Starting phenix.real_space_refine on Sat Feb 17 10:13:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0e_16364/02_2024/8c0e_16364.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0e_16364/02_2024/8c0e_16364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0e_16364/02_2024/8c0e_16364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0e_16364/02_2024/8c0e_16364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0e_16364/02_2024/8c0e_16364.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0e_16364/02_2024/8c0e_16364.pdb" } resolution = 3.6 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= 0.006 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 60 5.16 5 C 11582 2.51 5 N 3210 2.21 5 O 3533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 126": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 126": "OD1" <-> "OD2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 126": "OD1" <-> "OD2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E ASP 225": "OD1" <-> "OD2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "G ASP 157": "OD1" <-> "OD2" Residue "G ASP 225": "OD1" <-> "OD2" Residue "G PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 126": "OD1" <-> "OD2" Residue "H TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 144": "OD1" <-> "OD2" Residue "H ASP 157": "OD1" <-> "OD2" Residue "H ASP 225": "OD1" <-> "OD2" Residue "H PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18385 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "B" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2203 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 10, 'TRANS': 264} Chain breaks: 1 Chain: "C" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2214 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 1 Chain: "E" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "F" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2218 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "G" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "H" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2218 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Time building chain proxies: 9.09, per 1000 atoms: 0.49 Number of scatterers: 18385 At special positions: 0 Unit cell: (119.78, 119.78, 144.16, 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 60 16.00 O 3533 8.00 N 3210 7.00 C 11582 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: 6.64 Conformation dependent library (CDL) restraints added in 3.3 seconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 8 sheets defined 70.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 39 through 54 Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.519A pdb=" N GLY A 337 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.527A pdb=" N LYS B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 278 Processing helix chain 'B' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY B 337 " --> pdb=" O TRP B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY C 337 " --> pdb=" O TRP C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 241 removed outlier: 3.642A pdb=" N LEU D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 283 through 298 removed outlier: 3.730A pdb=" N ASP D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY D 337 " --> pdb=" O TRP D 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 82 " --> pdb=" O GLN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 99 through 113 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 125 through 130 removed outlier: 3.525A pdb=" N LYS E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 241 removed outlier: 3.640A pdb=" N LEU E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 removed outlier: 3.759A pdb=" N LEU E 263 " --> pdb=" O MET E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY E 337 " --> pdb=" O TRP E 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 54 Processing helix chain 'F' and resid 69 through 72 Processing helix chain 'F' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 82 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS F 129 " --> pdb=" O THR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 Processing helix chain 'F' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY F 337 " --> pdb=" O TRP F 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 54 Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 92 Processing helix chain 'G' and resid 99 through 113 Processing helix chain 'G' and resid 114 through 125 Processing helix chain 'G' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU G 179 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP G 287 " --> pdb=" O GLU G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY G 337 " --> pdb=" O TRP G 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 54 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 82 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 92 Processing helix chain 'H' and resid 99 through 113 Processing helix chain 'H' and resid 114 through 125 Processing helix chain 'H' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 150 removed outlier: 3.791A pdb=" N ILE H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 278 Processing helix chain 'H' and resid 283 through 298 removed outlier: 3.730A pdb=" N ASP H 287 " --> pdb=" O GLU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY H 337 " --> pdb=" O TRP H 333 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP A 163 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP A 65 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR A 311 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.842A pdb=" N ASP B 163 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 65 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TYR B 311 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP C 163 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP C 65 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR C 311 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP D 163 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP D 65 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR D 311 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP E 163 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP E 65 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR E 311 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 151 through 153 removed outlier: 3.842A pdb=" N ASP F 163 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP F 65 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR F 311 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP G 163 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP G 65 " --> pdb=" O TYR G 311 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR G 311 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP H 163 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP H 65 " --> pdb=" O TYR H 311 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR H 311 " --> pdb=" O ASP H 65 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3798 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: 5.01 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6170 1.34 - 1.46: 3246 1.46 - 1.57: 9201 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 18737 Sorted by residual: bond pdb=" C ILE A 255 " pdb=" N PRO A 256 " ideal model delta sigma weight residual 1.331 1.354 -0.023 1.21e-02 6.83e+03 3.55e+00 bond pdb=" C ARG H 265 " pdb=" N PRO H 266 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" C ARG D 265 " pdb=" N PRO D 266 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.89e+00 bond pdb=" C ILE E 255 " pdb=" N PRO E 256 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.21e-02 6.83e+03 2.36e+00 bond pdb=" C ARG A 265 " pdb=" N PRO A 266 " ideal model delta sigma weight residual 1.334 1.356 -0.021 1.51e-02 4.39e+03 2.00e+00 ... (remaining 18732 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.96: 449 106.96 - 113.73: 10082 113.73 - 120.50: 7629 120.50 - 127.27: 7051 127.27 - 134.05: 148 Bond angle restraints: 25359 Sorted by residual: angle pdb=" CB ARG G 313 " pdb=" CG ARG G 313 " pdb=" CD ARG G 313 " ideal model delta sigma weight residual 111.30 123.96 -12.66 2.30e+00 1.89e-01 3.03e+01 angle pdb=" CB ARG H 313 " pdb=" CG ARG H 313 " pdb=" CD ARG H 313 " ideal model delta sigma weight residual 111.30 123.94 -12.64 2.30e+00 1.89e-01 3.02e+01 angle pdb=" CB ARG F 313 " pdb=" CG ARG F 313 " pdb=" CD ARG F 313 " ideal model delta sigma weight residual 111.30 123.94 -12.64 2.30e+00 1.89e-01 3.02e+01 angle pdb=" CB ARG C 313 " pdb=" CG ARG C 313 " pdb=" CD ARG C 313 " ideal model delta sigma weight residual 111.30 123.93 -12.63 2.30e+00 1.89e-01 3.01e+01 angle pdb=" CB ARG B 313 " pdb=" CG ARG B 313 " pdb=" CD ARG B 313 " ideal model delta sigma weight residual 111.30 123.92 -12.62 2.30e+00 1.89e-01 3.01e+01 ... (remaining 25354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9468 17.95 - 35.91: 1448 35.91 - 53.86: 412 53.86 - 71.81: 42 71.81 - 89.76: 32 Dihedral angle restraints: 11402 sinusoidal: 4627 harmonic: 6775 Sorted by residual: dihedral pdb=" CA THR A 250 " pdb=" C THR A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta harmonic sigma weight residual 180.00 144.06 35.94 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA ASP E 249 " pdb=" C ASP E 249 " pdb=" N THR E 250 " pdb=" CA THR E 250 " ideal model delta harmonic sigma weight residual 180.00 144.74 35.26 0 5.00e+00 4.00e-02 4.97e+01 dihedral pdb=" CA THR E 250 " pdb=" C THR E 250 " pdb=" N PRO E 251 " pdb=" CA PRO E 251 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.34e+01 ... (remaining 11399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2076 0.041 - 0.081: 572 0.081 - 0.122: 92 0.122 - 0.162: 21 0.162 - 0.203: 10 Chirality restraints: 2771 Sorted by residual: chirality pdb=" CA PRO C 324 " pdb=" N PRO C 324 " pdb=" C PRO C 324 " pdb=" CB PRO C 324 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO B 324 " pdb=" N PRO B 324 " pdb=" C PRO B 324 " pdb=" CB PRO B 324 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA PRO F 324 " pdb=" N PRO F 324 " pdb=" C PRO F 324 " pdb=" CB PRO F 324 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2768 not shown) Planarity restraints: 3323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 241 " 0.051 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C GLN C 241 " -0.180 2.00e-02 2.50e+03 pdb=" O GLN C 241 " 0.070 2.00e-02 2.50e+03 pdb=" N GLY C 242 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 241 " -0.026 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C GLN E 241 " 0.090 2.00e-02 2.50e+03 pdb=" O GLN E 241 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY E 242 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 241 " -0.025 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C GLN A 241 " 0.086 2.00e-02 2.50e+03 pdb=" O GLN A 241 " -0.032 2.00e-02 2.50e+03 pdb=" N GLY A 242 " -0.029 2.00e-02 2.50e+03 ... (remaining 3320 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 549 2.71 - 3.26: 18529 3.26 - 3.81: 31020 3.81 - 4.35: 33628 4.35 - 4.90: 61068 Nonbonded interactions: 144794 Sorted by model distance: nonbonded pdb=" OG1 THR G 171 " pdb=" OD2 ASP G 174 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR E 171 " pdb=" OD2 ASP E 174 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR C 171 " pdb=" OD2 ASP C 174 " model vdw 2.167 2.440 nonbonded pdb=" OG1 THR A 171 " pdb=" OD2 ASP A 174 " model vdw 2.167 2.440 nonbonded pdb=" OG1 THR D 171 " pdb=" OD2 ASP D 174 " model vdw 2.167 2.440 ... (remaining 144789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 241 or resid 266 through 337)) selection = chain 'B' selection = (chain 'C' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'D' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'E' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'F' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'G' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'H' and (resid 39 through 241 or resid 266 through 337)) } 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 group one per residue 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: 1.060 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: 0.020 Extract box with map and model: 4.590 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 45.400 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 : 0.004 0.067 18737 Z= 0.226 Angle : 0.720 12.661 25359 Z= 0.368 Chirality : 0.039 0.203 2771 Planarity : 0.008 0.121 3323 Dihedral : 18.449 89.765 7028 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.12 % Favored : 96.53 % Rotamer: Outliers : 0.77 % Allowed : 28.16 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.05 % 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: 1.91 (0.18), residues: 2277 helix: 2.34 (0.14), residues: 1479 sheet: 0.25 (0.34), residues: 216 loop : -1.24 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.004 0.001 HIS F 193 PHE 0.014 0.001 PHE A 261 TYR 0.035 0.002 TYR H 115 ARG 0.007 0.001 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 255 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.7670 (tt0) cc_final: 0.7402 (tt0) REVERT: A 227 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6928 (mt-10) REVERT: A 267 MET cc_start: 0.6654 (mmm) cc_final: 0.6050 (tpp) REVERT: A 320 LYS cc_start: 0.8098 (pttp) cc_final: 0.7872 (mttt) REVERT: B 66 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8343 (ptmm) REVERT: C 170 GLU cc_start: 0.7719 (tt0) cc_final: 0.7503 (tt0) REVERT: C 267 MET cc_start: 0.6856 (mmm) cc_final: 0.6283 (tpp) REVERT: C 320 LYS cc_start: 0.8208 (pttp) cc_final: 0.7925 (mttt) REVERT: D 66 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8321 (ptmm) REVERT: E 106 ASP cc_start: 0.6900 (t0) cc_final: 0.6544 (m-30) REVERT: E 170 GLU cc_start: 0.7756 (tt0) cc_final: 0.7532 (tt0) REVERT: E 267 MET cc_start: 0.6439 (mmm) cc_final: 0.5822 (tpp) REVERT: E 292 MET cc_start: 0.8249 (mmm) cc_final: 0.8034 (tpp) REVERT: E 320 LYS cc_start: 0.8196 (pttp) cc_final: 0.7954 (mttt) REVERT: F 66 LYS cc_start: 0.8699 (ptpp) cc_final: 0.8320 (ptmm) REVERT: G 267 MET cc_start: 0.6595 (mmm) cc_final: 0.6139 (tpp) REVERT: G 320 LYS cc_start: 0.8150 (pttp) cc_final: 0.7926 (mttt) REVERT: H 66 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8330 (ptmm) outliers start: 15 outliers final: 0 residues processed: 268 average time/residue: 0.3543 time to fit residues: 135.5001 Evaluate side-chains 145 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 175 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 307 GLN B 193 HIS B 307 GLN C 307 GLN D 193 HIS D 216 GLN D 307 GLN E 307 GLN F 193 HIS F 307 GLN G 307 GLN H 193 HIS H 307 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18737 Z= 0.235 Angle : 0.604 8.089 25359 Z= 0.311 Chirality : 0.038 0.207 2771 Planarity : 0.008 0.125 3323 Dihedral : 4.460 34.322 2564 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.85 % Favored : 96.79 % Rotamer: Outliers : 3.66 % Allowed : 23.93 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.18), residues: 2277 helix: 2.50 (0.14), residues: 1479 sheet: -0.02 (0.33), residues: 216 loop : -1.27 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 333 HIS 0.002 0.001 HIS G 193 PHE 0.015 0.001 PHE E 328 TYR 0.013 0.002 TYR A 282 ARG 0.006 0.001 ARG H 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 162 time to evaluate : 1.931 Fit side-chains REVERT: A 227 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6979 (mt-10) REVERT: A 241 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6439 (mp10) REVERT: A 267 MET cc_start: 0.6601 (mmm) cc_final: 0.6013 (tpp) REVERT: A 320 LYS cc_start: 0.8164 (pttp) cc_final: 0.7926 (mttt) REVERT: B 43 PHE cc_start: 0.2830 (OUTLIER) cc_final: 0.2011 (m-10) REVERT: B 66 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8344 (ptmm) REVERT: B 157 ASP cc_start: 0.7231 (m-30) cc_final: 0.6864 (m-30) REVERT: C 267 MET cc_start: 0.6785 (mmm) cc_final: 0.6276 (tpp) REVERT: C 320 LYS cc_start: 0.8226 (pttp) cc_final: 0.7970 (mttt) REVERT: D 43 PHE cc_start: 0.2756 (OUTLIER) cc_final: 0.1936 (m-10) REVERT: D 66 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8339 (ptmm) REVERT: D 157 ASP cc_start: 0.7320 (m-30) cc_final: 0.6990 (m-30) REVERT: E 267 MET cc_start: 0.6458 (mmm) cc_final: 0.6214 (tpp) REVERT: E 320 LYS cc_start: 0.8186 (pttp) cc_final: 0.7971 (mttt) REVERT: F 43 PHE cc_start: 0.2822 (OUTLIER) cc_final: 0.1996 (m-10) REVERT: F 66 LYS cc_start: 0.8743 (ptpp) cc_final: 0.8362 (ptmm) REVERT: F 199 LYS cc_start: 0.7105 (mtpt) cc_final: 0.6889 (mttm) REVERT: G 267 MET cc_start: 0.6616 (mmm) cc_final: 0.6051 (tpp) REVERT: G 320 LYS cc_start: 0.8172 (pttp) cc_final: 0.7957 (mttt) REVERT: H 43 PHE cc_start: 0.2728 (OUTLIER) cc_final: 0.1968 (m-10) REVERT: H 66 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8326 (ptmm) REVERT: H 157 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: H 267 MET cc_start: 0.6112 (ptp) cc_final: 0.5726 (ptt) outliers start: 71 outliers final: 16 residues processed: 224 average time/residue: 0.3179 time to fit residues: 106.5589 Evaluate side-chains 174 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 298 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 240 GLN E 240 GLN E 241 GLN G 276 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 18737 Z= 0.293 Angle : 0.617 7.186 25359 Z= 0.321 Chirality : 0.039 0.215 2771 Planarity : 0.007 0.125 3323 Dihedral : 4.480 31.400 2564 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.50 % Favored : 97.15 % Rotamer: Outliers : 4.90 % Allowed : 22.74 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.05 % 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: 1.86 (0.18), residues: 2277 helix: 2.36 (0.14), residues: 1483 sheet: 0.19 (0.35), residues: 200 loop : -1.40 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 202 HIS 0.005 0.001 HIS H 193 PHE 0.018 0.001 PHE G 328 TYR 0.015 0.002 TYR C 282 ARG 0.007 0.001 ARG H 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 191 time to evaluate : 2.048 Fit side-chains REVERT: A 85 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4682 (mt) REVERT: A 137 LYS cc_start: 0.7880 (tppt) cc_final: 0.7403 (mtmt) REVERT: A 227 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7039 (mt-10) REVERT: A 236 LYS cc_start: 0.8773 (tttm) cc_final: 0.8475 (tttt) REVERT: A 311 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: A 320 LYS cc_start: 0.8260 (pttp) cc_final: 0.7966 (mttt) REVERT: B 43 PHE cc_start: 0.2665 (OUTLIER) cc_final: 0.1980 (m-10) REVERT: B 57 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6830 (mm-30) REVERT: B 85 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5180 (tp) REVERT: B 157 ASP cc_start: 0.7522 (m-30) cc_final: 0.7102 (m-30) REVERT: B 311 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: C 88 ARG cc_start: 0.7442 (mtt180) cc_final: 0.7115 (mtt90) REVERT: C 106 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6798 (m-30) REVERT: C 311 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: C 320 LYS cc_start: 0.8206 (pttp) cc_final: 0.7958 (mttt) REVERT: D 43 PHE cc_start: 0.2595 (OUTLIER) cc_final: 0.1917 (m-10) REVERT: D 57 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6830 (mm-30) REVERT: D 85 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.5252 (tp) REVERT: D 157 ASP cc_start: 0.7562 (m-30) cc_final: 0.7155 (m-30) REVERT: D 311 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: E 88 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7149 (mtt90) REVERT: E 106 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: E 110 MET cc_start: 0.7953 (ttm) cc_final: 0.7655 (ttm) REVERT: E 311 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: E 320 LYS cc_start: 0.8199 (pttp) cc_final: 0.7992 (mttt) REVERT: F 43 PHE cc_start: 0.2775 (OUTLIER) cc_final: 0.2064 (m-10) REVERT: F 57 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6843 (mm-30) REVERT: F 85 LEU cc_start: 0.5613 (OUTLIER) cc_final: 0.5315 (tp) REVERT: F 311 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: G 88 ARG cc_start: 0.7417 (mtt180) cc_final: 0.7078 (mtt90) REVERT: G 311 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: H 43 PHE cc_start: 0.2683 (OUTLIER) cc_final: 0.1999 (m-10) REVERT: H 57 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6767 (mm-30) REVERT: H 85 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.5125 (tp) REVERT: H 157 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: H 311 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7584 (m-80) outliers start: 95 outliers final: 36 residues processed: 273 average time/residue: 0.2987 time to fit residues: 123.4047 Evaluate side-chains 210 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 154 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 1.9990 chunk 153 optimal weight: 0.0770 chunk 105 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 136 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN C 240 GLN E 276 GLN G 240 GLN G 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18737 Z= 0.184 Angle : 0.532 7.288 25359 Z= 0.276 Chirality : 0.036 0.209 2771 Planarity : 0.007 0.125 3323 Dihedral : 4.310 30.960 2564 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.55 % Favored : 97.10 % Rotamer: Outliers : 3.20 % Allowed : 23.93 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.18), residues: 2277 helix: 2.66 (0.14), residues: 1479 sheet: 0.29 (0.36), residues: 200 loop : -1.41 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 202 HIS 0.002 0.001 HIS E 193 PHE 0.013 0.001 PHE B 306 TYR 0.009 0.001 TYR D 127 ARG 0.004 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 155 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6974 (mt-10) REVERT: A 267 MET cc_start: 0.6312 (tpp) cc_final: 0.5990 (tpp) REVERT: A 311 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: A 320 LYS cc_start: 0.8202 (pttp) cc_final: 0.7958 (mttt) REVERT: A 332 MET cc_start: 0.6053 (mmm) cc_final: 0.3699 (ppp) REVERT: B 43 PHE cc_start: 0.2608 (OUTLIER) cc_final: 0.1933 (m-10) REVERT: B 57 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6809 (mm-30) REVERT: B 157 ASP cc_start: 0.7501 (m-30) cc_final: 0.7081 (m-30) REVERT: B 311 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: C 106 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: C 267 MET cc_start: 0.6555 (tpp) cc_final: 0.6222 (tpp) REVERT: C 311 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: C 332 MET cc_start: 0.5846 (mmm) cc_final: 0.3854 (tmm) REVERT: D 57 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6795 (mm-30) REVERT: D 311 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: E 110 MET cc_start: 0.7864 (ttm) cc_final: 0.7581 (ttm) REVERT: E 267 MET cc_start: 0.6315 (tpp) cc_final: 0.5979 (tpp) REVERT: E 311 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: E 332 MET cc_start: 0.6102 (mmm) cc_final: 0.3773 (tmm) REVERT: F 43 PHE cc_start: 0.2655 (OUTLIER) cc_final: 0.1927 (m-10) REVERT: F 57 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6813 (mm-30) REVERT: F 199 LYS cc_start: 0.7727 (mttm) cc_final: 0.7505 (mptt) REVERT: F 267 MET cc_start: 0.5622 (ptp) cc_final: 0.5276 (ptp) REVERT: F 311 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: G 88 ARG cc_start: 0.7393 (mtt180) cc_final: 0.7132 (mtt90) REVERT: G 267 MET cc_start: 0.6480 (tpp) cc_final: 0.6093 (tpp) REVERT: G 311 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: G 332 MET cc_start: 0.5912 (mmm) cc_final: 0.3956 (tmm) REVERT: H 57 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6753 (mm-30) REVERT: H 157 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: H 267 MET cc_start: 0.5730 (ptp) cc_final: 0.5291 (ptt) REVERT: H 311 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: H 330 MET cc_start: 0.6077 (mmm) cc_final: 0.5851 (mmt) outliers start: 62 outliers final: 26 residues processed: 207 average time/residue: 0.3199 time to fit residues: 98.9725 Evaluate side-chains 180 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 84 ASN C 276 GLN D 84 ASN E 240 GLN E 241 GLN E 276 GLN F 84 ASN G 276 GLN H 84 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18737 Z= 0.318 Angle : 0.619 7.094 25359 Z= 0.320 Chirality : 0.039 0.212 2771 Planarity : 0.007 0.125 3323 Dihedral : 4.460 29.657 2564 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.85 % Favored : 96.79 % Rotamer: Outliers : 5.26 % Allowed : 22.18 % Favored : 72.56 % 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: 1.86 (0.18), residues: 2277 helix: 2.38 (0.14), residues: 1479 sheet: -0.07 (0.35), residues: 208 loop : -1.33 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 202 HIS 0.004 0.001 HIS B 193 PHE 0.014 0.002 PHE H 208 TYR 0.015 0.002 TYR F 286 ARG 0.007 0.001 ARG G 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 186 time to evaluate : 2.031 Fit side-chains REVERT: A 48 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6061 (tt) REVERT: A 88 ARG cc_start: 0.7525 (mtt90) cc_final: 0.7120 (ptp-170) REVERT: A 227 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6975 (mt-10) REVERT: A 236 LYS cc_start: 0.8728 (tttm) cc_final: 0.8472 (tttt) REVERT: A 267 MET cc_start: 0.6498 (tpp) cc_final: 0.6018 (tpp) REVERT: A 311 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8505 (m-80) REVERT: A 320 LYS cc_start: 0.8218 (pttp) cc_final: 0.7988 (mttt) REVERT: A 332 MET cc_start: 0.6179 (mmm) cc_final: 0.3792 (tmm) REVERT: B 43 PHE cc_start: 0.2688 (OUTLIER) cc_final: 0.2001 (m-10) REVERT: B 57 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6881 (mm-30) REVERT: B 71 MET cc_start: 0.9072 (ptp) cc_final: 0.8796 (ptp) REVERT: B 311 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: C 106 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: C 214 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7605 (mttt) REVERT: C 236 LYS cc_start: 0.8634 (tttm) cc_final: 0.8404 (tttt) REVERT: C 241 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: C 267 MET cc_start: 0.6382 (tpp) cc_final: 0.5946 (tpp) REVERT: C 311 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: C 332 MET cc_start: 0.6111 (mmm) cc_final: 0.3729 (tmm) REVERT: D 43 PHE cc_start: 0.2613 (OUTLIER) cc_final: 0.1903 (m-10) REVERT: D 57 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6882 (mm-30) REVERT: D 267 MET cc_start: 0.5699 (ptp) cc_final: 0.5305 (ptt) REVERT: D 311 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: E 48 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5867 (tt) REVERT: E 88 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7184 (mtt90) REVERT: E 110 MET cc_start: 0.7906 (ttm) cc_final: 0.7666 (ttm) REVERT: E 214 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7610 (mttt) REVERT: E 267 MET cc_start: 0.6632 (tpp) cc_final: 0.6009 (tpp) REVERT: E 271 ARG cc_start: 0.6888 (tpp80) cc_final: 0.6663 (ttt180) REVERT: E 311 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: E 332 MET cc_start: 0.6129 (mmm) cc_final: 0.3824 (tmm) REVERT: F 43 PHE cc_start: 0.2666 (OUTLIER) cc_final: 0.1970 (m-10) REVERT: F 57 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6867 (mm-30) REVERT: F 267 MET cc_start: 0.5587 (ptp) cc_final: 0.4972 (ptp) REVERT: F 311 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: G 48 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5716 (tt) REVERT: G 88 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7169 (mtt90) REVERT: G 214 LYS cc_start: 0.7811 (mmmm) cc_final: 0.7602 (mttt) REVERT: G 267 MET cc_start: 0.6477 (tpp) cc_final: 0.5986 (tpp) REVERT: G 311 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: G 332 MET cc_start: 0.6138 (mmm) cc_final: 0.3772 (tmm) REVERT: H 43 PHE cc_start: 0.2419 (OUTLIER) cc_final: 0.1684 (m-10) REVERT: H 57 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6866 (mm-30) REVERT: H 71 MET cc_start: 0.9075 (ptp) cc_final: 0.8799 (ptp) REVERT: H 157 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: H 311 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8033 (m-80) outliers start: 102 outliers final: 57 residues processed: 272 average time/residue: 0.3548 time to fit residues: 138.8823 Evaluate side-chains 231 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 156 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 3.9990 chunk 194 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 148 ASN D 148 ASN F 148 ASN G 240 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18737 Z= 0.192 Angle : 0.525 6.441 25359 Z= 0.275 Chirality : 0.035 0.209 2771 Planarity : 0.007 0.124 3323 Dihedral : 4.292 29.386 2564 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.59 % Favored : 97.06 % Rotamer: Outliers : 3.71 % Allowed : 23.72 % Favored : 72.56 % 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: 2.11 (0.18), residues: 2277 helix: 2.57 (0.14), residues: 1500 sheet: -0.19 (0.36), residues: 216 loop : -1.31 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 202 HIS 0.002 0.001 HIS A 193 PHE 0.012 0.001 PHE H 306 TYR 0.009 0.001 TYR F 286 ARG 0.005 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 155 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: A 137 LYS cc_start: 0.7353 (tptt) cc_final: 0.6535 (mtmt) REVERT: A 227 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6904 (mt-10) REVERT: A 267 MET cc_start: 0.6389 (tpp) cc_final: 0.5970 (tpp) REVERT: A 311 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: A 332 MET cc_start: 0.6169 (mmm) cc_final: 0.3814 (tmm) REVERT: B 43 PHE cc_start: 0.2564 (OUTLIER) cc_final: 0.1907 (m-10) REVERT: B 57 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6903 (mm-30) REVERT: B 71 MET cc_start: 0.9015 (ptp) cc_final: 0.8772 (ptp) REVERT: B 227 GLU cc_start: 0.7919 (tp30) cc_final: 0.7715 (tp30) REVERT: B 311 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: C 106 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6834 (m-30) REVERT: C 137 LYS cc_start: 0.7202 (tptt) cc_final: 0.6429 (mtmt) REVERT: C 241 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: C 267 MET cc_start: 0.6416 (tpp) cc_final: 0.6070 (tpp) REVERT: C 311 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: C 332 MET cc_start: 0.6182 (mmm) cc_final: 0.3880 (tmm) REVERT: D 43 PHE cc_start: 0.2601 (OUTLIER) cc_final: 0.1906 (m-10) REVERT: D 57 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6854 (mm-30) REVERT: D 267 MET cc_start: 0.5665 (ptp) cc_final: 0.5215 (ptt) REVERT: D 311 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: E 48 LEU cc_start: 0.6220 (tt) cc_final: 0.6011 (tt) REVERT: E 137 LYS cc_start: 0.7339 (tptt) cc_final: 0.6539 (mtmt) REVERT: E 240 GLN cc_start: 0.6894 (tt0) cc_final: 0.6654 (tt0) REVERT: E 267 MET cc_start: 0.6467 (tpp) cc_final: 0.5887 (tpp) REVERT: E 271 ARG cc_start: 0.6914 (tpp80) cc_final: 0.6685 (ttt180) REVERT: E 311 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: E 332 MET cc_start: 0.6249 (mmm) cc_final: 0.4030 (tmm) REVERT: F 43 PHE cc_start: 0.2661 (OUTLIER) cc_final: 0.1990 (m-10) REVERT: F 57 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6802 (mm-30) REVERT: F 199 LYS cc_start: 0.7889 (mttp) cc_final: 0.7684 (mptt) REVERT: F 267 MET cc_start: 0.5499 (ptp) cc_final: 0.4871 (ptp) REVERT: F 311 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: G 137 LYS cc_start: 0.7229 (tptt) cc_final: 0.6439 (mtmt) REVERT: G 267 MET cc_start: 0.6351 (tpp) cc_final: 0.5960 (tpp) REVERT: G 311 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: G 332 MET cc_start: 0.6142 (mmm) cc_final: 0.3857 (tmm) REVERT: H 43 PHE cc_start: 0.2428 (OUTLIER) cc_final: 0.1732 (m-10) REVERT: H 57 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6831 (mm-30) REVERT: H 71 MET cc_start: 0.9024 (ptp) cc_final: 0.8810 (ptp) REVERT: H 157 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: H 311 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7834 (m-80) outliers start: 72 outliers final: 46 residues processed: 221 average time/residue: 0.3313 time to fit residues: 107.7043 Evaluate side-chains 209 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 148 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN D 148 ASN F 148 ASN G 240 GLN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18737 Z= 0.234 Angle : 0.534 6.531 25359 Z= 0.278 Chirality : 0.036 0.208 2771 Planarity : 0.007 0.123 3323 Dihedral : 4.223 29.288 2564 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.99 % Favored : 96.66 % Rotamer: Outliers : 4.69 % Allowed : 22.49 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.18), residues: 2277 helix: 2.59 (0.14), residues: 1500 sheet: 0.09 (0.37), residues: 200 loop : -1.37 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 202 HIS 0.002 0.001 HIS F 193 PHE 0.013 0.001 PHE B 81 TYR 0.010 0.001 TYR B 286 ARG 0.008 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 156 time to evaluate : 2.101 Fit side-chains REVERT: A 48 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5782 (tt) REVERT: A 52 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6522 (t80) REVERT: A 137 LYS cc_start: 0.7356 (tptt) cc_final: 0.6524 (mtmt) REVERT: A 227 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6912 (mt-10) REVERT: A 267 MET cc_start: 0.6411 (tpp) cc_final: 0.6048 (tpp) REVERT: A 311 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: A 332 MET cc_start: 0.6213 (mmm) cc_final: 0.3855 (tmm) REVERT: B 43 PHE cc_start: 0.2423 (OUTLIER) cc_final: 0.1747 (m-10) REVERT: B 57 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6922 (mm-30) REVERT: B 71 MET cc_start: 0.9012 (ptp) cc_final: 0.8792 (ptp) REVERT: B 311 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: B 320 LYS cc_start: 0.7377 (tttm) cc_final: 0.6954 (mmmt) REVERT: C 52 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6534 (t80) REVERT: C 106 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: C 241 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6590 (mp10) REVERT: C 311 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: C 332 MET cc_start: 0.6243 (mmm) cc_final: 0.3935 (tmm) REVERT: D 43 PHE cc_start: 0.2427 (OUTLIER) cc_final: 0.1718 (m-10) REVERT: D 57 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6821 (mm-30) REVERT: D 267 MET cc_start: 0.5523 (ptp) cc_final: 0.5115 (ptt) REVERT: D 311 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: E 48 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5842 (tt) REVERT: E 52 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6698 (t80) REVERT: E 137 LYS cc_start: 0.7313 (tptt) cc_final: 0.6485 (mtmt) REVERT: E 267 MET cc_start: 0.6333 (tpp) cc_final: 0.5931 (tpp) REVERT: E 311 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: E 332 MET cc_start: 0.6184 (mmm) cc_final: 0.3954 (tmm) REVERT: F 43 PHE cc_start: 0.2551 (OUTLIER) cc_final: 0.1883 (m-10) REVERT: F 57 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6820 (mm-30) REVERT: F 199 LYS cc_start: 0.7899 (mttp) cc_final: 0.7545 (mptt) REVERT: F 267 MET cc_start: 0.5498 (ptp) cc_final: 0.4863 (ptp) REVERT: F 311 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: F 320 LYS cc_start: 0.7270 (tttm) cc_final: 0.6893 (mmmt) REVERT: G 48 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5727 (tt) REVERT: G 52 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6576 (t80) REVERT: G 137 LYS cc_start: 0.7348 (tptt) cc_final: 0.6516 (mtmt) REVERT: G 267 MET cc_start: 0.6432 (tpp) cc_final: 0.6063 (tpp) REVERT: G 311 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: G 332 MET cc_start: 0.6204 (mmm) cc_final: 0.3912 (tmm) REVERT: H 43 PHE cc_start: 0.2415 (OUTLIER) cc_final: 0.1713 (m-10) REVERT: H 57 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6842 (mm-30) REVERT: H 71 MET cc_start: 0.9008 (ptp) cc_final: 0.8800 (ptp) REVERT: H 88 ARG cc_start: 0.6815 (mtm-85) cc_final: 0.6614 (mtm110) REVERT: H 157 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: H 311 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7812 (m-80) outliers start: 91 outliers final: 63 residues processed: 238 average time/residue: 0.3276 time to fit residues: 114.7939 Evaluate side-chains 235 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 150 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 84 ASN B 148 ASN D 148 ASN F 148 ASN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18737 Z= 0.184 Angle : 0.513 6.723 25359 Z= 0.268 Chirality : 0.035 0.210 2771 Planarity : 0.007 0.122 3323 Dihedral : 4.148 28.648 2564 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.64 % Favored : 97.01 % Rotamer: Outliers : 4.02 % Allowed : 22.74 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.18), residues: 2277 helix: 2.76 (0.14), residues: 1500 sheet: -0.18 (0.36), residues: 216 loop : -1.33 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 202 HIS 0.002 0.001 HIS C 193 PHE 0.011 0.001 PHE H 306 TYR 0.009 0.001 TYR H 127 ARG 0.005 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 154 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5801 (tt) REVERT: A 52 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6524 (t80) REVERT: A 137 LYS cc_start: 0.7294 (tptt) cc_final: 0.6497 (mtmt) REVERT: A 227 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7111 (mt-10) REVERT: A 267 MET cc_start: 0.6296 (tpp) cc_final: 0.6039 (tpp) REVERT: A 311 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: A 332 MET cc_start: 0.6193 (mmm) cc_final: 0.3871 (tmm) REVERT: B 57 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6863 (mm-30) REVERT: B 71 MET cc_start: 0.9009 (ptp) cc_final: 0.8799 (ptp) REVERT: B 311 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: B 320 LYS cc_start: 0.7358 (tttm) cc_final: 0.6933 (mmmt) REVERT: C 52 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6398 (t80) REVERT: C 137 LYS cc_start: 0.7346 (tptt) cc_final: 0.6558 (mtmt) REVERT: C 241 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6423 (mp10) REVERT: C 311 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: C 332 MET cc_start: 0.6225 (mmm) cc_final: 0.3951 (tmm) REVERT: D 43 PHE cc_start: 0.2396 (OUTLIER) cc_final: 0.1685 (m-10) REVERT: D 57 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6809 (mm-30) REVERT: D 267 MET cc_start: 0.5448 (ptp) cc_final: 0.4977 (ptt) REVERT: D 311 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: E 52 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6454 (t80) REVERT: E 137 LYS cc_start: 0.7275 (tptt) cc_final: 0.6498 (mtmt) REVERT: E 267 MET cc_start: 0.6417 (tpp) cc_final: 0.6031 (tpp) REVERT: E 311 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: E 332 MET cc_start: 0.6166 (mmm) cc_final: 0.3962 (tmm) REVERT: F 57 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6829 (mm-30) REVERT: F 233 LEU cc_start: 0.8387 (mt) cc_final: 0.8142 (mt) REVERT: F 267 MET cc_start: 0.5365 (ptp) cc_final: 0.4736 (ptp) REVERT: F 311 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: G 48 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5665 (tt) REVERT: G 52 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6352 (t80) REVERT: G 311 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: G 332 MET cc_start: 0.6174 (mmm) cc_final: 0.3926 (tmm) REVERT: H 43 PHE cc_start: 0.2226 (OUTLIER) cc_final: 0.1491 (m-10) REVERT: H 57 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6776 (mm-30) REVERT: H 157 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: H 311 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7562 (m-80) outliers start: 78 outliers final: 56 residues processed: 225 average time/residue: 0.3541 time to fit residues: 116.4447 Evaluate side-chains 225 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 151 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 188 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 181 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN B 148 ASN D 148 ASN D 289 ASN E 240 GLN F 148 ASN G 241 GLN H 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 18737 Z= 0.208 Angle : 0.521 6.845 25359 Z= 0.271 Chirality : 0.036 0.207 2771 Planarity : 0.007 0.121 3323 Dihedral : 4.130 28.539 2564 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.85 % Favored : 96.79 % Rotamer: Outliers : 4.38 % Allowed : 22.33 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.18), residues: 2277 helix: 2.75 (0.14), residues: 1500 sheet: 0.09 (0.37), residues: 200 loop : -1.43 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 202 HIS 0.002 0.001 HIS F 193 PHE 0.009 0.001 PHE F 306 TYR 0.009 0.001 TYR D 286 ARG 0.004 0.000 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 154 time to evaluate : 2.168 Fit side-chains REVERT: A 48 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5909 (tt) REVERT: A 52 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6512 (t80) REVERT: A 227 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7109 (mt-10) REVERT: A 311 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: A 332 MET cc_start: 0.6058 (mmm) cc_final: 0.3873 (tmm) REVERT: B 57 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6880 (mm-30) REVERT: B 71 MET cc_start: 0.9010 (ptp) cc_final: 0.8801 (ptp) REVERT: B 311 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: B 320 LYS cc_start: 0.7370 (tttm) cc_final: 0.6936 (mmmt) REVERT: C 52 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.6436 (t80) REVERT: C 137 LYS cc_start: 0.7340 (tptt) cc_final: 0.6561 (mtmt) REVERT: C 241 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: C 311 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: C 332 MET cc_start: 0.6199 (mmm) cc_final: 0.4047 (tmm) REVERT: D 43 PHE cc_start: 0.2371 (OUTLIER) cc_final: 0.1702 (m-10) REVERT: D 57 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6839 (mm-30) REVERT: D 267 MET cc_start: 0.5272 (ptp) cc_final: 0.4826 (ptt) REVERT: D 311 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: E 48 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5898 (tt) REVERT: E 52 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6453 (t80) REVERT: E 267 MET cc_start: 0.6485 (tpp) cc_final: 0.6103 (tpp) REVERT: E 311 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: E 332 MET cc_start: 0.6161 (mmm) cc_final: 0.4093 (tmm) REVERT: F 57 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6843 (mm-30) REVERT: F 233 LEU cc_start: 0.8485 (mt) cc_final: 0.8228 (mt) REVERT: F 267 MET cc_start: 0.5080 (ptp) cc_final: 0.4657 (ptt) REVERT: F 311 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: G 48 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5798 (tt) REVERT: G 52 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6429 (t80) REVERT: G 137 LYS cc_start: 0.7290 (tptt) cc_final: 0.6539 (mtmt) REVERT: G 311 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: G 332 MET cc_start: 0.6147 (mmm) cc_final: 0.4027 (tmm) REVERT: H 43 PHE cc_start: 0.2248 (OUTLIER) cc_final: 0.1560 (m-10) REVERT: H 57 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6778 (mm-30) REVERT: H 157 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: H 311 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7521 (m-80) outliers start: 85 outliers final: 62 residues processed: 230 average time/residue: 0.3432 time to fit residues: 115.1361 Evaluate side-chains 233 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 152 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN C 276 GLN D 148 ASN E 240 GLN F 148 ASN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 18737 Z= 0.198 Angle : 0.517 7.210 25359 Z= 0.268 Chirality : 0.036 0.208 2771 Planarity : 0.007 0.121 3323 Dihedral : 4.104 28.452 2564 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % Rotamer: Outliers : 4.23 % Allowed : 22.43 % Favored : 73.34 % 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: 2.35 (0.18), residues: 2277 helix: 2.80 (0.14), residues: 1500 sheet: 0.10 (0.37), residues: 200 loop : -1.42 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 202 HIS 0.001 0.001 HIS D 193 PHE 0.011 0.001 PHE F 306 TYR 0.010 0.001 TYR H 127 ARG 0.012 0.000 ARG D 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 147 time to evaluate : 2.109 Fit side-chains REVERT: A 48 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5981 (tt) REVERT: A 52 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6558 (t80) REVERT: A 137 LYS cc_start: 0.7357 (tptt) cc_final: 0.6549 (mtmt) REVERT: A 227 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7098 (mt-10) REVERT: A 311 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: A 332 MET cc_start: 0.6026 (mmm) cc_final: 0.3982 (tmm) REVERT: B 57 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6878 (mm-30) REVERT: B 71 MET cc_start: 0.9008 (ptp) cc_final: 0.8806 (ptp) REVERT: B 267 MET cc_start: 0.5342 (ptp) cc_final: 0.4904 (ppp) REVERT: B 311 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: B 320 LYS cc_start: 0.7375 (tttm) cc_final: 0.6941 (mmmt) REVERT: C 52 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6475 (t80) REVERT: C 137 LYS cc_start: 0.7334 (tptt) cc_final: 0.6568 (mtmt) REVERT: C 241 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6322 (mp10) REVERT: C 311 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: C 332 MET cc_start: 0.6193 (mmm) cc_final: 0.4065 (tmm) REVERT: D 43 PHE cc_start: 0.2209 (OUTLIER) cc_final: 0.1520 (m-10) REVERT: D 57 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6836 (mm-30) REVERT: D 267 MET cc_start: 0.5249 (ptp) cc_final: 0.4883 (ptt) REVERT: D 311 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: E 48 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5919 (tt) REVERT: E 52 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6450 (t80) REVERT: E 137 LYS cc_start: 0.7309 (tptt) cc_final: 0.6518 (mtmt) REVERT: E 276 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7112 (mt0) REVERT: E 311 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: E 332 MET cc_start: 0.6156 (mmm) cc_final: 0.4111 (tmm) REVERT: F 57 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6814 (mm-30) REVERT: F 233 LEU cc_start: 0.8483 (mt) cc_final: 0.8208 (mt) REVERT: F 267 MET cc_start: 0.5045 (ptp) cc_final: 0.4628 (ptt) REVERT: F 311 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: G 48 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5969 (tt) REVERT: G 52 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6452 (t80) REVERT: G 137 LYS cc_start: 0.7376 (tptt) cc_final: 0.6577 (mtmt) REVERT: G 311 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: G 332 MET cc_start: 0.6153 (mmm) cc_final: 0.4050 (tmm) REVERT: H 43 PHE cc_start: 0.2080 (OUTLIER) cc_final: 0.1385 (m-10) REVERT: H 57 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6772 (mm-30) REVERT: H 157 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: H 311 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7515 (m-80) outliers start: 82 outliers final: 61 residues processed: 221 average time/residue: 0.3525 time to fit residues: 113.6711 Evaluate side-chains 226 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 145 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 40.0000 chunk 189 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 177 optimal weight: 0.0040 chunk 74 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.4472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN C 240 GLN C 241 GLN D 148 ASN E 78 GLN E 240 GLN F 148 ASN F 289 ASN G 212 GLN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.200848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.171904 restraints weight = 18670.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.156411 restraints weight = 33346.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.158318 restraints weight = 20388.756| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 18737 Z= 0.169 Angle : 0.504 7.340 25359 Z= 0.262 Chirality : 0.035 0.209 2771 Planarity : 0.007 0.120 3323 Dihedral : 4.031 28.328 2564 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.64 % Favored : 97.01 % Rotamer: Outliers : 3.76 % Allowed : 23.05 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.18), residues: 2277 helix: 2.86 (0.14), residues: 1507 sheet: -0.21 (0.37), residues: 216 loop : -1.46 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 202 HIS 0.002 0.001 HIS C 193 PHE 0.012 0.001 PHE F 306 TYR 0.009 0.001 TYR H 127 ARG 0.006 0.000 ARG D 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.25 seconds wall clock time: 61 minutes 40.02 seconds (3700.02 seconds total)