowed : 11.21 % Favored : 85.83 % 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: 1.67 (0.22), residues: 1500 helix: 2.04 (0.14), residues: 1220 sheet: -4.37 (0.56), residues: 44 loop : -2.98 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 193 HIS 0.004 0.001 HIS D 22 PHE 0.016 0.002 PHE A 205 TYR 0.020 0.002 TYR D 124 ARG 0.004 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.379 Fit side-chains REVERT: A 389 LEU cc_start: 0.8687 (mt) cc_final: 0.8464 (mt) REVERT: B 389 LEU cc_start: 0.8682 (mt) cc_final: 0.8458 (mt) REVERT: C 129 VAL cc_start: 0.7907 (t) cc_final: 0.7389 (m) REVERT: C 373 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8384 (mp) REVERT: C 389 LEU cc_start: 0.8691 (mt) cc_final: 0.8464 (mt) REVERT: D 389 LEU cc_start: 0.8697 (mt) cc_final: 0.8470 (mt) outliers start: 39 outliers final: 23 residues processed: 211 average time/residue: 1.2289 time to fit residues: 280.9037 Evaluate side-chains 203 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.0970 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN C 222 ASN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12208 Z= 0.220 Angle : 0.532 7.186 16584 Z= 0.272 Chirality : 0.036 0.132 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.000 17.865 1856 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.50 % Allowed : 13.94 % Favored : 83.56 % 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: 1.93 (0.22), residues: 1500 helix: 2.27 (0.14), residues: 1228 sheet: -4.33 (0.56), residues: 44 loop : -3.32 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 354 HIS 0.004 0.001 HIS D 22 PHE 0.014 0.001 PHE A 205 TYR 0.018 0.001 TYR A 124 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.375 Fit side-chains REVERT: A 129 VAL cc_start: 0.7886 (t) cc_final: 0.7351 (m) REVERT: A 365 VAL cc_start: 0.8763 (t) cc_final: 0.8463 (t) REVERT: A 389 LEU cc_start: 0.8591 (mt) cc_final: 0.8354 (mt) REVERT: B 121 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8187 (tmt) REVERT: B 129 VAL cc_start: 0.7895 (t) cc_final: 0.7347 (m) REVERT: B 365 VAL cc_start: 0.8762 (t) cc_final: 0.8462 (t) REVERT: B 389 LEU cc_start: 0.8588 (mt) cc_final: 0.8351 (mt) REVERT: C 129 VAL cc_start: 0.7891 (t) cc_final: 0.7345 (m) REVERT: C 365 VAL cc_start: 0.8762 (t) cc_final: 0.8462 (t) REVERT: C 389 LEU cc_start: 0.8581 (mt) cc_final: 0.8348 (mt) REVERT: D 129 VAL cc_start: 0.7892 (t) cc_final: 0.7353 (m) REVERT: D 365 VAL cc_start: 0.8761 (t) cc_final: 0.8461 (t) REVERT: D 389 LEU cc_start: 0.8589 (mt) cc_final: 0.8353 (mt) outliers start: 33 outliers final: 20 residues processed: 202 average time/residue: 1.2924 time to fit residues: 281.2836 Evaluate side-chains 197 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12208 Z= 0.246 Angle : 0.555 7.852 16584 Z= 0.281 Chirality : 0.037 0.133 2052 Planarity : 0.004 0.038 1992 Dihedral : 3.968 16.416 1856 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.79 % Allowed : 14.85 % Favored : 81.36 % 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: 1.90 (0.22), residues: 1500 helix: 2.24 (0.14), residues: 1228 sheet: -4.32 (0.56), residues: 44 loop : -3.32 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 354 HIS 0.003 0.001 HIS D 22 PHE 0.014 0.001 PHE A 203 TYR 0.019 0.001 TYR C 124 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 179 time to evaluate : 1.340 Fit side-chains REVERT: A 365 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8524 (t) REVERT: A 389 LEU cc_start: 0.8512 (mt) cc_final: 0.8288 (mt) REVERT: B 365 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8523 (t) REVERT: B 389 LEU cc_start: 0.8507 (mt) cc_final: 0.8286 (mt) REVERT: C 365 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8520 (t) REVERT: C 389 LEU cc_start: 0.8486 (mt) cc_final: 0.8262 (mt) REVERT: D 365 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8522 (t) REVERT: D 389 LEU cc_start: 0.8511 (mt) cc_final: 0.8284 (mt) outliers start: 50 outliers final: 25 residues processed: 217 average time/residue: 1.2965 time to fit residues: 303.8287 Evaluate side-chains 204 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 222 ASN A 410 GLN B 93 GLN B 222 ASN B 410 GLN C 93 GLN C 222 ASN C 410 GLN D 138 HIS D 222 ASN D 410 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12208 Z= 0.339 Angle : 0.605 8.445 16584 Z= 0.306 Chirality : 0.039 0.157 2052 Planarity : 0.004 0.039 1992 Dihedral : 4.136 18.371 1856 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.15 % Allowed : 13.71 % Favored : 81.14 % 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: 1.75 (0.22), residues: 1500 helix: 2.09 (0.14), residues: 1224 sheet: -4.34 (0.56), residues: 44 loop : -2.93 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 354 HIS 0.006 0.001 HIS D 22 PHE 0.016 0.002 PHE B 205 TYR 0.018 0.002 TYR C 124 ARG 0.003 0.000 ARG C 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 168 time to evaluate : 1.487 Fit side-chains REVERT: A 172 GLN cc_start: 0.7786 (mm110) cc_final: 0.7543 (mm-40) REVERT: A 193 TRP cc_start: 0.9538 (OUTLIER) cc_final: 0.7297 (m100) REVERT: B 172 GLN cc_start: 0.7793 (mm110) cc_final: 0.7544 (mm-40) REVERT: B 193 TRP cc_start: 0.9537 (OUTLIER) cc_final: 0.7297 (m100) REVERT: C 193 TRP cc_start: 0.9536 (OUTLIER) cc_final: 0.7298 (m100) REVERT: C 373 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 172 GLN cc_start: 0.7791 (mm110) cc_final: 0.7548 (mm-40) REVERT: D 193 TRP cc_start: 0.9538 (OUTLIER) cc_final: 0.7299 (m100) REVERT: D 389 LEU cc_start: 0.8655 (mt) cc_final: 0.8441 (mt) outliers start: 68 outliers final: 32 residues processed: 224 average time/residue: 1.2264 time to fit residues: 297.4148 Evaluate side-chains 199 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 88 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12208 Z= 0.257 Angle : 0.587 8.692 16584 Z= 0.293 Chirality : 0.038 0.137 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.056 17.211 1856 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.09 % Allowed : 15.91 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.22), residues: 1500 helix: 2.13 (0.14), residues: 1224 sheet: -4.32 (0.56), residues: 44 loop : -2.93 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 354 HIS 0.003 0.001 HIS D 22 PHE 0.014 0.001 PHE B 203 TYR 0.019 0.001 TYR B 124 ARG 0.003 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 169 time to evaluate : 1.485 Fit side-chains REVERT: A 151 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6870 (tp) REVERT: A 365 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8590 (t) REVERT: B 129 VAL cc_start: 0.7897 (t) cc_final: 0.7351 (m) REVERT: B 151 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6882 (tp) REVERT: B 193 TRP cc_start: 0.9507 (OUTLIER) cc_final: 0.7274 (m100) REVERT: B 365 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8596 (t) REVERT: C 151 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6873 (tp) REVERT: C 365 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8593 (t) REVERT: D 151 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6872 (tp) REVERT: D 365 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8591 (t) REVERT: D 389 LEU cc_start: 0.8517 (mt) cc_final: 0.8308 (mt) outliers start: 54 outliers final: 28 residues processed: 213 average time/residue: 1.3008 time to fit residues: 299.0921 Evaluate side-chains 201 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 93 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12208 Z= 0.270 Angle : 0.585 8.074 16584 Z= 0.294 Chirality : 0.038 0.139 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.064 18.036 1856 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.86 % Allowed : 16.59 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1500 helix: 2.13 (0.14), residues: 1224 sheet: -4.35 (0.55), residues: 44 loop : -2.96 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 193 HIS 0.004 0.001 HIS D 22 PHE 0.014 0.001 PHE B 203 TYR 0.018 0.001 TYR C 124 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 1.385 Fit side-chains REVERT: A 151 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6859 (tp) REVERT: A 365 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8601 (t) REVERT: B 151 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6954 (tp) REVERT: B 193 TRP cc_start: 0.9514 (OUTLIER) cc_final: 0.7199 (m100) REVERT: B 365 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8605 (t) REVERT: C 151 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6862 (tp) REVERT: C 365 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8599 (t) REVERT: D 151 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6858 (tp) REVERT: D 365 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8600 (t) REVERT: D 389 LEU cc_start: 0.8603 (mt) cc_final: 0.8393 (mt) outliers start: 51 outliers final: 28 residues processed: 216 average time/residue: 1.3317 time to fit residues: 310.1481 Evaluate side-chains 197 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9980 chunk 124 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 140 optimal weight: 0.0370 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12208 Z= 0.201 Angle : 0.555 8.975 16584 Z= 0.280 Chirality : 0.037 0.140 2052 Planarity : 0.004 0.037 1992 Dihedral : 3.951 16.836 1856 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.64 % Allowed : 16.74 % Favored : 79.62 % 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: 2.04 (0.22), residues: 1500 helix: 2.33 (0.14), residues: 1220 sheet: -4.34 (0.55), residues: 44 loop : -3.00 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 193 HIS 0.002 0.001 HIS D 326 PHE 0.013 0.001 PHE C 203 TYR 0.017 0.001 TYR C 124 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 163 time to evaluate : 1.343 Fit side-chains REVERT: A 151 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7043 (tp) REVERT: A 365 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8547 (t) REVERT: B 151 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7044 (tp) REVERT: B 365 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8545 (t) REVERT: C 151 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7047 (tp) REVERT: C 172 GLN cc_start: 0.7845 (mm110) cc_final: 0.7577 (mm-40) REVERT: C 365 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8547 (t) REVERT: D 151 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7043 (tp) REVERT: D 365 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8547 (t) REVERT: D 389 LEU cc_start: 0.8548 (mt) cc_final: 0.8314 (mt) outliers start: 48 outliers final: 29 residues processed: 206 average time/residue: 1.3059 time to fit residues: 289.9833 Evaluate side-chains 196 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 93 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 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 222 ASN A 410 GLN B 138 HIS B 139 HIS B 222 ASN B 410 GLN C 138 HIS C 139 HIS C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12208 Z= 0.281 Angle : 0.598 8.279 16584 Z= 0.300 Chirality : 0.039 0.145 2052 Planarity : 0.004 0.039 1992 Dihedral : 4.046 18.013 1856 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.56 % Allowed : 16.52 % Favored : 79.92 % 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: 1.92 (0.22), residues: 1500 helix: 2.21 (0.14), residues: 1224 sheet: -4.34 (0.55), residues: 44 loop : -2.92 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 193 HIS 0.004 0.001 HIS D 22 PHE 0.014 0.001 PHE C 203 TYR 0.017 0.001 TYR C 124 ARG 0.004 0.000 ARG D 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 1.336 Fit side-chains REVERT: A 121 MET cc_start: 0.8506 (tmt) cc_final: 0.8139 (tmt) REVERT: A 151 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6983 (tp) REVERT: A 193 TRP cc_start: 0.9512 (OUTLIER) cc_final: 0.7213 (m100) REVERT: A 365 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (t) REVERT: B 151 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6982 (tp) REVERT: B 193 TRP cc_start: 0.9510 (OUTLIER) cc_final: 0.7220 (m100) REVERT: B 365 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8597 (t) REVERT: C 121 MET cc_start: 0.8503 (tmt) cc_final: 0.8135 (tmt) REVERT: C 151 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6988 (tp) REVERT: C 193 TRP cc_start: 0.9512 (OUTLIER) cc_final: 0.7215 (m100) REVERT: C 365 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8596 (t) REVERT: D 121 MET cc_start: 0.8507 (tmt) cc_final: 0.8140 (tmt) REVERT: D 151 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6984 (tp) REVERT: D 193 TRP cc_start: 0.9513 (OUTLIER) cc_final: 0.7213 (m100) REVERT: D 365 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (t) REVERT: D 389 LEU cc_start: 0.8626 (mt) cc_final: 0.8410 (mt) outliers start: 47 outliers final: 29 residues processed: 208 average time/residue: 1.3371 time to fit residues: 299.6572 Evaluate side-chains 204 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 117 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111656 restraints weight = 21064.615| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.36 r_work: 0.3098 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12208 Z= 0.267 Angle : 0.626 13.948 16584 Z= 0.306 Chirality : 0.038 0.145 2052 Planarity : 0.004 0.039 1992 Dihedral : 4.055 17.468 1856 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.11 % Allowed : 17.73 % Favored : 79.17 % 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: 1.88 (0.22), residues: 1500 helix: 2.19 (0.14), residues: 1224 sheet: -4.35 (0.55), residues: 44 loop : -2.93 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.004 0.001 HIS D 22 PHE 0.014 0.001 PHE A 203 TYR 0.017 0.001 TYR C 124 ARG 0.005 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4764.97 seconds wall clock time: 90 minutes 14.02 seconds (5414.02 seconds total)