Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 17:52:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d68_27220/04_2023/8d68_27220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d68_27220/04_2023/8d68_27220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d68_27220/04_2023/8d68_27220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d68_27220/04_2023/8d68_27220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d68_27220/04_2023/8d68_27220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d68_27220/04_2023/8d68_27220_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 30 5.16 5 C 8545 2.51 5 N 2130 2.21 5 O 2345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 13": "OD1" <-> "OD2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "E ASP 13": "OD1" <-> "OD2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13055 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "B" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "C" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "D" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "E" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AGLN A 233 " occ=0.30 ... (16 atoms not shown) pdb=" NE2BGLN A 233 " occ=0.70 residue: pdb=" N AGLN B 233 " occ=0.30 ... (16 atoms not shown) pdb=" NE2BGLN B 233 " occ=0.70 residue: pdb=" N AGLN C 233 " occ=0.30 ... (16 atoms not shown) pdb=" NE2BGLN C 233 " occ=0.70 residue: pdb=" N AGLN D 233 " occ=0.30 ... (16 atoms not shown) pdb=" NE2BGLN D 233 " occ=0.70 residue: pdb=" N AGLN E 233 " occ=0.30 ... (16 atoms not shown) pdb=" NE2BGLN E 233 " occ=0.70 Time building chain proxies: 12.57, per 1000 atoms: 0.96 Number of scatterers: 13055 At special positions: 0 Unit cell: (93.96, 95.12, 128.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 5 15.00 O 2345 8.00 N 2130 7.00 C 8545 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 3.3 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2950 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 15 sheets defined 30.4% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.754A pdb=" N ASN A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 222 removed outlier: 3.833A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Proline residue: A 211 - end of helix removed outlier: 4.218A pdb=" N VAL A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.278A pdb=" N TYR A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 261 through 287 Processing helix chain 'A' and resid 300 through 320 Proline residue: A 305 - end of helix removed outlier: 3.691A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.754A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 222 removed outlier: 3.834A pdb=" N ILE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) Proline residue: B 211 - end of helix removed outlier: 4.218A pdb=" N VAL B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 233 through 245 removed outlier: 4.278A pdb=" N TYR B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 261 through 287 Processing helix chain 'B' and resid 300 through 320 Proline residue: B 305 - end of helix removed outlier: 3.691A pdb=" N ILE B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 69 removed outlier: 3.755A pdb=" N ASN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 222 removed outlier: 3.833A pdb=" N ILE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) Proline residue: C 211 - end of helix removed outlier: 4.218A pdb=" N VAL C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.278A pdb=" N TYR C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 261 through 287 Processing helix chain 'C' and resid 300 through 320 Proline residue: C 305 - end of helix removed outlier: 3.691A pdb=" N ILE C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 69 removed outlier: 3.755A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 222 removed outlier: 3.833A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) Proline residue: D 211 - end of helix removed outlier: 4.218A pdb=" N VAL D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 233 through 245 removed outlier: 4.278A pdb=" N TYR D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 261 through 287 Processing helix chain 'D' and resid 300 through 320 Proline residue: D 305 - end of helix removed outlier: 3.691A pdb=" N ILE D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 316 " --> pdb=" O GLY D 312 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 removed outlier: 3.754A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 222 removed outlier: 3.834A pdb=" N ILE E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU E 210 " --> pdb=" O TRP E 206 " (cutoff:3.500A) Proline residue: E 211 - end of helix removed outlier: 4.218A pdb=" N VAL E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 233 through 245 removed outlier: 4.278A pdb=" N TYR E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 261 through 287 Processing helix chain 'E' and resid 300 through 320 Proline residue: E 305 - end of helix removed outlier: 3.692A pdb=" N ILE E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 316 " --> pdb=" O GLY E 312 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.825A pdb=" N LYS A 22 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR A 38 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE A 20 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 40 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE A 18 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN A 42 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 16 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N THR A 44 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL A 14 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL A 147 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE A 20 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 removed outlier: 4.469A pdb=" N ASP A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 167 through 174 Processing sheet with id= D, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.825A pdb=" N LYS B 22 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR B 38 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE B 20 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL B 40 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE B 18 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN B 42 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 16 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N THR B 44 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL B 14 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL B 147 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 20 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 76 through 78 removed outlier: 4.469A pdb=" N ASP B 196 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 167 through 174 Processing sheet with id= G, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.825A pdb=" N LYS C 22 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR C 38 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE C 20 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL C 40 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE C 18 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN C 42 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL C 16 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N THR C 44 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL C 14 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL C 147 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE C 20 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.469A pdb=" N ASP C 196 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 167 through 174 Processing sheet with id= J, first strand: chain 'D' and resid 56 through 58 removed outlier: 3.825A pdb=" N LYS D 22 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL D 40 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE D 18 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN D 42 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL D 16 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N THR D 44 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL D 14 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL D 147 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE D 20 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 76 through 78 removed outlier: 4.469A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 167 through 174 Processing sheet with id= M, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.824A pdb=" N LYS E 22 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR E 38 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE E 20 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL E 40 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE E 18 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN E 42 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL E 16 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N THR E 44 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL E 14 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL E 147 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE E 20 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 76 through 78 removed outlier: 4.469A pdb=" N ASP E 196 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 167 through 174 510 hydrogen bonds defined for protein. 1500 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: 3.54 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2048 1.30 - 1.43: 3840 1.43 - 1.55: 7452 1.55 - 1.68: 10 1.68 - 1.81: 50 Bond restraints: 13400 Sorted by residual: bond pdb=" C BGLN D 233 " pdb=" N THR D 234 " ideal model delta sigma weight residual 1.335 1.241 0.094 1.31e-02 5.83e+03 5.14e+01 bond pdb=" C LEU C 232 " pdb=" N BGLN C 233 " ideal model delta sigma weight residual 1.335 1.237 0.097 1.36e-02 5.41e+03 5.12e+01 bond pdb=" C LEU E 232 " pdb=" N BGLN E 233 " ideal model delta sigma weight residual 1.335 1.422 -0.087 1.38e-02 5.25e+03 3.97e+01 bond pdb=" C BGLN A 233 " pdb=" N THR A 234 " ideal model delta sigma weight residual 1.335 1.412 -0.077 1.31e-02 5.83e+03 3.50e+01 bond pdb=" C BGLN B 233 " pdb=" N THR B 234 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.31e-02 5.83e+03 3.22e+01 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 100.18 - 107.00: 395 107.00 - 113.83: 7333 113.83 - 120.65: 5711 120.65 - 127.47: 4601 127.47 - 134.29: 145 Bond angle restraints: 18185 Sorted by residual: angle pdb=" O13 PGW A 401 " pdb=" P PGW A 401 " pdb=" O14 PGW A 401 " ideal model delta sigma weight residual 119.81 107.80 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O13 PGW B 401 " pdb=" P PGW B 401 " pdb=" O14 PGW B 401 " ideal model delta sigma weight residual 119.81 107.80 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O13 PGW D 401 " pdb=" P PGW D 401 " pdb=" O14 PGW D 401 " ideal model delta sigma weight residual 119.81 107.81 12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O13 PGW E 401 " pdb=" P PGW E 401 " pdb=" O14 PGW E 401 " ideal model delta sigma weight residual 119.81 107.81 12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O13 PGW C 401 " pdb=" P PGW C 401 " pdb=" O14 PGW C 401 " ideal model delta sigma weight residual 119.81 107.82 11.99 3.00e+00 1.11e-01 1.60e+01 ... (remaining 18180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 7261 21.73 - 43.45: 449 43.45 - 65.18: 90 65.18 - 86.90: 20 86.90 - 108.63: 10 Dihedral angle restraints: 7830 sinusoidal: 3250 harmonic: 4580 Sorted by residual: dihedral pdb=" CA VAL E 291 " pdb=" C VAL E 291 " pdb=" N GLU E 292 " pdb=" CA GLU E 292 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL D 291 " pdb=" C VAL D 291 " pdb=" N GLU D 292 " pdb=" CA GLU D 292 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL A 291 " pdb=" C VAL A 291 " pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 7827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 955 0.035 - 0.071: 664 0.071 - 0.106: 239 0.106 - 0.142: 97 0.142 - 0.177: 25 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA TRP E 206 " pdb=" N TRP E 206 " pdb=" C TRP E 206 " pdb=" CB TRP E 206 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA TRP C 206 " pdb=" N TRP C 206 " pdb=" C TRP C 206 " pdb=" CB TRP C 206 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA TRP D 206 " pdb=" N TRP D 206 " pdb=" C TRP D 206 " pdb=" CB TRP D 206 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 1977 not shown) Planarity restraints: 2300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 256 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 257 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 257 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 257 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 256 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO E 257 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 257 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 257 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 256 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO D 257 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 257 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 257 " -0.025 5.00e-02 4.00e+02 ... (remaining 2297 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1712 2.75 - 3.29: 11059 3.29 - 3.82: 18358 3.82 - 4.36: 21177 4.36 - 4.90: 39458 Nonbonded interactions: 91764 Sorted by model distance: nonbonded pdb=" ND2 ASN A 27 " pdb=" OE1 GLU A 30 " model vdw 2.212 2.520 nonbonded pdb=" ND2 ASN C 27 " pdb=" OE1 GLU C 30 " model vdw 2.212 2.520 nonbonded pdb=" ND2 ASN D 27 " pdb=" OE1 GLU D 30 " model vdw 2.212 2.520 nonbonded pdb=" ND2 ASN E 27 " pdb=" OE1 GLU E 30 " model vdw 2.212 2.520 nonbonded pdb=" ND2 ASN B 27 " pdb=" OE1 GLU B 30 " model vdw 2.213 2.520 ... (remaining 91759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 232 or resid 234 through 321 or resid 401 throu \ gh 402)) selection = (chain 'B' and (resid 11 through 232 or resid 234 through 321 or resid 401 throu \ gh 402)) selection = (chain 'C' and (resid 11 through 232 or resid 234 through 321 or resid 401 throu \ gh 402)) selection = (chain 'D' and (resid 11 through 232 or resid 234 through 321 or resid 401 throu \ gh 402)) selection = (chain 'E' and (resid 11 through 232 or resid 234 through 321 or resid 401 throu \ gh 402)) } 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=0.30 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: 0.340 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: 2.460 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 41.030 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.008 0.097 13400 Z= 0.524 Angle : 1.061 12.008 18185 Z= 0.532 Chirality : 0.056 0.177 1980 Planarity : 0.005 0.045 2300 Dihedral : 15.514 108.626 4880 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 0.00 % 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: -1.43 (0.21), residues: 1560 helix: 0.90 (0.25), residues: 455 sheet: -0.34 (0.23), residues: 425 loop : -2.74 (0.23), residues: 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.424 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3431 time to fit residues: 51.8987 Evaluate side-chains 86 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 121 optimal weight: 0.0570 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13400 Z= 0.208 Angle : 0.632 6.776 18185 Z= 0.338 Chirality : 0.048 0.163 1980 Planarity : 0.004 0.040 2300 Dihedral : 11.618 75.016 1900 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.07 % 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: -1.24 (0.21), residues: 1560 helix: 1.01 (0.25), residues: 495 sheet: -0.38 (0.24), residues: 410 loop : -2.65 (0.22), residues: 655 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.608 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.2815 time to fit residues: 37.2855 Evaluate side-chains 83 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1140 time to fit residues: 2.4038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 0.0770 chunk 152 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 13400 Z= 0.153 Angle : 0.537 6.183 18185 Z= 0.285 Chirality : 0.046 0.149 1980 Planarity : 0.004 0.038 2300 Dihedral : 9.951 68.898 1900 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.07 % 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: -0.79 (0.22), residues: 1560 helix: 1.54 (0.25), residues: 500 sheet: -0.04 (0.24), residues: 410 loop : -2.64 (0.22), residues: 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.550 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.2380 time to fit residues: 36.8187 Evaluate side-chains 92 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1041 time to fit residues: 2.0443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 134 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 13400 Z= 0.154 Angle : 0.538 7.050 18185 Z= 0.286 Chirality : 0.046 0.153 1980 Planarity : 0.004 0.037 2300 Dihedral : 9.369 66.595 1900 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 0.00 % 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: -0.62 (0.22), residues: 1560 helix: 1.66 (0.25), residues: 500 sheet: 0.13 (0.25), residues: 410 loop : -2.57 (0.22), residues: 650 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.520 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2609 time to fit residues: 36.6809 Evaluate side-chains 89 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 134 optimal weight: 0.0170 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 overall best weight: 2.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13400 Z= 0.282 Angle : 0.658 7.886 18185 Z= 0.354 Chirality : 0.049 0.167 1980 Planarity : 0.004 0.037 2300 Dihedral : 9.646 68.934 1900 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 0.43 % 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: -0.79 (0.21), residues: 1560 helix: 1.39 (0.25), residues: 495 sheet: 0.19 (0.25), residues: 395 loop : -2.57 (0.22), residues: 670 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.520 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 0.2628 time to fit residues: 34.8999 Evaluate side-chains 88 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1124 time to fit residues: 3.3346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 13400 Z= 0.176 Angle : 0.562 7.062 18185 Z= 0.300 Chirality : 0.046 0.154 1980 Planarity : 0.004 0.038 2300 Dihedral : 9.061 67.881 1900 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.00 % 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: -0.71 (0.22), residues: 1560 helix: 1.57 (0.25), residues: 495 sheet: 0.06 (0.24), residues: 410 loop : -2.56 (0.22), residues: 655 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.398 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2665 time to fit residues: 36.7976 Evaluate side-chains 88 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 0.0170 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 149 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 13400 Z= 0.122 Angle : 0.491 6.635 18185 Z= 0.258 Chirality : 0.045 0.144 1980 Planarity : 0.003 0.038 2300 Dihedral : 8.192 61.373 1900 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.07 % 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: -0.42 (0.22), residues: 1560 helix: 1.74 (0.26), residues: 505 sheet: 0.27 (0.25), residues: 410 loop : -2.42 (0.22), residues: 645 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.443 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.2609 time to fit residues: 42.8864 Evaluate side-chains 100 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.0060 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 13400 Z= 0.133 Angle : 0.502 7.505 18185 Z= 0.265 Chirality : 0.045 0.146 1980 Planarity : 0.003 0.036 2300 Dihedral : 7.972 61.754 1900 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.07 % 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: -0.31 (0.22), residues: 1560 helix: 1.76 (0.25), residues: 505 sheet: 0.31 (0.25), residues: 410 loop : -2.28 (0.23), residues: 645 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.387 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.2609 time to fit residues: 37.6182 Evaluate side-chains 96 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1189 time to fit residues: 2.4042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 0.0670 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 13400 Z= 0.153 Angle : 0.527 7.320 18185 Z= 0.281 Chirality : 0.046 0.155 1980 Planarity : 0.003 0.036 2300 Dihedral : 7.821 61.643 1900 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.07 % 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: -0.31 (0.22), residues: 1560 helix: 1.76 (0.25), residues: 505 sheet: 0.29 (0.25), residues: 410 loop : -2.26 (0.23), residues: 645 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.577 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2762 time to fit residues: 40.5088 Evaluate side-chains 98 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1171 time to fit residues: 2.3738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 12 optimal weight: 0.0370 chunk 94 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN E 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 13400 Z= 0.126 Angle : 0.497 7.201 18185 Z= 0.262 Chirality : 0.045 0.145 1980 Planarity : 0.003 0.037 2300 Dihedral : 7.475 61.020 1900 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.00 % 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: -0.26 (0.22), residues: 1560 helix: 1.76 (0.25), residues: 510 sheet: 0.36 (0.25), residues: 410 loop : -2.25 (0.23), residues: 640 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.513 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2633 time to fit residues: 39.3967 Evaluate side-chains 97 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 139 GLN C 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.144563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.113198 restraints weight = 56256.953| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 5.07 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 13400 Z= 0.298 Angle : 0.659 8.242 18185 Z= 0.356 Chirality : 0.050 0.171 1980 Planarity : 0.004 0.036 2300 Dihedral : 8.198 58.751 1900 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 0.00 % 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: -0.62 (0.21), residues: 1560 helix: 1.52 (0.25), residues: 495 sheet: 0.14 (0.25), residues: 410 loop : -2.42 (0.22), residues: 655 =============================================================================== Job complete usr+sys time: 2079.40 seconds wall clock time: 38 minutes 41.58 seconds (2321.58 seconds total)