Starting phenix.real_space_refine on Fri Mar 15 20:08:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/03_2024/7l6u_23208.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/03_2024/7l6u_23208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/03_2024/7l6u_23208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/03_2024/7l6u_23208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/03_2024/7l6u_23208.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/03_2024/7l6u_23208.pdb" } resolution = 3.3 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= 0.064 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 30 5.16 5 C 8255 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 258": "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: 12675 Number of models: 1 Model: "" Number of chains: 5 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} Time building chain proxies: 6.80, per 1000 atoms: 0.54 Number of scatterers: 12675 At special positions: 0 Unit cell: (92.064, 93.16, 121.656, 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 30 16.00 O 2275 8.00 N 2115 7.00 C 8255 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: 4.38 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... Secondary structure from input PDB file: 45 helices and 15 sheets defined 38.3% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS A 54 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 removed outlier: 3.709A pdb=" N GLN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.541A pdb=" N THR A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS B 54 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 removed outlier: 3.709A pdb=" N GLN B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.541A pdb=" N THR B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS C 54 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 321 removed outlier: 4.260A pdb=" N GLN C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.541A pdb=" N THR C 321 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS D 54 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.664A pdb=" N ASN D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 253 removed outlier: 3.832A pdb=" N PHE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.541A pdb=" N THR D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E 237 " --> pdb=" O GLN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 321 removed outlier: 4.260A pdb=" N GLN E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.541A pdb=" N THR E 321 " --> pdb=" O ILE E 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.286A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A 14 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 143 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.780A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.780A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B 14 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER B 143 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C 14 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER C 143 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 14 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER D 143 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.286A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL E 14 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER E 143 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1905 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: 3.83 Time building geometry restraints manager: 4.81 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: 3037 1.33 - 1.45: 2787 1.45 - 1.57: 7141 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 13015 Sorted by residual: bond pdb=" C VAL A 58 " pdb=" N GLU A 59 " ideal model delta sigma weight residual 1.332 1.221 0.112 1.40e-02 5.10e+03 6.36e+01 bond pdb=" C VAL C 58 " pdb=" N GLU C 59 " ideal model delta sigma weight residual 1.332 1.222 0.111 1.40e-02 5.10e+03 6.23e+01 bond pdb=" C VAL D 58 " pdb=" N GLU D 59 " ideal model delta sigma weight residual 1.332 1.222 0.110 1.40e-02 5.10e+03 6.19e+01 bond pdb=" C VAL E 58 " pdb=" N GLU E 59 " ideal model delta sigma weight residual 1.332 1.223 0.110 1.40e-02 5.10e+03 6.13e+01 bond pdb=" C VAL B 58 " pdb=" N GLU B 59 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.40e-02 5.10e+03 6.11e+01 ... (remaining 13010 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.77: 375 106.77 - 113.59: 7169 113.59 - 120.40: 5097 120.40 - 127.22: 4929 127.22 - 134.04: 165 Bond angle restraints: 17735 Sorted by residual: angle pdb=" N VAL A 291 " pdb=" CA VAL A 291 " pdb=" C VAL A 291 " ideal model delta sigma weight residual 113.71 107.58 6.13 9.50e-01 1.11e+00 4.17e+01 angle pdb=" N VAL B 291 " pdb=" CA VAL B 291 " pdb=" C VAL B 291 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.12e+01 angle pdb=" N VAL E 291 " pdb=" CA VAL E 291 " pdb=" C VAL E 291 " ideal model delta sigma weight residual 113.71 107.62 6.09 9.50e-01 1.11e+00 4.11e+01 angle pdb=" N VAL D 291 " pdb=" CA VAL D 291 " pdb=" C VAL D 291 " ideal model delta sigma weight residual 113.71 107.63 6.08 9.50e-01 1.11e+00 4.10e+01 angle pdb=" N VAL C 291 " pdb=" CA VAL C 291 " pdb=" C VAL C 291 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 ... (remaining 17730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 6653 15.94 - 31.89: 751 31.89 - 47.83: 175 47.83 - 63.78: 26 63.78 - 79.72: 10 Dihedral angle restraints: 7615 sinusoidal: 3060 harmonic: 4555 Sorted by residual: dihedral pdb=" CA GLN C 182 " pdb=" C GLN C 182 " pdb=" N PRO C 183 " pdb=" CA PRO C 183 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN A 182 " pdb=" C GLN A 182 " pdb=" N PRO A 183 " pdb=" CA PRO A 183 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN D 182 " pdb=" C GLN D 182 " pdb=" N PRO D 183 " pdb=" CA PRO D 183 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1519 0.059 - 0.117: 396 0.117 - 0.176: 55 0.176 - 0.235: 0 0.235 - 0.293: 5 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CA GLU B 59 " pdb=" N GLU B 59 " pdb=" C GLU B 59 " pdb=" CB GLU B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA GLU D 59 " pdb=" N GLU D 59 " pdb=" C GLU D 59 " pdb=" CB GLU D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1972 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 59 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLU A 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU A 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN A 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 59 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU B 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU B 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN B 60 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 59 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLU E 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU E 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN E 60 " -0.021 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4737 2.87 - 3.38: 11474 3.38 - 3.89: 19850 3.89 - 4.39: 22253 4.39 - 4.90: 40341 Nonbonded interactions: 98655 Sorted by model distance: nonbonded pdb=" OH TYR D 33 " pdb=" O VAL D 127 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR E 33 " pdb=" O VAL E 127 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR A 33 " pdb=" O VAL A 127 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR B 33 " pdb=" O VAL B 127 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR C 33 " pdb=" O VAL C 127 " model vdw 2.366 2.440 ... (remaining 98650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 2.520 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.780 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.009 0.112 13015 Z= 0.590 Angle : 0.786 8.281 17735 Z= 0.454 Chirality : 0.054 0.293 1975 Planarity : 0.005 0.070 2260 Dihedral : 14.086 79.721 4675 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.72 % Allowed : 0.79 % Favored : 98.49 % 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: -1.06 (0.22), residues: 1545 helix: 0.42 (0.22), residues: 515 sheet: -0.18 (0.26), residues: 480 loop : -2.25 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 160 HIS 0.003 0.001 HIS D 285 PHE 0.025 0.002 PHE B 247 TYR 0.021 0.002 TYR A 248 ARG 0.003 0.000 ARG A 199 *********************** 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 117 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.368 Fit side-chains REVERT: A 142 PHE cc_start: 0.6837 (t80) cc_final: 0.6603 (t80) REVERT: B 138 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: B 142 PHE cc_start: 0.6826 (t80) cc_final: 0.6556 (t80) REVERT: C 142 PHE cc_start: 0.7021 (t80) cc_final: 0.6643 (t80) REVERT: D 142 PHE cc_start: 0.6975 (t80) cc_final: 0.6681 (t80) REVERT: E 138 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: E 142 PHE cc_start: 0.6831 (t80) cc_final: 0.6586 (t80) outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 0.3062 time to fit residues: 49.4086 Evaluate side-chains 90 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 138 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 140 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: B 60 ASN B 138 GLN D 251 ASN E 138 GLN E 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13015 Z= 0.178 Angle : 0.576 7.003 17735 Z= 0.296 Chirality : 0.045 0.153 1975 Planarity : 0.004 0.054 2260 Dihedral : 6.017 59.581 1731 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % 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: -0.39 (0.23), residues: 1545 helix: 1.00 (0.23), residues: 535 sheet: 0.25 (0.26), residues: 480 loop : -2.07 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 43 HIS 0.004 0.001 HIS E 285 PHE 0.028 0.001 PHE E 247 TYR 0.015 0.001 TYR A 248 ARG 0.002 0.000 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 134 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.406 Fit side-chains REVERT: B 142 PHE cc_start: 0.6760 (t80) cc_final: 0.6419 (t80) REVERT: C 142 PHE cc_start: 0.6905 (t80) cc_final: 0.6453 (t80) REVERT: D 86 ASP cc_start: 0.8311 (t0) cc_final: 0.8051 (t0) REVERT: D 93 MET cc_start: 0.7923 (ttm) cc_final: 0.7619 (ttp) REVERT: D 142 PHE cc_start: 0.6865 (t80) cc_final: 0.6482 (t80) REVERT: E 142 PHE cc_start: 0.6666 (t80) cc_final: 0.6375 (t80) REVERT: E 185 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7548 (tp-100) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.2514 time to fit residues: 48.9324 Evaluate side-chains 101 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN B 89 ASN B 251 ASN C 89 ASN C 103 ASN C 251 ASN D 89 ASN D 138 GLN D 251 ASN E 89 ASN E 233 GLN E 285 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 13015 Z= 0.523 Angle : 0.718 7.480 17735 Z= 0.370 Chirality : 0.051 0.199 1975 Planarity : 0.005 0.049 2260 Dihedral : 5.254 26.947 1710 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.79 % Allowed : 9.42 % Favored : 89.78 % 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: -0.73 (0.22), residues: 1545 helix: 0.61 (0.22), residues: 535 sheet: 0.13 (0.26), residues: 480 loop : -2.19 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 224 HIS 0.005 0.001 HIS E 285 PHE 0.046 0.002 PHE A 142 TYR 0.020 0.002 TYR A 248 ARG 0.002 0.000 ARG E 163 *********************** 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 110 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.384 Fit side-chains REVERT: B 142 PHE cc_start: 0.6737 (t80) cc_final: 0.6449 (t80) REVERT: C 142 PHE cc_start: 0.6915 (t80) cc_final: 0.6347 (t80) REVERT: D 86 ASP cc_start: 0.8487 (t0) cc_final: 0.8207 (t0) REVERT: D 142 PHE cc_start: 0.6895 (t80) cc_final: 0.6567 (t80) REVERT: D 224 TRP cc_start: 0.7409 (m100) cc_final: 0.7182 (m100) REVERT: E 264 GLN cc_start: 0.8567 (mt0) cc_final: 0.8362 (mt0) outliers start: 11 outliers final: 4 residues processed: 110 average time/residue: 0.2684 time to fit residues: 42.9441 Evaluate side-chains 85 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13015 Z= 0.292 Angle : 0.618 6.849 17735 Z= 0.318 Chirality : 0.047 0.153 1975 Planarity : 0.004 0.048 2260 Dihedral : 4.876 26.099 1710 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.51 % Allowed : 10.72 % 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: -0.49 (0.22), residues: 1545 helix: 0.83 (0.23), residues: 535 sheet: 0.30 (0.26), residues: 480 loop : -2.12 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.003 0.001 HIS D 285 PHE 0.034 0.002 PHE A 142 TYR 0.017 0.001 TYR C 248 ARG 0.002 0.000 ARG C 91 *********************** 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 126 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.380 Fit side-chains REVERT: D 86 ASP cc_start: 0.8476 (t0) cc_final: 0.8216 (t0) REVERT: D 93 MET cc_start: 0.8019 (ttm) cc_final: 0.7676 (ttp) REVERT: E 185 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7618 (tp-100) outliers start: 21 outliers final: 15 residues processed: 124 average time/residue: 0.2513 time to fit residues: 45.5442 Evaluate side-chains 104 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 0.0770 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 0.0170 chunk 134 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13015 Z= 0.161 Angle : 0.549 7.383 17735 Z= 0.280 Chirality : 0.044 0.142 1975 Planarity : 0.004 0.045 2260 Dihedral : 4.381 24.462 1710 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.29 % Allowed : 11.80 % Favored : 86.91 % 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: -0.05 (0.23), residues: 1545 helix: 1.23 (0.23), residues: 535 sheet: 0.82 (0.27), residues: 450 loop : -2.09 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 43 HIS 0.004 0.001 HIS D 285 PHE 0.025 0.001 PHE A 142 TYR 0.017 0.001 TYR D 248 ARG 0.002 0.000 ARG C 91 *********************** 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 144 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.490 Fit side-chains REVERT: D 86 ASP cc_start: 0.8417 (t0) cc_final: 0.8160 (t0) REVERT: D 93 MET cc_start: 0.7883 (ttm) cc_final: 0.7590 (ttp) REVERT: D 138 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: D 224 TRP cc_start: 0.7574 (m100) cc_final: 0.7328 (m100) REVERT: E 185 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7399 (tp-100) outliers start: 18 outliers final: 15 residues processed: 138 average time/residue: 0.2425 time to fit residues: 49.2127 Evaluate side-chains 115 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN E 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 13015 Z= 0.432 Angle : 0.663 6.856 17735 Z= 0.342 Chirality : 0.049 0.181 1975 Planarity : 0.005 0.043 2260 Dihedral : 4.955 25.826 1710 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.80 % Allowed : 12.88 % Favored : 85.32 % 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: 0.86 (0.23), residues: 540 sheet: 0.40 (0.26), residues: 480 loop : -2.04 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 160 HIS 0.004 0.001 HIS A 285 PHE 0.033 0.002 PHE A 142 TYR 0.019 0.002 TYR C 248 ARG 0.002 0.000 ARG B 91 *********************** 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 117 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.419 Fit side-chains REVERT: B 113 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7274 (p0) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.2537 time to fit residues: 42.0574 Evaluate side-chains 102 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 149 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 92 optimal weight: 20.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13015 Z= 0.162 Angle : 0.544 6.378 17735 Z= 0.277 Chirality : 0.044 0.143 1975 Planarity : 0.004 0.043 2260 Dihedral : 4.387 24.227 1710 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.44 % Allowed : 13.17 % Favored : 85.40 % 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: 0.05 (0.23), residues: 1545 helix: 1.37 (0.23), residues: 535 sheet: 0.83 (0.27), residues: 455 loop : -2.06 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.003 0.000 HIS D 285 PHE 0.025 0.001 PHE A 142 TYR 0.020 0.001 TYR C 248 ARG 0.002 0.000 ARG C 286 *********************** 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 135 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.344 Fit side-chains REVERT: D 93 MET cc_start: 0.7940 (ttm) cc_final: 0.7631 (ttp) REVERT: D 224 TRP cc_start: 0.7495 (m100) cc_final: 0.7286 (m100) outliers start: 20 outliers final: 18 residues processed: 129 average time/residue: 0.2477 time to fit residues: 46.6400 Evaluate side-chains 121 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 20.0000 chunk 89 optimal weight: 0.0570 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 117 optimal weight: 0.3980 chunk 135 optimal weight: 1.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13015 Z= 0.210 Angle : 0.564 6.353 17735 Z= 0.290 Chirality : 0.045 0.143 1975 Planarity : 0.004 0.042 2260 Dihedral : 4.414 24.265 1710 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.87 % Allowed : 13.74 % Favored : 84.39 % 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: 0.19 (0.23), residues: 1545 helix: 1.38 (0.23), residues: 535 sheet: 0.90 (0.27), residues: 470 loop : -1.95 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 43 HIS 0.003 0.001 HIS D 285 PHE 0.026 0.001 PHE A 142 TYR 0.023 0.001 TYR C 248 ARG 0.001 0.000 ARG C 65 *********************** 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 131 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.477 Fit side-chains REVERT: D 93 MET cc_start: 0.8016 (ttm) cc_final: 0.7709 (ttp) REVERT: D 141 ARG cc_start: 0.7353 (ttt180) cc_final: 0.7104 (ttt-90) REVERT: D 224 TRP cc_start: 0.7511 (m100) cc_final: 0.7046 (m100) outliers start: 26 outliers final: 22 residues processed: 126 average time/residue: 0.2514 time to fit residues: 46.3231 Evaluate side-chains 116 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN E 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13015 Z= 0.244 Angle : 0.573 6.386 17735 Z= 0.294 Chirality : 0.046 0.145 1975 Planarity : 0.004 0.042 2260 Dihedral : 4.485 24.277 1710 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.65 % Allowed : 14.17 % Favored : 84.17 % 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: 0.18 (0.23), residues: 1545 helix: 1.39 (0.23), residues: 535 sheet: 0.92 (0.27), residues: 470 loop : -1.99 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 224 HIS 0.003 0.001 HIS B 285 PHE 0.027 0.001 PHE A 142 TYR 0.021 0.001 TYR C 248 ARG 0.001 0.000 ARG B 91 *********************** 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 121 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.443 Fit side-chains REVERT: D 93 MET cc_start: 0.7992 (ttm) cc_final: 0.7673 (ttp) outliers start: 23 outliers final: 23 residues processed: 117 average time/residue: 0.2674 time to fit residues: 45.5965 Evaluate side-chains 119 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 0.0770 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13015 Z= 0.343 Angle : 0.621 6.516 17735 Z= 0.320 Chirality : 0.047 0.162 1975 Planarity : 0.004 0.042 2260 Dihedral : 4.743 24.944 1710 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.65 % Allowed : 14.39 % Favored : 83.96 % 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: -0.06 (0.22), residues: 1545 helix: 1.14 (0.22), residues: 540 sheet: 0.77 (0.26), residues: 470 loop : -2.08 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 43 HIS 0.004 0.001 HIS E 285 PHE 0.031 0.002 PHE A 142 TYR 0.018 0.002 TYR C 248 ARG 0.002 0.000 ARG B 91 ********************** 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 117 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.491 Fit side-chains outliers start: 23 outliers final: 21 residues processed: 113 average time/residue: 0.2526 time to fit residues: 41.3935 Evaluate side-chains 114 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.173318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.141632 restraints weight = 14512.652| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.13 r_work: 0.3608 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13015 Z= 0.289 Angle : 0.596 6.476 17735 Z= 0.307 Chirality : 0.046 0.149 1975 Planarity : 0.004 0.042 2260 Dihedral : 4.658 24.756 1710 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.58 % Allowed : 14.53 % Favored : 83.88 % 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: -0.02 (0.22), residues: 1545 helix: 1.20 (0.22), residues: 540 sheet: 0.73 (0.26), residues: 475 loop : -2.04 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 224 HIS 0.004 0.001 HIS B 285 PHE 0.029 0.002 PHE A 142 TYR 0.020 0.001 TYR C 248 ARG 0.001 0.000 ARG B 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.54 seconds wall clock time: 41 minutes 1.20 seconds (2461.20 seconds total)