Starting phenix.real_space_refine (version: dev) on Mon Dec 12 14:12:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/12_2022/7oe2_12859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/12_2022/7oe2_12859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/12_2022/7oe2_12859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/12_2022/7oe2_12859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/12_2022/7oe2_12859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/12_2022/7oe2_12859.pdb" } resolution = 2.4 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= -0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 14": "OD1" <-> "OD2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 14": "OD1" <-> "OD2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 14": "OD1" <-> "OD2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10589 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2034 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain: "B" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2034 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain: "C" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2034 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain: "D" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2034 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain: "E" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2034 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain: "1" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 53 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "2" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 53 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "3" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 53 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "4" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 53 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "5" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 53 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.05, per 1000 atoms: 0.57 Number of scatterers: 10589 At special positions: 0 Unit cell: (95.192, 146.7, 134.964, 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 25 16.00 O 2144 8.00 N 1805 7.00 C 6615 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: 4.40 Conformation dependent library (CDL) restraints added in 1.6 seconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 25 sheets defined 42.2% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 12 through 31 removed outlier: 3.561A pdb=" N ILE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.644A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 101 through 122 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 162 Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 12 through 31 removed outlier: 3.561A pdb=" N ILE B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 3.645A pdb=" N LEU B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 101 through 122 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 162 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 12 through 31 removed outlier: 3.562A pdb=" N ILE C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.644A pdb=" N LEU C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 162 Processing helix chain 'C' and resid 173 through 183 Processing helix chain 'C' and resid 190 through 198 Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 12 through 31 removed outlier: 3.562A pdb=" N ILE D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.644A pdb=" N LEU D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 147 through 162 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 190 through 198 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 12 through 31 removed outlier: 3.562A pdb=" N ILE E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 removed outlier: 3.644A pdb=" N LEU E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 101 through 122 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 147 through 162 Processing helix chain 'E' and resid 173 through 183 Processing helix chain 'E' and resid 190 through 198 Processing helix chain 'E' and resid 256 through 258 No H-bonds generated for 'chain 'E' and resid 256 through 258' Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP A 38 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 226 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG A 40 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP A 38 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 226 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG A 40 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE A 245 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR A 234 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA A 247 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 232 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 57 removed outlier: 7.280A pdb=" N THR A 52 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN A 73 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU A 54 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 removed outlier: 6.921A pdb=" N LEU A 140 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 204 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP B 38 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 226 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 40 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP B 38 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 226 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 40 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE B 245 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR B 234 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 247 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 232 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 57 removed outlier: 7.281A pdb=" N THR B 52 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN B 73 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU B 54 " --> pdb=" O GLN B 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 141 removed outlier: 6.921A pdb=" N LEU B 140 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 204 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 185 Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.275A pdb=" N ASP C 38 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 226 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG C 40 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.275A pdb=" N ASP C 38 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 226 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG C 40 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 245 " --> pdb=" O TYR C 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR C 234 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA C 247 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE C 232 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 49 through 57 removed outlier: 7.282A pdb=" N THR C 52 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN C 73 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU C 54 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 141 removed outlier: 6.921A pdb=" N LEU C 140 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 204 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB7, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP D 38 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 226 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG D 40 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP D 38 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 226 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG D 40 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE D 245 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR D 234 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA D 247 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE D 232 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 57 removed outlier: 7.282A pdb=" N THR D 52 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN D 73 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU D 54 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 140 through 141 removed outlier: 6.920A pdb=" N LEU D 140 " --> pdb=" O ARG D 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 204 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 184 through 185 Processing sheet with id=AC3, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP E 38 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL E 226 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG E 40 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP E 38 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL E 226 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG E 40 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE E 245 " --> pdb=" O TYR E 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR E 234 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA E 247 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE E 232 " --> pdb=" O ALA E 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 49 through 57 removed outlier: 7.282A pdb=" N THR E 52 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN E 73 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU E 54 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 140 through 141 removed outlier: 6.920A pdb=" N LEU E 140 " --> pdb=" O ARG E 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 204 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 184 through 185 500 hydrogen bonds defined for protein. 1395 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: 3.27 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3566 1.34 - 1.46: 2099 1.46 - 1.58: 4935 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 10650 Sorted by residual: bond pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 1.515 1.496 0.019 1.43e-02 4.89e+03 1.75e+00 bond pdb=" CA GLY B 166 " pdb=" C GLY B 166 " ideal model delta sigma weight residual 1.515 1.497 0.018 1.43e-02 4.89e+03 1.58e+00 bond pdb=" CA GLY E 166 " pdb=" C GLY E 166 " ideal model delta sigma weight residual 1.515 1.497 0.018 1.43e-02 4.89e+03 1.56e+00 bond pdb=" CA GLY A 166 " pdb=" C GLY A 166 " ideal model delta sigma weight residual 1.515 1.497 0.018 1.43e-02 4.89e+03 1.55e+00 bond pdb=" CA GLY C 41 " pdb=" C GLY C 41 " ideal model delta sigma weight residual 1.515 1.497 0.018 1.43e-02 4.89e+03 1.54e+00 ... (remaining 10645 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.69: 330 106.69 - 113.55: 5886 113.55 - 120.41: 4032 120.41 - 127.27: 4132 127.27 - 134.13: 110 Bond angle restraints: 14490 Sorted by residual: angle pdb=" N GLY E 227 " pdb=" CA GLY E 227 " pdb=" C GLY E 227 " ideal model delta sigma weight residual 113.18 106.57 6.61 2.37e+00 1.78e-01 7.78e+00 angle pdb=" N GLY B 227 " pdb=" CA GLY B 227 " pdb=" C GLY B 227 " ideal model delta sigma weight residual 113.18 106.59 6.59 2.37e+00 1.78e-01 7.74e+00 angle pdb=" N GLY C 227 " pdb=" CA GLY C 227 " pdb=" C GLY C 227 " ideal model delta sigma weight residual 113.18 106.59 6.59 2.37e+00 1.78e-01 7.72e+00 angle pdb=" N GLY D 227 " pdb=" CA GLY D 227 " pdb=" C GLY D 227 " ideal model delta sigma weight residual 113.18 106.64 6.54 2.37e+00 1.78e-01 7.62e+00 angle pdb=" N GLY A 227 " pdb=" CA GLY A 227 " pdb=" C GLY A 227 " ideal model delta sigma weight residual 113.18 106.64 6.54 2.37e+00 1.78e-01 7.62e+00 ... (remaining 14485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5502 17.89 - 35.79: 618 35.79 - 53.68: 185 53.68 - 71.58: 20 71.58 - 89.47: 35 Dihedral angle restraints: 6360 sinusoidal: 2440 harmonic: 3920 Sorted by residual: dihedral pdb=" CA ARG D 264 " pdb=" C ARG D 264 " pdb=" N TYR D 265 " pdb=" CA TYR D 265 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG E 264 " pdb=" C ARG E 264 " pdb=" N TYR E 265 " pdb=" CA TYR E 265 " ideal model delta harmonic sigma weight residual 180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG B 264 " pdb=" C ARG B 264 " pdb=" N TYR B 265 " pdb=" CA TYR B 265 " ideal model delta harmonic sigma weight residual -180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 6357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 682 0.032 - 0.063: 566 0.063 - 0.095: 282 0.095 - 0.126: 84 0.126 - 0.158: 26 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CB VAL D 92 " pdb=" CA VAL D 92 " pdb=" CG1 VAL D 92 " pdb=" CG2 VAL D 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CB VAL A 92 " pdb=" CA VAL A 92 " pdb=" CG1 VAL A 92 " pdb=" CG2 VAL A 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CB VAL C 92 " pdb=" CA VAL C 92 " pdb=" CG1 VAL C 92 " pdb=" CG2 VAL C 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 1637 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 152 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C VAL D 152 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL D 152 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU D 153 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 152 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C VAL B 152 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL B 152 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 153 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 152 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C VAL A 152 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL A 152 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 153 " 0.010 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 564 2.72 - 3.27: 10100 3.27 - 3.81: 19178 3.81 - 4.36: 23739 4.36 - 4.90: 36477 Nonbonded interactions: 90058 Sorted by model distance: nonbonded pdb=" OE2 GLU D 115 " pdb=" O HOH D 301 " model vdw 2.179 2.440 nonbonded pdb=" OE2 GLU E 115 " pdb=" O HOH E 301 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR E 188 " pdb=" NH2 ARG E 196 " model vdw 2.324 2.520 nonbonded pdb=" OH TYR B 188 " pdb=" NH2 ARG B 196 " model vdw 2.324 2.520 nonbonded pdb=" OH TYR D 188 " pdb=" NH2 ARG D 196 " model vdw 2.325 2.520 ... (remaining 90053 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' } 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 6615 2.51 5 N 1805 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 8.380 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: 41.060 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.100 Process input model: 30.770 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.006 0.032 10650 Z= 0.422 Angle : 0.682 6.612 14490 Z= 0.386 Chirality : 0.054 0.158 1640 Planarity : 0.005 0.031 1920 Dihedral : 17.807 89.472 3840 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 2.44 % 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: 0.75 (0.23), residues: 1355 helix: 0.52 (0.25), residues: 415 sheet: 1.63 (0.30), residues: 315 loop : -0.03 (0.26), residues: 625 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.424 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 152 average time/residue: 1.5649 time to fit residues: 252.6121 Evaluate side-chains 107 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.5017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 10650 Z= 0.136 Angle : 0.459 5.094 14490 Z= 0.245 Chirality : 0.042 0.128 1640 Planarity : 0.004 0.028 1920 Dihedral : 4.122 13.931 1490 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1355 helix: 1.50 (0.26), residues: 445 sheet: 1.59 (0.31), residues: 315 loop : 0.14 (0.26), residues: 595 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.302 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 137 average time/residue: 1.5770 time to fit residues: 229.6272 Evaluate side-chains 117 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 1 average time/residue: 0.2850 time to fit residues: 2.1229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 0.0670 overall best weight: 0.9528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN B 73 GLN C 73 GLN D 73 GLN E 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 10650 Z= 0.135 Angle : 0.431 4.862 14490 Z= 0.226 Chirality : 0.041 0.131 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.741 12.691 1490 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.97 % 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: 1.51 (0.24), residues: 1355 helix: 2.21 (0.26), residues: 415 sheet: 1.22 (0.33), residues: 260 loop : 0.23 (0.25), residues: 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 1.4479 time to fit residues: 204.1304 Evaluate side-chains 118 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.5395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.021 10650 Z= 0.242 Angle : 0.472 5.626 14490 Z= 0.244 Chirality : 0.043 0.133 1640 Planarity : 0.003 0.028 1920 Dihedral : 4.039 13.832 1490 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 3.10 % 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: 1.56 (0.24), residues: 1355 helix: 2.13 (0.26), residues: 415 sheet: 1.25 (0.32), residues: 295 loop : 0.28 (0.26), residues: 645 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.267 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 131 average time/residue: 1.4528 time to fit residues: 203.1371 Evaluate side-chains 116 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.6322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 10650 Z= 0.192 Angle : 0.445 5.293 14490 Z= 0.230 Chirality : 0.042 0.132 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.850 12.641 1490 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.97 % 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: 1.55 (0.24), residues: 1355 helix: 2.17 (0.26), residues: 415 sheet: 1.10 (0.32), residues: 260 loop : 0.36 (0.25), residues: 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.311 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 124 average time/residue: 1.4656 time to fit residues: 194.0241 Evaluate side-chains 116 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.8888 time to fit residues: 3.5771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8085 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 10650 Z= 0.157 Angle : 0.426 4.978 14490 Z= 0.221 Chirality : 0.041 0.131 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.680 12.445 1490 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.07 % 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: 1.59 (0.23), residues: 1355 helix: 2.24 (0.26), residues: 415 sheet: 1.07 (0.32), residues: 260 loop : 0.39 (0.25), residues: 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.256 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 127 average time/residue: 1.4478 time to fit residues: 198.2708 Evaluate side-chains 123 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 1.7262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 10650 Z= 0.254 Angle : 0.476 6.046 14490 Z= 0.243 Chirality : 0.043 0.133 1640 Planarity : 0.003 0.028 1920 Dihedral : 3.967 13.005 1490 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.88 % 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: 1.55 (0.23), residues: 1355 helix: 2.15 (0.26), residues: 415 sheet: 0.99 (0.32), residues: 265 loop : 0.43 (0.25), residues: 675 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 123 average time/residue: 1.4875 time to fit residues: 195.5585 Evaluate side-chains 120 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.7634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 10650 Z= 0.150 Angle : 0.438 7.788 14490 Z= 0.224 Chirality : 0.041 0.131 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.703 12.835 1490 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 2.07 % 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: 1.61 (0.23), residues: 1355 helix: 2.26 (0.26), residues: 415 sheet: 1.04 (0.32), residues: 260 loop : 0.42 (0.25), residues: 680 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.261 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 19 residues processed: 126 average time/residue: 1.4715 time to fit residues: 197.7431 Evaluate side-chains 124 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.4775 time to fit residues: 3.1032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 10650 Z= 0.226 Angle : 0.465 6.517 14490 Z= 0.237 Chirality : 0.042 0.133 1640 Planarity : 0.003 0.028 1920 Dihedral : 3.849 12.442 1490 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.78 % 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: 1.62 (0.23), residues: 1355 helix: 2.21 (0.26), residues: 415 sheet: 1.08 (0.32), residues: 260 loop : 0.45 (0.25), residues: 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 18 residues processed: 123 average time/residue: 1.4965 time to fit residues: 196.3089 Evaluate side-chains 121 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.6824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 85 optimal weight: 0.0570 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS D 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10650 Z= 0.132 Angle : 0.426 4.820 14490 Z= 0.218 Chirality : 0.041 0.130 1640 Planarity : 0.003 0.026 1920 Dihedral : 3.525 11.912 1490 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1355 helix: 2.35 (0.26), residues: 415 sheet: 1.07 (0.31), residues: 290 loop : 0.52 (0.25), residues: 650 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 1.4948 time to fit residues: 207.0109 Evaluate side-chains 126 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.5129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.047805 restraints weight = 27086.034| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.92 r_work: 0.2565 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10650 Z= 0.166 Angle : 0.448 5.108 14490 Z= 0.227 Chirality : 0.042 0.131 1640 Planarity : 0.003 0.026 1920 Dihedral : 3.628 11.990 1490 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.78 % 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: 1.76 (0.23), residues: 1355 helix: 2.34 (0.26), residues: 415 sheet: 1.11 (0.31), residues: 290 loop : 0.54 (0.25), residues: 650 =============================================================================== Job complete usr+sys time: 4167.56 seconds wall clock time: 74 minutes 40.87 seconds (4480.87 seconds total)