Starting phenix.real_space_refine on Thu Feb 15 00:43:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/02_2024/7oe2_12859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/02_2024/7oe2_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_12859/02_2024/7oe2_12859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/02_2024/7oe2_12859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/02_2024/7oe2_12859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe2_12859/02_2024/7oe2_12859.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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. 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-5238/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: 5.79, per 1000 atoms: 0.55 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: 3.94 Conformation dependent library (CDL) restraints added in 1.8 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: 1.56 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: 3.43 Time building geometry restraints manager: 4.24 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 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: 14.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 38.810 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.740 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.44 % Allowed : 15.87 % Favored : 81.69 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 45 HIS 0.006 0.002 HIS C 121 PHE 0.018 0.004 PHE D 181 TYR 0.008 0.002 TYR B 168 ARG 0.008 0.001 ARG E 264 *********************** 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 : 1.260 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 152 average time/residue: 1.6766 time to fit residues: 269.6898 Evaluate side-chains 107 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 92 VAL 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: 0.7980 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.1721 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= 0.140 Angle : 0.460 5.163 14490 Z= 0.245 Chirality : 0.042 0.129 1640 Planarity : 0.004 0.029 1920 Dihedral : 4.519 29.450 1501 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.88 % Allowed : 16.43 % Favored : 81.69 % 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: 1.52 (0.26), residues: 445 sheet: 1.59 (0.31), residues: 315 loop : 0.11 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 45 HIS 0.001 0.000 HIS B 121 PHE 0.008 0.001 PHE B 82 TYR 0.007 0.001 TYR E 265 ARG 0.006 0.001 ARG E 264 *********************** 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 132 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.261 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 132 average time/residue: 1.8271 time to fit residues: 254.5819 Evaluate side-chains 111 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 265 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 40 optimal weight: 0.2980 chunk 94 optimal weight: 20.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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: 0.7656 moved from start: 0.2050 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= 0.184 Angle : 0.454 5.250 14490 Z= 0.238 Chirality : 0.042 0.132 1640 Planarity : 0.004 0.028 1920 Dihedral : 4.235 26.819 1495 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.97 % Allowed : 17.28 % Favored : 80.75 % 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: 1.54 (0.24), residues: 1355 helix: 2.14 (0.26), residues: 415 sheet: 1.39 (0.32), residues: 295 loop : 0.16 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 45 HIS 0.001 0.000 HIS A 121 PHE 0.008 0.001 PHE C 181 TYR 0.005 0.001 TYR C 177 ARG 0.004 0.000 ARG D 264 *********************** 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 127 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 124 average time/residue: 1.7522 time to fit residues: 229.7042 Evaluate side-chains 111 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 92 VAL 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: 2.9990 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7684 moved from start: 0.2210 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= 0.239 Angle : 0.467 5.596 14490 Z= 0.243 Chirality : 0.043 0.132 1640 Planarity : 0.004 0.029 1920 Dihedral : 4.330 28.517 1495 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.16 % Allowed : 17.75 % Favored : 80.09 % 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: 1.54 (0.24), residues: 1355 helix: 2.11 (0.26), residues: 415 sheet: 1.29 (0.32), residues: 295 loop : 0.24 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 45 HIS 0.002 0.000 HIS C 121 PHE 0.009 0.001 PHE C 181 TYR 0.010 0.001 TYR E 265 ARG 0.003 0.000 ARG D 264 *********************** 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 128 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 124 average time/residue: 1.7270 time to fit residues: 227.5454 Evaluate side-chains 115 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 92 VAL 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: 2.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.2324 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= 0.205 Angle : 0.450 5.279 14490 Z= 0.233 Chirality : 0.042 0.132 1640 Planarity : 0.003 0.028 1920 Dihedral : 4.160 26.598 1495 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.97 % Allowed : 17.46 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1355 helix: 2.17 (0.26), residues: 415 sheet: 1.12 (0.32), residues: 260 loop : 0.32 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 45 HIS 0.001 0.000 HIS C 121 PHE 0.008 0.001 PHE E 82 TYR 0.023 0.001 TYR E 265 ARG 0.003 0.000 ARG E 264 *********************** 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 127 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 124 average time/residue: 1.6753 time to fit residues: 220.1475 Evaluate side-chains 115 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 31 optimal weight: 0.0060 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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: 0.7625 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10650 Z= 0.124 Angle : 0.421 5.191 14490 Z= 0.217 Chirality : 0.041 0.130 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.778 22.259 1495 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.13 % Allowed : 18.59 % Favored : 80.28 % 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: 1.60 (0.23), residues: 1355 helix: 2.33 (0.26), residues: 415 sheet: 1.06 (0.32), residues: 260 loop : 0.34 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 45 HIS 0.001 0.000 HIS A 237 PHE 0.007 0.001 PHE E 82 TYR 0.006 0.001 TYR D 177 ARG 0.003 0.000 ARG B 264 *********************** 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 128 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.312 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 125 average time/residue: 1.6337 time to fit residues: 216.8216 Evaluate side-chains 117 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2601 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= 0.154 Angle : 0.431 4.919 14490 Z= 0.221 Chirality : 0.041 0.131 1640 Planarity : 0.003 0.026 1920 Dihedral : 3.821 23.245 1495 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.03 % Allowed : 19.44 % Favored : 79.53 % 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: 1.65 (0.23), residues: 1355 helix: 2.36 (0.26), residues: 415 sheet: 1.11 (0.32), residues: 260 loop : 0.37 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 45 HIS 0.001 0.000 HIS A 237 PHE 0.008 0.001 PHE C 82 TYR 0.012 0.001 TYR D 265 ARG 0.003 0.000 ARG D 264 *********************** 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 121 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.191 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 121 average time/residue: 1.6956 time to fit residues: 217.3889 Evaluate side-chains 117 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 98 optimal weight: 0.0870 chunk 113 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- 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: 0.7691 moved from start: 0.2459 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= 0.276 Angle : 0.499 7.386 14490 Z= 0.253 Chirality : 0.043 0.133 1640 Planarity : 0.003 0.027 1920 Dihedral : 4.236 27.813 1495 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.22 % Allowed : 19.53 % Favored : 79.25 % 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: 1.58 (0.23), residues: 1355 helix: 2.21 (0.26), residues: 415 sheet: 1.11 (0.32), residues: 260 loop : 0.38 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 45 HIS 0.002 0.001 HIS C 121 PHE 0.011 0.001 PHE C 181 TYR 0.007 0.001 TYR A 222 ARG 0.002 0.000 ARG D 56 *********************** 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 119 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 118 average time/residue: 1.6544 time to fit residues: 206.7570 Evaluate side-chains 116 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.2502 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= 0.220 Angle : 0.468 5.929 14490 Z= 0.238 Chirality : 0.042 0.132 1640 Planarity : 0.003 0.028 1920 Dihedral : 4.132 26.640 1495 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.75 % Allowed : 19.81 % Favored : 79.44 % 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: 1.60 (0.23), residues: 1355 helix: 2.24 (0.26), residues: 415 sheet: 1.06 (0.32), residues: 260 loop : 0.41 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 45 HIS 0.001 0.000 HIS C 121 PHE 0.009 0.001 PHE B 82 TYR 0.006 0.001 TYR A 222 ARG 0.003 0.000 ARG D 56 *********************** 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 115 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.239 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 115 average time/residue: 1.7334 time to fit residues: 210.8619 Evaluate side-chains 115 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 129 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.7624 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10650 Z= 0.124 Angle : 0.431 5.923 14490 Z= 0.220 Chirality : 0.041 0.129 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.701 21.823 1495 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.85 % Allowed : 19.81 % Favored : 79.34 % 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: 1.66 (0.24), residues: 1355 helix: 2.42 (0.26), residues: 415 sheet: 0.84 (0.32), residues: 270 loop : 0.47 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 45 HIS 0.001 0.000 HIS A 237 PHE 0.007 0.001 PHE B 82 TYR 0.007 0.001 TYR A 177 ARG 0.003 0.000 ARG D 56 ********************** 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 126 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 126 average time/residue: 1.7104 time to fit residues: 227.7458 Evaluate side-chains 122 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.2964 r_free = 0.2964 target = 0.057837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.046924 restraints weight = 27130.216| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.93 r_work: 0.2538 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10650 Z= 0.225 Angle : 0.470 5.870 14490 Z= 0.239 Chirality : 0.042 0.134 1640 Planarity : 0.003 0.027 1920 Dihedral : 4.036 25.869 1495 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.85 % Allowed : 20.09 % Favored : 79.06 % 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: 1.68 (0.23), residues: 1355 helix: 2.31 (0.26), residues: 415 sheet: 1.10 (0.32), residues: 260 loop : 0.46 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 45 HIS 0.001 0.001 HIS D 237 PHE 0.010 0.001 PHE B 181 TYR 0.006 0.001 TYR A 222 ARG 0.003 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.72 seconds wall clock time: 81 minutes 58.33 seconds (4918.33 seconds total)