Starting phenix.real_space_refine on Fri Mar 6 15:22:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lu4_63387/03_2026/9lu4_63387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lu4_63387/03_2026/9lu4_63387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lu4_63387/03_2026/9lu4_63387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lu4_63387/03_2026/9lu4_63387.map" model { file = "/net/cci-nas-00/data/ceres_data/9lu4_63387/03_2026/9lu4_63387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lu4_63387/03_2026/9lu4_63387.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 20100 2.51 5 N 5184 2.21 5 O 5748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 249 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31182 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1219 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1219 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1219 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1219 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1219 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1219 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 6.83, per 1000 atoms: 0.22 Number of scatterers: 31182 At special positions: 0 Unit cell: (181.944, 181.944, 105.336, 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 150 16.00 O 5748 8.00 N 5184 7.00 C 20100 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 - 3.00 Amino acid : True - 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: 2.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 30 sheets defined 36.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.776A pdb=" N ILE D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 116 removed outlier: 3.832A pdb=" N ALA D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 149 Processing helix chain 'D' and resid 244 through 266 removed outlier: 3.721A pdb=" N HIS D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 301 Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 30 through 49 removed outlier: 3.798A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.785A pdb=" N ALA B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 149 Processing helix chain 'B' and resid 244 through 266 removed outlier: 3.718A pdb=" N HIS B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'L' and resid 8 through 21 Processing helix chain 'L' and resid 30 through 49 removed outlier: 3.706A pdb=" N ILE L 34 " --> pdb=" O THR L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 116 removed outlier: 3.781A pdb=" N ALA L 115 " --> pdb=" O LEU L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 149 Processing helix chain 'L' and resid 244 through 266 removed outlier: 3.752A pdb=" N HIS L 266 " --> pdb=" O ILE L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 301 Processing helix chain 'J' and resid 8 through 21 Processing helix chain 'J' and resid 30 through 49 removed outlier: 3.792A pdb=" N ILE J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 116 removed outlier: 3.787A pdb=" N ALA J 115 " --> pdb=" O LEU J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 149 Processing helix chain 'J' and resid 244 through 266 removed outlier: 3.728A pdb=" N HIS J 266 " --> pdb=" O ILE J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 301 Processing helix chain 'F' and resid 8 through 21 Processing helix chain 'F' and resid 30 through 49 removed outlier: 3.831A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 116 removed outlier: 3.787A pdb=" N ALA F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 149 Processing helix chain 'F' and resid 244 through 266 removed outlier: 3.713A pdb=" N HIS F 266 " --> pdb=" O ILE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 301 Processing helix chain 'H' and resid 8 through 21 Processing helix chain 'H' and resid 30 through 49 removed outlier: 3.737A pdb=" N ILE H 34 " --> pdb=" O THR H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 116 removed outlier: 3.787A pdb=" N ALA H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 149 Processing helix chain 'H' and resid 244 through 266 removed outlier: 3.724A pdb=" N HIS H 266 " --> pdb=" O ILE H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 301 Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 31 through 49 Processing helix chain 'C' and resid 109 through 116 removed outlier: 3.819A pdb=" N ALA C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 149 Processing helix chain 'C' and resid 244 through 266 removed outlier: 3.937A pdb=" N HIS C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 301 Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 31 through 49 Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.802A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 244 through 266 removed outlier: 3.926A pdb=" N HIS A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 301 Processing helix chain 'K' and resid 8 through 21 Processing helix chain 'K' and resid 31 through 49 Processing helix chain 'K' and resid 109 through 116 removed outlier: 3.784A pdb=" N ALA K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 149 Processing helix chain 'K' and resid 244 through 266 removed outlier: 3.937A pdb=" N HIS K 266 " --> pdb=" O ILE K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 301 Processing helix chain 'I' and resid 8 through 21 Processing helix chain 'I' and resid 31 through 49 Processing helix chain 'I' and resid 109 through 116 removed outlier: 3.784A pdb=" N ALA I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 149 Processing helix chain 'I' and resid 244 through 266 removed outlier: 3.891A pdb=" N HIS I 266 " --> pdb=" O ILE I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 301 Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 31 through 49 Processing helix chain 'E' and resid 109 through 116 removed outlier: 3.800A pdb=" N ALA E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 149 Processing helix chain 'E' and resid 244 through 266 removed outlier: 3.953A pdb=" N HIS E 266 " --> pdb=" O ILE E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 301 Processing helix chain 'G' and resid 8 through 21 Processing helix chain 'G' and resid 31 through 49 Processing helix chain 'G' and resid 109 through 116 removed outlier: 3.795A pdb=" N ALA G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 Processing helix chain 'G' and resid 244 through 266 removed outlier: 3.936A pdb=" N HIS G 266 " --> pdb=" O ILE G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 301 Processing helix chain 'M' and resid 32 through 35 Processing helix chain 'M' and resid 36 through 52 removed outlier: 3.955A pdb=" N GLN M 40 " --> pdb=" O TYR M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 4.153A pdb=" N SER M 92 " --> pdb=" O TYR M 89 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE M 93 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU M 94 " --> pdb=" O ASN M 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 89 through 94' Processing helix chain 'M' and resid 119 through 126 Processing helix chain 'R' and resid 36 through 52 removed outlier: 3.899A pdb=" N GLN R 40 " --> pdb=" O TYR R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 94 removed outlier: 4.147A pdb=" N SER R 92 " --> pdb=" O TYR R 89 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE R 93 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU R 94 " --> pdb=" O ASN R 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 89 through 94' Processing helix chain 'R' and resid 119 through 126 Processing helix chain 'Q' and resid 32 through 35 Processing helix chain 'Q' and resid 36 through 52 removed outlier: 3.946A pdb=" N GLN Q 40 " --> pdb=" O TYR Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 94 removed outlier: 4.126A pdb=" N SER Q 92 " --> pdb=" O TYR Q 89 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE Q 93 " --> pdb=" O LEU Q 90 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU Q 94 " --> pdb=" O ASN Q 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 89 through 94' Processing helix chain 'Q' and resid 119 through 126 Processing helix chain 'P' and resid 36 through 52 removed outlier: 3.902A pdb=" N GLN P 40 " --> pdb=" O TYR P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 94 removed outlier: 4.155A pdb=" N SER P 92 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE P 93 " --> pdb=" O LEU P 90 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU P 94 " --> pdb=" O ASN P 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 89 through 94' Processing helix chain 'P' and resid 119 through 126 Processing helix chain 'O' and resid 32 through 35 Processing helix chain 'O' and resid 36 through 52 removed outlier: 3.931A pdb=" N GLN O 40 " --> pdb=" O TYR O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 94 removed outlier: 4.104A pdb=" N SER O 92 " --> pdb=" O TYR O 89 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE O 93 " --> pdb=" O LEU O 90 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU O 94 " --> pdb=" O ASN O 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 89 through 94' Processing helix chain 'O' and resid 119 through 126 Processing helix chain 'N' and resid 32 through 35 Processing helix chain 'N' and resid 36 through 52 removed outlier: 3.974A pdb=" N GLN N 40 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 94 removed outlier: 4.135A pdb=" N SER N 92 " --> pdb=" O TYR N 89 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE N 93 " --> pdb=" O LEU N 90 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU N 94 " --> pdb=" O ASN N 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 89 through 94' Processing helix chain 'N' and resid 119 through 126 Processing sheet with id=AA1, first strand: chain 'D' and resid 81 through 88 removed outlier: 6.082A pdb=" N VAL D 84 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TRP D 187 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG D 86 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 185 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE D 182 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE D 60 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D 184 " --> pdb=" O HIS D 58 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS D 58 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.569A pdb=" N GLN D 169 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.762A pdb=" N TRP B 187 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL B 84 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLU B 185 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 182 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE B 60 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 184 " --> pdb=" O HIS B 58 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS B 58 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.526A pdb=" N LYS B 171 " --> pdb=" O TRP B 162 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 169 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 81 through 88 removed outlier: 6.123A pdb=" N VAL L 84 " --> pdb=" O TRP L 187 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TRP L 187 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ARG L 86 " --> pdb=" O GLU L 185 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU L 185 " --> pdb=" O ARG L 86 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE L 182 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE L 60 " --> pdb=" O ILE L 182 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL L 184 " --> pdb=" O HIS L 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS L 58 " --> pdb=" O VAL L 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 161 through 164 removed outlier: 3.518A pdb=" N LYS L 171 " --> pdb=" O TRP L 162 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN L 169 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 81 through 84 removed outlier: 6.764A pdb=" N TRP J 187 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL J 84 " --> pdb=" O GLU J 185 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU J 185 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE J 182 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE J 60 " --> pdb=" O ILE J 182 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL J 184 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS J 58 " --> pdb=" O VAL J 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 161 through 164 removed outlier: 3.534A pdb=" N GLN J 169 " --> pdb=" O ASN J 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 81 through 84 removed outlier: 6.759A pdb=" N TRP F 187 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL F 84 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU F 185 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE F 182 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE F 60 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL F 184 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS F 58 " --> pdb=" O VAL F 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.524A pdb=" N LYS F 171 " --> pdb=" O TRP F 162 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN F 169 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 81 through 88 removed outlier: 6.126A pdb=" N VAL H 84 " --> pdb=" O TRP H 187 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TRP H 187 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG H 86 " --> pdb=" O GLU H 185 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU H 185 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE H 182 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE H 60 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL H 184 " --> pdb=" O HIS H 58 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS H 58 " --> pdb=" O VAL H 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.525A pdb=" N LYS H 171 " --> pdb=" O TRP H 162 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN H 169 " --> pdb=" O ASN H 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 81 through 84 removed outlier: 6.769A pdb=" N TRP C 187 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL C 84 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU C 185 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 182 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C 60 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 184 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS C 58 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.525A pdb=" N LYS C 171 " --> pdb=" O TRP C 162 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 169 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 81 through 88 removed outlier: 6.109A pdb=" N VAL A 84 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TRP A 187 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ARG A 86 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 185 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 182 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 60 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 184 " --> pdb=" O HIS A 58 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS A 58 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 161 through 164 Processing sheet with id=AB8, first strand: chain 'K' and resid 81 through 88 removed outlier: 6.138A pdb=" N VAL K 84 " --> pdb=" O TRP K 187 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP K 187 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ARG K 86 " --> pdb=" O GLU K 185 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU K 185 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL K 184 " --> pdb=" O HIS K 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS K 58 " --> pdb=" O VAL K 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 161 through 164 removed outlier: 3.532A pdb=" N GLN K 169 " --> pdb=" O ASN K 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 81 through 84 removed outlier: 6.770A pdb=" N TRP I 187 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL I 84 " --> pdb=" O GLU I 185 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU I 185 " --> pdb=" O VAL I 84 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE I 182 " --> pdb=" O PHE I 60 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE I 60 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL I 184 " --> pdb=" O HIS I 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS I 58 " --> pdb=" O VAL I 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 161 through 164 Processing sheet with id=AC3, first strand: chain 'E' and resid 81 through 88 removed outlier: 6.135A pdb=" N VAL E 84 " --> pdb=" O TRP E 187 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP E 187 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG E 86 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU E 185 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE E 182 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE E 60 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL E 184 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS E 58 " --> pdb=" O VAL E 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.500A pdb=" N GLN E 169 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 81 through 88 removed outlier: 6.131A pdb=" N VAL G 84 " --> pdb=" O TRP G 187 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TRP G 187 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ARG G 86 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU G 185 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE G 182 " --> pdb=" O PHE G 60 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE G 60 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL G 184 " --> pdb=" O HIS G 58 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS G 58 " --> pdb=" O VAL G 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 161 through 164 Processing sheet with id=AC7, first strand: chain 'M' and resid 84 through 88 removed outlier: 3.631A pdb=" N SER M 145 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE M 149 " --> pdb=" O GLY M 172 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY M 172 " --> pdb=" O ILE M 149 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG M 167 " --> pdb=" O ILE M 118 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 84 through 88 removed outlier: 3.618A pdb=" N SER R 145 " --> pdb=" O PHE R 140 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE R 149 " --> pdb=" O GLY R 172 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY R 172 " --> pdb=" O ILE R 149 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG R 167 " --> pdb=" O ILE R 118 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 84 through 88 removed outlier: 3.661A pdb=" N SER Q 145 " --> pdb=" O PHE Q 140 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE Q 149 " --> pdb=" O GLY Q 172 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY Q 172 " --> pdb=" O ILE Q 149 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG Q 167 " --> pdb=" O ILE Q 118 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 84 through 88 removed outlier: 3.628A pdb=" N SER P 145 " --> pdb=" O PHE P 140 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE P 149 " --> pdb=" O GLY P 172 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY P 172 " --> pdb=" O ILE P 149 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG P 167 " --> pdb=" O ILE P 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 84 through 88 removed outlier: 3.617A pdb=" N SER O 145 " --> pdb=" O PHE O 140 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE O 149 " --> pdb=" O GLY O 172 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY O 172 " --> pdb=" O ILE O 149 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG O 167 " --> pdb=" O ILE O 118 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 84 through 88 removed outlier: 3.605A pdb=" N SER N 145 " --> pdb=" O PHE N 140 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE N 149 " --> pdb=" O GLY N 172 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY N 172 " --> pdb=" O ILE N 149 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG N 167 " --> pdb=" O ILE N 118 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3513 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: 6.48 Time building geometry restraints manager: 3.48 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: 10086 1.34 - 1.46: 7519 1.46 - 1.58: 14057 1.58 - 1.69: 0 1.69 - 1.81: 270 Bond restraints: 31932 Sorted by residual: bond pdb=" C LEU E 271 " pdb=" N PRO E 272 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.08e-02 8.57e+03 2.53e+00 bond pdb=" C LEU G 271 " pdb=" N PRO G 272 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.08e-02 8.57e+03 2.50e+00 bond pdb=" C LEU B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.19e-02 7.06e+03 1.89e+00 bond pdb=" CA ARG N 54 " pdb=" CB ARG N 54 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.62e-02 3.81e+03 1.84e+00 bond pdb=" C LEU J 271 " pdb=" N PRO J 272 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.19e-02 7.06e+03 1.74e+00 ... (remaining 31927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 41973 1.49 - 2.99: 1040 2.99 - 4.48: 109 4.48 - 5.98: 24 5.98 - 7.47: 6 Bond angle restraints: 43152 Sorted by residual: angle pdb=" N LYS I 70 " pdb=" CA LYS I 70 " pdb=" C LYS I 70 " ideal model delta sigma weight residual 114.56 108.59 5.97 1.27e+00 6.20e-01 2.21e+01 angle pdb=" N LYS G 70 " pdb=" CA LYS G 70 " pdb=" C LYS G 70 " ideal model delta sigma weight residual 114.56 108.63 5.93 1.27e+00 6.20e-01 2.18e+01 angle pdb=" N LYS K 70 " pdb=" CA LYS K 70 " pdb=" C LYS K 70 " ideal model delta sigma weight residual 114.56 108.65 5.91 1.27e+00 6.20e-01 2.17e+01 angle pdb=" N LYS E 70 " pdb=" CA LYS E 70 " pdb=" C LYS E 70 " ideal model delta sigma weight residual 114.56 108.66 5.90 1.27e+00 6.20e-01 2.16e+01 angle pdb=" N LYS C 70 " pdb=" CA LYS C 70 " pdb=" C LYS C 70 " ideal model delta sigma weight residual 114.56 108.66 5.90 1.27e+00 6.20e-01 2.16e+01 ... (remaining 43147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 17870 17.88 - 35.76: 694 35.76 - 53.64: 98 53.64 - 71.51: 59 71.51 - 89.39: 23 Dihedral angle restraints: 18744 sinusoidal: 7692 harmonic: 11052 Sorted by residual: dihedral pdb=" CA THR G 30 " pdb=" C THR G 30 " pdb=" N PRO G 31 " pdb=" CA PRO G 31 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA THR K 30 " pdb=" C THR K 30 " pdb=" N PRO K 31 " pdb=" CA PRO K 31 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA THR C 30 " pdb=" C THR C 30 " pdb=" N PRO C 31 " pdb=" CA PRO C 31 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 18741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3004 0.029 - 0.058: 919 0.058 - 0.086: 303 0.086 - 0.115: 244 0.115 - 0.144: 30 Chirality restraints: 4500 Sorted by residual: chirality pdb=" CA PRO A 31 " pdb=" N PRO A 31 " pdb=" C PRO A 31 " pdb=" CB PRO A 31 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA PRO E 31 " pdb=" N PRO E 31 " pdb=" C PRO E 31 " pdb=" CB PRO E 31 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO K 31 " pdb=" N PRO K 31 " pdb=" C PRO K 31 " pdb=" CB PRO K 31 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 4497 not shown) Planarity restraints: 5622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN N 119 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO N 120 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO N 120 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 120 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN P 119 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO P 120 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO P 120 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO P 120 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 119 " 0.029 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO O 120 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO O 120 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO O 120 " 0.025 5.00e-02 4.00e+02 ... (remaining 5619 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9285 2.82 - 3.34: 28761 3.34 - 3.86: 49900 3.86 - 4.38: 55361 4.38 - 4.90: 97090 Nonbonded interactions: 240397 Sorted by model distance: nonbonded pdb=" NH1 ARG D 281 " pdb=" OE2 GLU D 285 " model vdw 2.302 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" O ASP D 180 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR G 90 " pdb=" O ASP G 180 " model vdw 2.324 3.040 nonbonded pdb=" O GLY D 52 " pdb=" OG SER D 190 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR F 90 " pdb=" O ASP F 180 " model vdw 2.335 3.040 ... (remaining 240392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.190 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 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 : 0.002 0.022 31932 Z= 0.133 Angle : 0.566 7.471 43152 Z= 0.369 Chirality : 0.038 0.144 4500 Planarity : 0.004 0.045 5622 Dihedral : 10.479 89.392 11736 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.93 % Allowed : 7.50 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.12), residues: 3762 helix: 0.81 (0.13), residues: 1332 sheet: -2.53 (0.18), residues: 690 loop : -4.13 (0.10), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 19 TYR 0.005 0.001 TYR D 129 PHE 0.006 0.001 PHE J 141 TRP 0.005 0.000 TRP M 84 HIS 0.001 0.000 HIS G 58 Details of bonding type rmsd covalent geometry : bond 0.00208 (31932) covalent geometry : angle 0.56578 (43152) hydrogen bonds : bond 0.18670 ( 1209) hydrogen bonds : angle 5.34840 ( 3513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 803 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.0225 (t80) cc_final: -0.0598 (t80) REVERT: D 11 GLU cc_start: 0.9418 (tp30) cc_final: 0.8641 (tp30) REVERT: D 39 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8270 (tm-30) REVERT: D 134 PHE cc_start: 0.8530 (t80) cc_final: 0.8261 (m-10) REVERT: D 138 LEU cc_start: -0.3493 (OUTLIER) cc_final: -0.3699 (tp) REVERT: D 148 MET cc_start: 0.4075 (ttp) cc_final: 0.3669 (ttp) REVERT: D 257 GLU cc_start: 0.8547 (tp30) cc_final: 0.8138 (tp30) REVERT: D 261 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8468 (mm-40) REVERT: D 283 ILE cc_start: 0.8923 (tt) cc_final: 0.8397 (mt) REVERT: D 289 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8852 (pt0) REVERT: D 295 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8402 (tm-30) REVERT: B 4 TYR cc_start: -0.1701 (t80) cc_final: -0.3313 (t80) REVERT: B 11 GLU cc_start: 0.8711 (tp30) cc_final: 0.8223 (tp30) REVERT: B 29 LEU cc_start: 0.8205 (mt) cc_final: 0.7754 (mt) REVERT: B 148 MET cc_start: 0.4560 (ttp) cc_final: 0.4238 (ttm) REVERT: B 187 TRP cc_start: 0.8122 (m100) cc_final: 0.5914 (m-10) REVERT: B 257 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: B 261 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8654 (mm-40) REVERT: B 278 ASP cc_start: 0.7493 (t70) cc_final: 0.6787 (p0) REVERT: B 289 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7821 (pt0) REVERT: B 295 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7815 (tm-30) REVERT: L 11 GLU cc_start: 0.9406 (tp30) cc_final: 0.8835 (tp30) REVERT: L 129 TYR cc_start: 0.5542 (t80) cc_final: 0.5294 (t80) REVERT: L 134 PHE cc_start: 0.8174 (t80) cc_final: 0.7789 (m-10) REVERT: L 257 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8450 (tp30) REVERT: L 261 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8825 (mm-40) REVERT: L 283 ILE cc_start: 0.9223 (tt) cc_final: 0.8973 (mt) REVERT: L 289 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8639 (pt0) REVERT: J 4 TYR cc_start: 0.0914 (t80) cc_final: 0.0518 (t80) REVERT: J 11 GLU cc_start: 0.9367 (tp30) cc_final: 0.8590 (tp30) REVERT: J 28 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.9122 (pt0) REVERT: J 29 LEU cc_start: 0.8965 (mt) cc_final: 0.8753 (mt) REVERT: J 39 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8579 (tm-30) REVERT: J 134 PHE cc_start: 0.8179 (t80) cc_final: 0.7893 (m-10) REVERT: J 148 MET cc_start: 0.4578 (ttp) cc_final: 0.4348 (ttp) REVERT: J 187 TRP cc_start: 0.8083 (m100) cc_final: 0.6701 (m-10) REVERT: J 257 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: J 261 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8381 (mm-40) REVERT: J 283 ILE cc_start: 0.8643 (tt) cc_final: 0.7822 (mt) REVERT: J 289 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8711 (pt0) REVERT: J 295 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8512 (tm-30) REVERT: F 11 GLU cc_start: 0.8983 (tp30) cc_final: 0.8711 (tp30) REVERT: F 261 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8595 (mm-40) REVERT: H 4 TYR cc_start: 0.2286 (t80) cc_final: 0.0969 (t80) REVERT: H 11 GLU cc_start: 0.9366 (tp30) cc_final: 0.8484 (tp30) REVERT: H 29 LEU cc_start: 0.8783 (mt) cc_final: 0.8576 (mt) REVERT: H 187 TRP cc_start: 0.6597 (m100) cc_final: 0.4892 (m-10) REVERT: H 257 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: H 261 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8551 (mm-40) REVERT: H 278 ASP cc_start: 0.7511 (t70) cc_final: 0.7160 (p0) REVERT: C 39 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8734 (tm-30) REVERT: C 71 THR cc_start: 0.3385 (t) cc_final: 0.2887 (m) REVERT: C 256 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7228 (ttpp) REVERT: C 265 ARG cc_start: 0.6772 (tpt-90) cc_final: 0.6447 (tpp80) REVERT: C 269 MET cc_start: -0.2916 (mmt) cc_final: -0.3143 (mmt) REVERT: C 284 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8971 (pp20) REVERT: C 288 LEU cc_start: 0.9337 (mt) cc_final: 0.9034 (mt) REVERT: C 289 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8583 (pt0) REVERT: A 191 TYR cc_start: 0.8202 (t80) cc_final: 0.7998 (t80) REVERT: A 288 LEU cc_start: 0.9610 (mt) cc_final: 0.8791 (mt) REVERT: K 39 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8927 (tm-30) REVERT: K 256 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8439 (ttpt) REVERT: K 269 MET cc_start: -0.0600 (mmt) cc_final: -0.0902 (mmt) REVERT: K 288 LEU cc_start: 0.9765 (mt) cc_final: 0.9421 (pp) REVERT: I 71 THR cc_start: 0.3288 (t) cc_final: 0.2923 (m) REVERT: I 191 TYR cc_start: 0.8375 (t80) cc_final: 0.8093 (t80) REVERT: I 249 ASP cc_start: 0.9321 (m-30) cc_final: 0.9086 (m-30) REVERT: I 256 LYS cc_start: 0.9223 (ttmm) cc_final: 0.8249 (ttpp) REVERT: I 257 GLU cc_start: 0.9237 (tp30) cc_final: 0.9020 (tm-30) REVERT: I 265 ARG cc_start: 0.7420 (tpt-90) cc_final: 0.7002 (tpp80) REVERT: I 284 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8759 (pp20) REVERT: I 288 LEU cc_start: 0.9662 (mt) cc_final: 0.8868 (mt) REVERT: I 289 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8757 (pt0) REVERT: E 39 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8865 (tm-30) REVERT: E 71 THR cc_start: 0.5134 (t) cc_final: 0.4625 (m) REVERT: E 134 PHE cc_start: 0.8661 (t80) cc_final: 0.8396 (m-10) REVERT: E 178 LYS cc_start: 0.8052 (ptmm) cc_final: 0.7706 (mmmm) REVERT: E 256 LYS cc_start: 0.9156 (ttmm) cc_final: 0.8701 (ttpt) REVERT: E 288 LEU cc_start: 0.9746 (mt) cc_final: 0.9389 (pp) REVERT: G 288 LEU cc_start: 0.9634 (mt) cc_final: 0.9320 (pp) REVERT: G 289 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9042 (pt0) REVERT: M 159 TYR cc_start: 0.8671 (p90) cc_final: 0.8448 (p90) REVERT: R 33 PHE cc_start: 0.4805 (m-10) cc_final: 0.3892 (m-10) REVERT: R 142 MET cc_start: 0.8468 (mmm) cc_final: 0.8248 (ptp) REVERT: R 146 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9027 (tp) REVERT: Q 33 PHE cc_start: 0.5081 (m-10) cc_final: 0.4045 (m-10) REVERT: Q 146 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8646 (tp) REVERT: Q 159 TYR cc_start: 0.8512 (p90) cc_final: 0.8215 (p90) REVERT: P 33 PHE cc_start: 0.6356 (m-10) cc_final: 0.5893 (m-10) REVERT: P 130 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7037 (ptpp) REVERT: P 158 PHE cc_start: 0.7630 (t80) cc_final: 0.7113 (t80) REVERT: P 159 TYR cc_start: 0.8544 (p90) cc_final: 0.8274 (p90) REVERT: O 33 PHE cc_start: 0.5765 (m-10) cc_final: 0.5051 (m-10) REVERT: O 146 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9247 (tp) REVERT: N 33 PHE cc_start: 0.3800 (m-10) cc_final: 0.2791 (m-10) outliers start: 129 outliers final: 23 residues processed: 875 average time/residue: 0.2087 time to fit residues: 279.6290 Evaluate side-chains 417 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 384 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 171 LYS Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 161 LEU Chi-restraints excluded: chain P residue 130 LYS Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 161 LEU Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 161 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN B 26 ASN B 143 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 26 ASN L 49 HIS ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN J 26 ASN ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 26 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN H 26 ASN H 143 GLN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 49 HIS ** C 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS C 267 GLN ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN A 49 HIS A 143 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS A 267 GLN ** K 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 ASN K 49 HIS K 143 GLN ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 HIS I 8 ASN I 49 HIS I 143 GLN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 HIS I 267 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 143 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 49 HIS G 143 GLN ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 HIS G 267 GLN ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 ASN M 126 GLN M 163 GLN ** R 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 ASN R 126 GLN R 163 GLN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 ASN Q 126 GLN Q 163 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 ASN P 126 GLN P 163 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 ASN O 126 GLN O 163 GLN N 119 ASN N 126 GLN N 163 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.096340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.073176 restraints weight = 164614.806| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 6.42 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 31932 Z= 0.238 Angle : 0.762 9.540 43152 Z= 0.389 Chirality : 0.046 0.229 4500 Planarity : 0.005 0.064 5622 Dihedral : 5.555 59.653 4312 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 5.85 % Allowed : 13.77 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.13), residues: 3762 helix: 1.16 (0.14), residues: 1356 sheet: -1.94 (0.21), residues: 618 loop : -3.58 (0.12), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 294 TYR 0.033 0.002 TYR I 4 PHE 0.022 0.002 PHE M 33 TRP 0.019 0.002 TRP B 187 HIS 0.010 0.002 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00491 (31932) covalent geometry : angle 0.76177 (43152) hydrogen bonds : bond 0.03793 ( 1209) hydrogen bonds : angle 4.35874 ( 3513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 410 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8743 (p0) REVERT: D 11 GLU cc_start: 0.9467 (tp30) cc_final: 0.9195 (tm-30) REVERT: D 12 LEU cc_start: 0.9811 (OUTLIER) cc_final: 0.9514 (mt) REVERT: D 121 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6257 (pmm) REVERT: D 257 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8882 (tp30) REVERT: D 284 GLU cc_start: 0.9138 (pp20) cc_final: 0.8909 (pp20) REVERT: D 287 ARG cc_start: 0.9323 (tmm-80) cc_final: 0.9090 (ttp80) REVERT: D 289 GLU cc_start: 0.9279 (mt-10) cc_final: 0.9052 (mt-10) REVERT: D 295 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8607 (tm-30) REVERT: B 121 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6881 (pmm) REVERT: B 154 MET cc_start: 0.5199 (pmm) cc_final: 0.4952 (pmm) REVERT: B 257 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8869 (tp30) REVERT: B 275 VAL cc_start: 0.3870 (OUTLIER) cc_final: 0.3333 (m) REVERT: B 283 ILE cc_start: 0.9756 (mt) cc_final: 0.9535 (mt) REVERT: B 289 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8921 (mt-10) REVERT: L 121 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7156 (pmm) REVERT: L 154 MET cc_start: 0.5098 (pmm) cc_final: 0.4819 (pmm) REVERT: L 187 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.7415 (m-10) REVERT: L 256 LYS cc_start: 0.9515 (ttmm) cc_final: 0.9236 (ttmt) REVERT: L 257 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8877 (tp30) REVERT: L 289 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8842 (mt-10) REVERT: J 8 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8627 (p0) REVERT: J 16 ILE cc_start: 0.9693 (OUTLIER) cc_final: 0.9489 (tp) REVERT: J 28 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: J 121 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6334 (pmm) REVERT: J 154 MET cc_start: 0.4504 (pmm) cc_final: 0.4271 (pmm) REVERT: J 173 MET cc_start: 0.1639 (mmm) cc_final: -0.0071 (mmm) REVERT: J 256 LYS cc_start: 0.9469 (ttmm) cc_final: 0.9163 (ttmt) REVERT: J 257 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8952 (tp30) REVERT: J 270 MET cc_start: 0.5975 (mtt) cc_final: 0.5632 (mpp) REVERT: J 289 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8913 (mt-10) REVERT: J 295 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8584 (tm-30) REVERT: F 8 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8845 (p0) REVERT: F 121 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7190 (pmm) REVERT: F 154 MET cc_start: 0.5230 (pmm) cc_final: 0.4894 (pmm) REVERT: F 173 MET cc_start: 0.0670 (mmm) cc_final: -0.0817 (mmm) REVERT: F 187 TRP cc_start: 0.7937 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: H 121 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6898 (pmm) REVERT: H 154 MET cc_start: 0.5006 (pmm) cc_final: 0.4735 (pmm) REVERT: H 257 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8872 (tp30) REVERT: H 261 GLN cc_start: 0.9447 (mm-40) cc_final: 0.8935 (mm-40) REVERT: H 295 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8727 (tm-30) REVERT: C 8 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8665 (p0) REVERT: C 178 LYS cc_start: 0.8285 (mmmm) cc_final: 0.8060 (mmmm) REVERT: C 249 ASP cc_start: 0.9329 (m-30) cc_final: 0.9123 (m-30) REVERT: C 256 LYS cc_start: 0.9451 (ttmm) cc_final: 0.8873 (ttpp) REVERT: C 295 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8549 (tm-30) REVERT: C 299 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8607 (mp) REVERT: A 4 TYR cc_start: 0.6940 (p90) cc_final: 0.6328 (p90) REVERT: A 92 ILE cc_start: 0.3700 (OUTLIER) cc_final: 0.3436 (pt) REVERT: A 178 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7964 (mmmm) REVERT: A 285 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8728 (mt-10) REVERT: A 287 ARG cc_start: 0.9203 (tmm-80) cc_final: 0.8361 (ttp80) REVERT: A 288 LEU cc_start: 0.9522 (mt) cc_final: 0.8852 (mt) REVERT: K 4 TYR cc_start: 0.7056 (p90) cc_final: 0.5787 (p90) REVERT: K 8 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8453 (p0) REVERT: K 62 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7527 (m) REVERT: K 150 MET cc_start: 0.8766 (ptp) cc_final: 0.8342 (pmm) REVERT: K 287 ARG cc_start: 0.9520 (ttp80) cc_final: 0.8393 (tmm-80) REVERT: K 288 LEU cc_start: 0.9544 (mt) cc_final: 0.8999 (mt) REVERT: K 294 ARG cc_start: 0.9338 (mmm-85) cc_final: 0.9065 (mmm-85) REVERT: I 8 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8633 (p0) REVERT: I 62 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7438 (m) REVERT: I 249 ASP cc_start: 0.9401 (m-30) cc_final: 0.9134 (m-30) REVERT: I 256 LYS cc_start: 0.9374 (ttmm) cc_final: 0.8804 (ttpp) REVERT: I 257 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9079 (tm-30) REVERT: I 280 GLN cc_start: 0.9145 (mp10) cc_final: 0.8764 (mp10) REVERT: E 4 TYR cc_start: 0.7099 (p90) cc_final: 0.5693 (p90) REVERT: E 62 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7475 (m) REVERT: E 150 MET cc_start: 0.8743 (ptp) cc_final: 0.8302 (pmm) REVERT: E 178 LYS cc_start: 0.8597 (ptmm) cc_final: 0.8014 (mmmm) REVERT: E 280 GLN cc_start: 0.8970 (mp10) cc_final: 0.8751 (mp10) REVERT: E 284 GLU cc_start: 0.9138 (pp20) cc_final: 0.8932 (pp20) REVERT: E 287 ARG cc_start: 0.9507 (ttp80) cc_final: 0.8353 (tmm-80) REVERT: E 288 LEU cc_start: 0.9556 (mt) cc_final: 0.9000 (mt) REVERT: E 294 ARG cc_start: 0.9333 (mmm-85) cc_final: 0.9074 (mmm-85) REVERT: G 4 TYR cc_start: 0.6752 (p90) cc_final: 0.6326 (p90) REVERT: G 8 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8637 (p0) REVERT: G 92 ILE cc_start: 0.3895 (OUTLIER) cc_final: 0.3608 (pt) REVERT: G 150 MET cc_start: 0.8589 (ptp) cc_final: 0.8369 (pmm) REVERT: G 280 GLN cc_start: 0.9094 (mp10) cc_final: 0.8832 (mp10) REVERT: G 287 ARG cc_start: 0.9515 (ttp80) cc_final: 0.9007 (tmm-80) REVERT: G 290 LYS cc_start: 0.9568 (ptpt) cc_final: 0.9354 (ptpp) REVERT: M 130 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.9161 (tmtt) REVERT: M 159 TYR cc_start: 0.8366 (p90) cc_final: 0.7268 (p90) REVERT: R 130 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9195 (ptpp) REVERT: Q 130 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9216 (ptpp) REVERT: P 34 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8242 (m110) REVERT: N 130 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9146 (ptpp) outliers start: 192 outliers final: 34 residues processed: 556 average time/residue: 0.1806 time to fit residues: 161.8468 Evaluate side-chains 399 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 187 TRP Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 285 GLU Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 187 TRP Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 80 ASN Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain R residue 78 ASN Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 133 LYS Chi-restraints excluded: chain Q residue 161 LEU Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain O residue 78 ASN Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 161 LEU Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 370 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 353 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 266 HIS ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 ASN K 7 GLN K 243 ASN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 GLN E 5 ASN E 7 GLN E 8 ASN E 239 GLN E 243 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.095902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.073341 restraints weight = 164054.416| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 6.44 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31932 Z= 0.150 Angle : 0.652 10.551 43152 Z= 0.331 Chirality : 0.044 0.190 4500 Planarity : 0.005 0.057 5622 Dihedral : 4.768 58.452 4268 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.11 % Allowed : 15.66 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.14), residues: 3762 helix: 1.39 (0.14), residues: 1356 sheet: -1.76 (0.20), residues: 702 loop : -3.51 (0.12), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 287 TYR 0.022 0.001 TYR I 4 PHE 0.017 0.001 PHE Q 158 TRP 0.013 0.001 TRP J 187 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00323 (31932) covalent geometry : angle 0.65159 (43152) hydrogen bonds : bond 0.03279 ( 1209) hydrogen bonds : angle 4.16258 ( 3513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 382 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.5791 (pmm) REVERT: D 154 MET cc_start: 0.5422 (pmm) cc_final: 0.4995 (pmm) REVERT: D 257 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8786 (tp30) REVERT: D 287 ARG cc_start: 0.9384 (tmm-80) cc_final: 0.8861 (tmm-80) REVERT: D 295 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8580 (tm-30) REVERT: B 11 GLU cc_start: 0.9425 (tp30) cc_final: 0.9112 (tm-30) REVERT: B 121 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6538 (pmm) REVERT: B 154 MET cc_start: 0.4991 (pmm) cc_final: 0.4676 (pmm) REVERT: B 187 TRP cc_start: 0.7404 (m-10) cc_final: 0.7078 (m-10) REVERT: B 257 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8693 (tp30) REVERT: B 295 GLU cc_start: 0.8960 (tp30) cc_final: 0.8578 (tp30) REVERT: L 12 LEU cc_start: 0.9457 (mm) cc_final: 0.9216 (mm) REVERT: L 121 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6735 (pmm) REVERT: L 154 MET cc_start: 0.4778 (pmm) cc_final: 0.4511 (pmm) REVERT: L 173 MET cc_start: 0.1845 (mmm) cc_final: 0.1429 (mmm) REVERT: L 187 TRP cc_start: 0.7454 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: L 257 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8617 (tp30) REVERT: J 121 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6046 (pmm) REVERT: J 256 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9052 (ttmt) REVERT: J 257 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8742 (tp30) REVERT: J 284 GLU cc_start: 0.9286 (pp20) cc_final: 0.9074 (pp20) REVERT: J 295 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8530 (tm-30) REVERT: F 121 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6248 (pmm) REVERT: F 148 MET cc_start: 0.2993 (ttt) cc_final: 0.2469 (ttp) REVERT: F 154 MET cc_start: 0.4809 (pmm) cc_final: 0.4535 (pmm) REVERT: F 177 GLN cc_start: 0.8357 (mp10) cc_final: 0.8145 (mp10) REVERT: F 187 TRP cc_start: 0.7822 (OUTLIER) cc_final: 0.7044 (m-10) REVERT: H 121 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6454 (pmm) REVERT: H 154 MET cc_start: 0.4997 (pmm) cc_final: 0.4672 (pmm) REVERT: H 257 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8755 (tp30) REVERT: H 289 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8556 (mt-10) REVERT: H 295 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8670 (tp30) REVERT: C 114 MET cc_start: 0.5912 (ptp) cc_final: 0.5391 (ppp) REVERT: C 173 MET cc_start: 0.7961 (mmm) cc_final: 0.7747 (mmm) REVERT: C 178 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8292 (mmmm) REVERT: C 249 ASP cc_start: 0.9248 (m-30) cc_final: 0.9044 (m-30) REVERT: C 256 LYS cc_start: 0.9482 (ttmm) cc_final: 0.9129 (ttmt) REVERT: A 4 TYR cc_start: 0.7193 (p90) cc_final: 0.6959 (p90) REVERT: A 92 ILE cc_start: 0.3592 (OUTLIER) cc_final: 0.3339 (pt) REVERT: A 114 MET cc_start: 0.5578 (ptp) cc_final: 0.5279 (ppp) REVERT: A 173 MET cc_start: 0.7663 (mmm) cc_final: 0.7365 (mmm) REVERT: A 178 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8182 (mmmm) REVERT: A 284 GLU cc_start: 0.8998 (pp20) cc_final: 0.8675 (pp20) REVERT: A 285 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8706 (mt-10) REVERT: A 287 ARG cc_start: 0.9176 (tmm-80) cc_final: 0.8674 (tmm-80) REVERT: A 290 LYS cc_start: 0.9577 (ptpt) cc_final: 0.9354 (ptpp) REVERT: K 4 TYR cc_start: 0.6732 (p90) cc_final: 0.5495 (p90) REVERT: K 114 MET cc_start: 0.5583 (ptp) cc_final: 0.5202 (ppp) REVERT: K 150 MET cc_start: 0.8719 (ptp) cc_final: 0.8359 (pmm) REVERT: K 285 GLU cc_start: 0.8672 (pt0) cc_final: 0.8286 (pt0) REVERT: K 287 ARG cc_start: 0.9350 (ttp80) cc_final: 0.8947 (tmm-80) REVERT: K 288 LEU cc_start: 0.9638 (mt) cc_final: 0.9389 (mt) REVERT: K 294 ARG cc_start: 0.9252 (mmm-85) cc_final: 0.8944 (mmm-85) REVERT: I 178 LYS cc_start: 0.8476 (mmmm) cc_final: 0.8272 (mmmm) REVERT: I 191 TYR cc_start: 0.7956 (t80) cc_final: 0.7753 (t80) REVERT: I 249 ASP cc_start: 0.9334 (m-30) cc_final: 0.9083 (m-30) REVERT: I 256 LYS cc_start: 0.9319 (ttmm) cc_final: 0.9090 (ttpp) REVERT: I 257 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8823 (tp30) REVERT: I 288 LEU cc_start: 0.9529 (mt) cc_final: 0.9263 (mt) REVERT: I 291 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8830 (pp20) REVERT: E 4 TYR cc_start: 0.6995 (p90) cc_final: 0.5536 (p90) REVERT: E 8 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8362 (p0) REVERT: E 114 MET cc_start: 0.5647 (ptp) cc_final: 0.5273 (ppp) REVERT: E 150 MET cc_start: 0.8646 (ptp) cc_final: 0.8327 (pmm) REVERT: E 173 MET cc_start: 0.7940 (mmm) cc_final: 0.7661 (mmm) REVERT: E 178 LYS cc_start: 0.8551 (ptmm) cc_final: 0.8208 (mmmm) REVERT: E 280 GLN cc_start: 0.9018 (mp10) cc_final: 0.8801 (mp10) REVERT: E 284 GLU cc_start: 0.9066 (pp20) cc_final: 0.8865 (pp20) REVERT: E 287 ARG cc_start: 0.9350 (ttp80) cc_final: 0.8994 (tmm-80) REVERT: E 294 ARG cc_start: 0.9263 (mmm-85) cc_final: 0.8965 (mmm-85) REVERT: G 92 ILE cc_start: 0.3290 (OUTLIER) cc_final: 0.3009 (pt) REVERT: G 150 MET cc_start: 0.8584 (ptp) cc_final: 0.8336 (pmm) REVERT: G 173 MET cc_start: 0.7496 (mmm) cc_final: 0.7173 (mmm) REVERT: G 178 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8154 (mmmm) REVERT: G 280 GLN cc_start: 0.8830 (mp10) cc_final: 0.8617 (mp10) REVERT: G 284 GLU cc_start: 0.9067 (pp20) cc_final: 0.8660 (pp20) REVERT: G 287 ARG cc_start: 0.9512 (ttp80) cc_final: 0.8737 (tmm-80) REVERT: G 288 LEU cc_start: 0.9661 (mt) cc_final: 0.9322 (mt) REVERT: G 290 LYS cc_start: 0.9543 (ptpt) cc_final: 0.9341 (ptpp) REVERT: M 142 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8311 (ptt) REVERT: M 159 TYR cc_start: 0.7874 (p90) cc_final: 0.7615 (p90) REVERT: R 158 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: Q 158 PHE cc_start: 0.7831 (t80) cc_final: 0.7423 (m-80) REVERT: P 142 MET cc_start: 0.8655 (ptp) cc_final: 0.8167 (ptp) REVERT: O 158 PHE cc_start: 0.7799 (t80) cc_final: 0.7599 (m-80) REVERT: N 142 MET cc_start: 0.8645 (ptp) cc_final: 0.8389 (ptp) outliers start: 102 outliers final: 25 residues processed: 455 average time/residue: 0.1863 time to fit residues: 136.5068 Evaluate side-chains 381 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 337 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 187 TRP Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 285 GLU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 187 TRP Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain R residue 158 PHE Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain P residue 159 TYR Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain N residue 159 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 235 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 50.0000 chunk 359 optimal weight: 10.0000 chunk 172 optimal weight: 0.0470 chunk 173 optimal weight: 20.0000 chunk 257 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN K 126 ASN ** I 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN E 239 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN G 126 ASN G 143 GLN ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.092848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.069609 restraints weight = 167871.568| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 6.34 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31932 Z= 0.205 Angle : 0.691 13.314 43152 Z= 0.352 Chirality : 0.045 0.206 4500 Planarity : 0.005 0.063 5622 Dihedral : 4.580 43.750 4241 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.86 % Allowed : 16.33 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.13), residues: 3762 helix: 1.27 (0.14), residues: 1380 sheet: -1.75 (0.19), residues: 738 loop : -3.48 (0.12), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 287 TYR 0.017 0.001 TYR C 191 PHE 0.016 0.001 PHE O 33 TRP 0.009 0.001 TRP J 246 HIS 0.005 0.001 HIS L 266 Details of bonding type rmsd covalent geometry : bond 0.00430 (31932) covalent geometry : angle 0.69097 (43152) hydrogen bonds : bond 0.03351 ( 1209) hydrogen bonds : angle 4.17239 ( 3513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 323 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9282 (mm) REVERT: D 154 MET cc_start: 0.5950 (pmm) cc_final: 0.5547 (pmm) REVERT: D 257 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8891 (tp30) REVERT: D 287 ARG cc_start: 0.9406 (tmm-80) cc_final: 0.8840 (tmm-80) REVERT: D 295 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 148 MET cc_start: 0.3262 (ttt) cc_final: 0.2862 (ttm) REVERT: B 154 MET cc_start: 0.5045 (pmm) cc_final: 0.4723 (pmm) REVERT: B 257 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8732 (tp30) REVERT: B 295 GLU cc_start: 0.9145 (tp30) cc_final: 0.8707 (tp30) REVERT: L 12 LEU cc_start: 0.9428 (mm) cc_final: 0.9175 (mm) REVERT: L 154 MET cc_start: 0.5317 (pmm) cc_final: 0.4994 (pmm) REVERT: L 187 TRP cc_start: 0.7710 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: L 256 LYS cc_start: 0.9512 (ttmt) cc_final: 0.9131 (ttpp) REVERT: L 257 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8719 (tp30) REVERT: J 12 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9157 (mm) REVERT: J 28 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: J 154 MET cc_start: 0.5890 (pmm) cc_final: 0.5574 (pmm) REVERT: J 256 LYS cc_start: 0.9493 (ttmm) cc_final: 0.9171 (ttmt) REVERT: J 257 GLU cc_start: 0.9220 (tp30) cc_final: 0.8950 (tp30) REVERT: J 295 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8666 (tm-30) REVERT: F 12 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9252 (mm) REVERT: F 154 MET cc_start: 0.5400 (pmm) cc_final: 0.5047 (pmm) REVERT: F 187 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.6877 (m-10) REVERT: F 295 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8602 (tm-30) REVERT: H 154 MET cc_start: 0.4975 (pmm) cc_final: 0.4618 (pmm) REVERT: H 249 ASP cc_start: 0.9283 (m-30) cc_final: 0.8983 (m-30) REVERT: H 257 GLU cc_start: 0.9300 (tp30) cc_final: 0.8742 (tp30) REVERT: H 289 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8728 (mt-10) REVERT: C 178 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8405 (mmmm) REVERT: C 249 ASP cc_start: 0.9341 (m-30) cc_final: 0.9140 (m-30) REVERT: C 299 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 92 ILE cc_start: 0.3564 (OUTLIER) cc_final: 0.3317 (pt) REVERT: A 178 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8317 (mmmm) REVERT: A 284 GLU cc_start: 0.9099 (pp20) cc_final: 0.8762 (pp20) REVERT: A 285 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8835 (mt-10) REVERT: A 287 ARG cc_start: 0.9373 (tmm-80) cc_final: 0.9071 (tmm-80) REVERT: A 290 LYS cc_start: 0.9618 (ptpt) cc_final: 0.9336 (ptpp) REVERT: K 4 TYR cc_start: 0.6656 (p90) cc_final: 0.5602 (p90) REVERT: K 62 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7630 (m) REVERT: K 287 ARG cc_start: 0.9583 (ttp80) cc_final: 0.8899 (tmm-80) REVERT: K 288 LEU cc_start: 0.9622 (mt) cc_final: 0.9269 (mt) REVERT: I 62 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7745 (m) REVERT: I 178 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8381 (mmmm) REVERT: I 191 TYR cc_start: 0.8110 (t80) cc_final: 0.7781 (t80) REVERT: I 249 ASP cc_start: 0.9389 (m-30) cc_final: 0.9133 (m-30) REVERT: I 256 LYS cc_start: 0.9456 (ttmm) cc_final: 0.9042 (ttpp) REVERT: I 257 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9010 (tp30) REVERT: I 284 GLU cc_start: 0.9148 (pp20) cc_final: 0.8946 (pp20) REVERT: I 294 ARG cc_start: 0.9342 (mmm-85) cc_final: 0.9089 (mmm-85) REVERT: E 4 TYR cc_start: 0.7316 (p90) cc_final: 0.5957 (p90) REVERT: E 62 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7554 (m) REVERT: E 150 MET cc_start: 0.8776 (ptp) cc_final: 0.8422 (pmm) REVERT: E 154 MET cc_start: 0.7859 (pmm) cc_final: 0.7585 (pmm) REVERT: E 280 GLN cc_start: 0.9084 (mp10) cc_final: 0.8717 (mp10) REVERT: E 284 GLU cc_start: 0.9288 (pp20) cc_final: 0.8880 (pp20) REVERT: E 287 ARG cc_start: 0.9643 (ttp80) cc_final: 0.9106 (tmm-80) REVERT: G 92 ILE cc_start: 0.3793 (OUTLIER) cc_final: 0.3547 (pt) REVERT: G 178 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8449 (mmmm) REVERT: G 191 TYR cc_start: 0.8026 (t80) cc_final: 0.7779 (t80) REVERT: G 280 GLN cc_start: 0.9012 (mp10) cc_final: 0.8688 (mp10) REVERT: G 287 ARG cc_start: 0.9589 (ttp80) cc_final: 0.8839 (tmm-80) REVERT: G 288 LEU cc_start: 0.9629 (mt) cc_final: 0.9259 (mt) REVERT: G 290 LYS cc_start: 0.9609 (ptpt) cc_final: 0.9351 (ptpp) REVERT: G 295 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8574 (tm-30) REVERT: M 158 PHE cc_start: 0.7870 (t80) cc_final: 0.7316 (t80) outliers start: 94 outliers final: 35 residues processed: 390 average time/residue: 0.1949 time to fit residues: 120.1583 Evaluate side-chains 344 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 187 TRP Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 285 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 187 TRP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 80 ASN Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain R residue 78 ASN Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain Q residue 176 TYR Chi-restraints excluded: chain P residue 159 TYR Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain O residue 78 ASN Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 176 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 296 optimal weight: 10.0000 chunk 150 optimal weight: 0.0870 chunk 300 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 105 optimal weight: 0.3980 chunk 177 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 362 optimal weight: 10.0000 overall best weight: 4.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS Q 38 ASN N 38 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.082720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.059524 restraints weight = 173553.391| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 6.65 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31932 Z= 0.211 Angle : 0.700 11.211 43152 Z= 0.355 Chirality : 0.045 0.194 4500 Planarity : 0.005 0.054 5622 Dihedral : 4.601 39.496 4234 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.23 % Allowed : 16.09 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 3762 helix: 1.27 (0.14), residues: 1380 sheet: -1.75 (0.19), residues: 738 loop : -3.37 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 287 TYR 0.018 0.001 TYR J 4 PHE 0.012 0.001 PHE O 33 TRP 0.010 0.001 TRP J 246 HIS 0.004 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00443 (31932) covalent geometry : angle 0.70007 (43152) hydrogen bonds : bond 0.03401 ( 1209) hydrogen bonds : angle 4.32656 ( 3513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 293 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.6308 (pmm) cc_final: 0.5936 (pmm) REVERT: D 257 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8903 (tp30) REVERT: D 287 ARG cc_start: 0.9463 (tmm-80) cc_final: 0.8970 (tmm-80) REVERT: B 148 MET cc_start: 0.3535 (ttt) cc_final: 0.3142 (ttm) REVERT: B 151 MET cc_start: 0.2819 (OUTLIER) cc_final: 0.2501 (ttp) REVERT: B 154 MET cc_start: 0.5509 (pmm) cc_final: 0.5222 (pmm) REVERT: B 249 ASP cc_start: 0.9294 (m-30) cc_final: 0.9027 (m-30) REVERT: B 257 GLU cc_start: 0.9225 (tp30) cc_final: 0.8730 (tp30) REVERT: B 269 MET cc_start: 0.4869 (mmp) cc_final: 0.4614 (mmp) REVERT: B 295 GLU cc_start: 0.9289 (tp30) cc_final: 0.8848 (tp30) REVERT: L 12 LEU cc_start: 0.9465 (mm) cc_final: 0.9247 (mm) REVERT: L 148 MET cc_start: 0.3763 (ttp) cc_final: 0.3330 (ttm) REVERT: L 154 MET cc_start: 0.5864 (pmm) cc_final: 0.5535 (pmm) REVERT: L 257 GLU cc_start: 0.9208 (tp30) cc_final: 0.8733 (tp30) REVERT: L 289 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8793 (mp0) REVERT: J 12 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9179 (mm) REVERT: J 154 MET cc_start: 0.6129 (pmm) cc_final: 0.5780 (pmm) REVERT: J 256 LYS cc_start: 0.9521 (ttmm) cc_final: 0.9142 (ttmt) REVERT: J 295 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8766 (tm-30) REVERT: F 148 MET cc_start: 0.3186 (ttp) cc_final: 0.2784 (ttm) REVERT: F 151 MET cc_start: 0.2402 (OUTLIER) cc_final: 0.1914 (ttp) REVERT: F 154 MET cc_start: 0.5934 (pmm) cc_final: 0.5623 (pmm) REVERT: F 187 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.7215 (m-10) REVERT: F 289 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8668 (mt-10) REVERT: F 295 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8749 (tm-30) REVERT: H 154 MET cc_start: 0.5385 (pmm) cc_final: 0.5061 (pmm) REVERT: H 249 ASP cc_start: 0.9278 (m-30) cc_final: 0.8967 (m-30) REVERT: H 257 GLU cc_start: 0.9318 (tp30) cc_final: 0.8688 (tp30) REVERT: C 114 MET cc_start: 0.6053 (ptp) cc_final: 0.5665 (ppp) REVERT: C 173 MET cc_start: 0.7681 (mmm) cc_final: 0.7464 (mmm) REVERT: C 178 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8433 (mmmm) REVERT: C 249 ASP cc_start: 0.9364 (m-30) cc_final: 0.9104 (m-30) REVERT: C 256 LYS cc_start: 0.9523 (ttmm) cc_final: 0.9273 (ptmm) REVERT: A 92 ILE cc_start: 0.3453 (OUTLIER) cc_final: 0.3206 (pt) REVERT: A 114 MET cc_start: 0.5855 (ptp) cc_final: 0.5552 (ppp) REVERT: A 173 MET cc_start: 0.7610 (mmm) cc_final: 0.7315 (mmm) REVERT: A 178 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8439 (mmmm) REVERT: A 284 GLU cc_start: 0.9113 (pp20) cc_final: 0.8786 (pp20) REVERT: A 285 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8804 (mt-10) REVERT: A 287 ARG cc_start: 0.9630 (tmm-80) cc_final: 0.9168 (tmm-80) REVERT: A 290 LYS cc_start: 0.9639 (ptpt) cc_final: 0.9253 (ptpp) REVERT: K 114 MET cc_start: 0.5857 (ptp) cc_final: 0.5364 (ppp) REVERT: K 150 MET cc_start: 0.8789 (ptp) cc_final: 0.8525 (pmm) REVERT: K 287 ARG cc_start: 0.9619 (ttp80) cc_final: 0.9069 (tmm-80) REVERT: I 178 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8467 (mmmm) REVERT: I 191 TYR cc_start: 0.7861 (t80) cc_final: 0.7511 (t80) REVERT: I 249 ASP cc_start: 0.9422 (m-30) cc_final: 0.9160 (m-30) REVERT: I 254 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9363 (tp) REVERT: I 256 LYS cc_start: 0.9511 (ttmm) cc_final: 0.8994 (ttpp) REVERT: I 257 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8990 (tm-30) REVERT: I 284 GLU cc_start: 0.9279 (pp20) cc_final: 0.8916 (pp20) REVERT: I 294 ARG cc_start: 0.9397 (mmm-85) cc_final: 0.9094 (mmm-85) REVERT: E 4 TYR cc_start: 0.7479 (p90) cc_final: 0.6095 (p90) REVERT: E 62 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7457 (m) REVERT: E 114 MET cc_start: 0.5982 (ptp) cc_final: 0.5524 (ppp) REVERT: E 150 MET cc_start: 0.8832 (ptp) cc_final: 0.8465 (pmm) REVERT: E 280 GLN cc_start: 0.9038 (mp10) cc_final: 0.8732 (mp10) REVERT: G 92 ILE cc_start: 0.3667 (OUTLIER) cc_final: 0.3428 (pt) REVERT: G 173 MET cc_start: 0.7625 (mmm) cc_final: 0.7341 (mmm) REVERT: G 178 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8531 (mmmm) REVERT: G 280 GLN cc_start: 0.8986 (mp10) cc_final: 0.8660 (mp10) REVERT: G 287 ARG cc_start: 0.9621 (ttp80) cc_final: 0.9075 (tmm-80) REVERT: G 290 LYS cc_start: 0.9613 (ptpt) cc_final: 0.9289 (ptpp) REVERT: M 53 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8474 (ppp) REVERT: P 53 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8273 (tmm) REVERT: O 53 MET cc_start: 0.8582 (ppp) cc_final: 0.8292 (ppp) REVERT: N 158 PHE cc_start: 0.8268 (t80) cc_final: 0.8023 (t80) outliers start: 106 outliers final: 43 residues processed: 368 average time/residue: 0.1878 time to fit residues: 111.0702 Evaluate side-chains 329 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 274 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 184 VAL Chi-restraints excluded: chain L residue 285 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 187 TRP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain R residue 176 TYR Chi-restraints excluded: chain Q residue 36 TYR Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain Q residue 176 TYR Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 159 TYR Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 176 TYR Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 176 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 17 optimal weight: 40.0000 chunk 210 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 40.0000 chunk 51 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.083913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.060989 restraints weight = 170595.741| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 6.67 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31932 Z= 0.126 Angle : 0.638 10.407 43152 Z= 0.324 Chirality : 0.044 0.294 4500 Planarity : 0.004 0.049 5622 Dihedral : 4.336 23.658 4226 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.38 % Allowed : 17.67 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 3762 helix: 1.54 (0.14), residues: 1380 sheet: -1.49 (0.20), residues: 702 loop : -3.33 (0.12), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 287 TYR 0.018 0.001 TYR E 298 PHE 0.014 0.001 PHE G 110 TRP 0.015 0.001 TRP B 187 HIS 0.003 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00277 (31932) covalent geometry : angle 0.63761 (43152) hydrogen bonds : bond 0.03140 ( 1209) hydrogen bonds : angle 4.21235 ( 3513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 327 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.6122 (pmm) cc_final: 0.5689 (pmm) REVERT: D 257 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8889 (tp30) REVERT: D 287 ARG cc_start: 0.9496 (tmm-80) cc_final: 0.8969 (tmm-80) REVERT: B 148 MET cc_start: 0.3763 (ttt) cc_final: 0.3400 (ttm) REVERT: B 151 MET cc_start: 0.2385 (OUTLIER) cc_final: 0.2047 (ttp) REVERT: B 154 MET cc_start: 0.5464 (pmm) cc_final: 0.5119 (pmm) REVERT: B 249 ASP cc_start: 0.9303 (m-30) cc_final: 0.9001 (m-30) REVERT: B 256 LYS cc_start: 0.9551 (ttmt) cc_final: 0.9139 (ttpp) REVERT: B 269 MET cc_start: 0.4865 (mmp) cc_final: 0.4600 (mmp) REVERT: B 280 GLN cc_start: 0.8478 (mp10) cc_final: 0.8229 (mp10) REVERT: B 295 GLU cc_start: 0.9249 (tp30) cc_final: 0.8784 (tp30) REVERT: L 12 LEU cc_start: 0.9520 (mm) cc_final: 0.9206 (mm) REVERT: L 148 MET cc_start: 0.3791 (ttp) cc_final: 0.3396 (ttm) REVERT: L 151 MET cc_start: 0.2526 (OUTLIER) cc_final: 0.2041 (ttp) REVERT: L 154 MET cc_start: 0.5859 (pmm) cc_final: 0.5550 (pmm) REVERT: L 256 LYS cc_start: 0.9577 (ttmt) cc_final: 0.9184 (ttpp) REVERT: L 257 GLU cc_start: 0.9244 (tp30) cc_final: 0.8796 (tp30) REVERT: L 289 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8665 (mm-30) REVERT: J 12 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9124 (mm) REVERT: J 154 MET cc_start: 0.6104 (pmm) cc_final: 0.5716 (pmm) REVERT: J 249 ASP cc_start: 0.9267 (m-30) cc_final: 0.8993 (m-30) REVERT: J 256 LYS cc_start: 0.9535 (ttmm) cc_final: 0.9174 (ttmt) REVERT: J 270 MET cc_start: 0.5515 (mtt) cc_final: 0.5094 (ptp) REVERT: J 294 ARG cc_start: 0.9508 (mmm-85) cc_final: 0.9304 (mmm-85) REVERT: J 295 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8718 (tm-30) REVERT: F 148 MET cc_start: 0.3323 (ttp) cc_final: 0.2931 (ttm) REVERT: F 151 MET cc_start: 0.2752 (ttp) cc_final: 0.2266 (ttp) REVERT: F 154 MET cc_start: 0.5953 (pmm) cc_final: 0.5612 (pmm) REVERT: F 249 ASP cc_start: 0.9273 (m-30) cc_final: 0.8967 (m-30) REVERT: F 289 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8713 (mt-10) REVERT: F 295 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8659 (tm-30) REVERT: H 154 MET cc_start: 0.5332 (pmm) cc_final: 0.4908 (pmm) REVERT: H 249 ASP cc_start: 0.9329 (m-30) cc_final: 0.8995 (m-30) REVERT: H 256 LYS cc_start: 0.9573 (ttmm) cc_final: 0.9281 (ttmm) REVERT: H 257 GLU cc_start: 0.9329 (tp30) cc_final: 0.9107 (tm-30) REVERT: H 289 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8698 (pt0) REVERT: C 114 MET cc_start: 0.6049 (ptp) cc_final: 0.5780 (ppp) REVERT: C 178 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8417 (mmmm) REVERT: C 256 LYS cc_start: 0.9539 (ttmm) cc_final: 0.9283 (ptmm) REVERT: C 284 GLU cc_start: 0.9395 (pp20) cc_final: 0.9118 (pp20) REVERT: C 291 GLU cc_start: 0.9600 (OUTLIER) cc_final: 0.9119 (pp20) REVERT: A 92 ILE cc_start: 0.3682 (OUTLIER) cc_final: 0.3444 (pt) REVERT: A 173 MET cc_start: 0.7601 (mmm) cc_final: 0.7340 (mmm) REVERT: A 178 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8356 (mmmm) REVERT: A 280 GLN cc_start: 0.8933 (mp10) cc_final: 0.8619 (mp10) REVERT: A 284 GLU cc_start: 0.9111 (pp20) cc_final: 0.8758 (pp20) REVERT: A 285 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 287 ARG cc_start: 0.9646 (tmm-80) cc_final: 0.9154 (tmm-80) REVERT: A 290 LYS cc_start: 0.9604 (ptpt) cc_final: 0.9269 (ptpp) REVERT: K 114 MET cc_start: 0.5873 (ptp) cc_final: 0.5425 (ppp) REVERT: K 150 MET cc_start: 0.8766 (ptp) cc_final: 0.8398 (pmm) REVERT: K 280 GLN cc_start: 0.8998 (mp10) cc_final: 0.8736 (mp10) REVERT: K 284 GLU cc_start: 0.9193 (pp20) cc_final: 0.8481 (pp20) REVERT: K 287 ARG cc_start: 0.9621 (ttp80) cc_final: 0.8873 (tmm-80) REVERT: K 288 LEU cc_start: 0.9626 (mt) cc_final: 0.9093 (mt) REVERT: I 48 TYR cc_start: 0.8771 (t80) cc_final: 0.8550 (t80) REVERT: I 178 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8533 (mmmm) REVERT: I 191 TYR cc_start: 0.7794 (t80) cc_final: 0.7504 (t80) REVERT: I 249 ASP cc_start: 0.9444 (m-30) cc_final: 0.9161 (m-30) REVERT: I 254 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9426 (tp) REVERT: I 256 LYS cc_start: 0.9539 (ttmm) cc_final: 0.9121 (ttpp) REVERT: I 257 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8991 (tp30) REVERT: I 284 GLU cc_start: 0.9292 (pp20) cc_final: 0.9002 (pp20) REVERT: I 287 ARG cc_start: 0.9627 (ttp80) cc_final: 0.9142 (ttp80) REVERT: I 289 GLU cc_start: 0.9093 (mp0) cc_final: 0.8859 (mp0) REVERT: I 294 ARG cc_start: 0.9346 (mmm-85) cc_final: 0.9050 (mmm-85) REVERT: E 4 TYR cc_start: 0.7547 (p90) cc_final: 0.6999 (p90) REVERT: E 114 MET cc_start: 0.6108 (ptp) cc_final: 0.5690 (ppp) REVERT: E 256 LYS cc_start: 0.9240 (ttmt) cc_final: 0.8898 (ttpp) REVERT: E 280 GLN cc_start: 0.9059 (mp10) cc_final: 0.8795 (mp10) REVERT: G 92 ILE cc_start: 0.3536 (OUTLIER) cc_final: 0.3301 (pt) REVERT: G 173 MET cc_start: 0.7541 (mmm) cc_final: 0.7284 (mmm) REVERT: G 178 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8543 (mmmm) REVERT: G 280 GLN cc_start: 0.9012 (mp10) cc_final: 0.8711 (mp10) REVERT: G 290 LYS cc_start: 0.9566 (ptpt) cc_final: 0.9262 (ptpp) REVERT: M 53 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8485 (ppp) REVERT: O 53 MET cc_start: 0.8602 (ppp) cc_final: 0.8285 (ppp) REVERT: O 158 PHE cc_start: 0.8126 (t80) cc_final: 0.7724 (m-80) REVERT: N 53 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8353 (ppp) REVERT: N 142 MET cc_start: 0.8866 (ptp) cc_final: 0.8558 (ptp) REVERT: N 158 PHE cc_start: 0.8187 (t80) cc_final: 0.7897 (t80) outliers start: 78 outliers final: 38 residues processed: 374 average time/residue: 0.1891 time to fit residues: 111.7731 Evaluate side-chains 348 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 184 VAL Chi-restraints excluded: chain L residue 285 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain P residue 159 TYR Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain N residue 53 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 116 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 136 optimal weight: 40.0000 chunk 252 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 321 optimal weight: 9.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 ASN D 49 HIS ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN ** R 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 ASN P 40 GLN P 164 ASN O 40 GLN O 144 ASN O 164 ASN N 40 GLN N 144 ASN N 164 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.082132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.058760 restraints weight = 173465.609| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 6.78 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.7785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31932 Z= 0.228 Angle : 0.731 12.959 43152 Z= 0.371 Chirality : 0.046 0.206 4500 Planarity : 0.005 0.050 5622 Dihedral : 4.641 25.026 4224 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.41 % Allowed : 19.20 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 3762 helix: 1.12 (0.14), residues: 1416 sheet: -1.72 (0.19), residues: 738 loop : -3.18 (0.13), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 294 TYR 0.018 0.002 TYR A 298 PHE 0.014 0.001 PHE G 110 TRP 0.011 0.001 TRP B 246 HIS 0.005 0.001 HIS P 35 Details of bonding type rmsd covalent geometry : bond 0.00483 (31932) covalent geometry : angle 0.73102 (43152) hydrogen bonds : bond 0.03524 ( 1209) hydrogen bonds : angle 4.45666 ( 3513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 289 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.6310 (pmm) cc_final: 0.5948 (pmm) REVERT: D 257 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8943 (tp30) REVERT: D 287 ARG cc_start: 0.9503 (tmm-80) cc_final: 0.8969 (tmm-80) REVERT: B 249 ASP cc_start: 0.9331 (m-30) cc_final: 0.9038 (m-30) REVERT: B 269 MET cc_start: 0.5149 (mmp) cc_final: 0.4874 (mmp) REVERT: B 280 GLN cc_start: 0.8496 (mp10) cc_final: 0.8231 (mp10) REVERT: B 295 GLU cc_start: 0.9311 (tp30) cc_final: 0.8879 (tp30) REVERT: L 12 LEU cc_start: 0.9514 (mm) cc_final: 0.9245 (mm) REVERT: J 12 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9129 (mm) REVERT: J 154 MET cc_start: 0.6382 (pmm) cc_final: 0.6019 (pmm) REVERT: J 249 ASP cc_start: 0.9285 (m-30) cc_final: 0.9004 (m-30) REVERT: J 256 LYS cc_start: 0.9523 (ttmm) cc_final: 0.9289 (ttmt) REVERT: J 295 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8823 (tm-30) REVERT: F 249 ASP cc_start: 0.9277 (m-30) cc_final: 0.8975 (m-30) REVERT: F 289 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8707 (mt-10) REVERT: F 294 ARG cc_start: 0.9494 (mmm-85) cc_final: 0.9269 (mmm-85) REVERT: F 295 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8812 (tm-30) REVERT: H 154 MET cc_start: 0.5813 (pmm) cc_final: 0.5437 (pmm) REVERT: H 249 ASP cc_start: 0.9321 (m-30) cc_final: 0.8972 (m-30) REVERT: H 289 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8879 (pt0) REVERT: C 114 MET cc_start: 0.6193 (ptp) cc_final: 0.5833 (ppp) REVERT: C 256 LYS cc_start: 0.9493 (ttmm) cc_final: 0.9245 (ptmm) REVERT: C 284 GLU cc_start: 0.9512 (pp20) cc_final: 0.9117 (pp20) REVERT: C 287 ARG cc_start: 0.9632 (ttp80) cc_final: 0.9345 (ttp80) REVERT: A 92 ILE cc_start: 0.3869 (OUTLIER) cc_final: 0.3500 (pt) REVERT: A 173 MET cc_start: 0.7502 (mmm) cc_final: 0.7299 (mmm) REVERT: A 284 GLU cc_start: 0.9168 (pp20) cc_final: 0.8549 (pp20) REVERT: A 285 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8946 (mt-10) REVERT: A 287 ARG cc_start: 0.9660 (tmm-80) cc_final: 0.9127 (tmm-80) REVERT: A 290 LYS cc_start: 0.9611 (ptpt) cc_final: 0.9272 (ptpp) REVERT: K 114 MET cc_start: 0.5978 (ptp) cc_final: 0.5626 (ppp) REVERT: K 287 ARG cc_start: 0.9631 (ttp80) cc_final: 0.9092 (tmm-80) REVERT: I 48 TYR cc_start: 0.8711 (t80) cc_final: 0.8450 (t80) REVERT: I 178 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8625 (mmmm) REVERT: I 249 ASP cc_start: 0.9385 (m-30) cc_final: 0.9113 (m-30) REVERT: I 254 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9369 (tp) REVERT: I 256 LYS cc_start: 0.9538 (ttmm) cc_final: 0.9088 (ttpp) REVERT: I 257 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.9003 (tm-30) REVERT: I 284 GLU cc_start: 0.9354 (pp20) cc_final: 0.9084 (pp20) REVERT: I 287 ARG cc_start: 0.9622 (ttp80) cc_final: 0.9133 (ttp80) REVERT: I 294 ARG cc_start: 0.9387 (mmm-85) cc_final: 0.9004 (mmm-85) REVERT: E 62 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7655 (m) REVERT: E 114 MET cc_start: 0.6033 (ptp) cc_final: 0.5640 (ppp) REVERT: E 150 MET cc_start: 0.8817 (ptp) cc_final: 0.8540 (pmm) REVERT: G 92 ILE cc_start: 0.3926 (OUTLIER) cc_final: 0.3594 (pt) REVERT: G 178 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8691 (mmmm) REVERT: G 280 GLN cc_start: 0.9004 (mp10) cc_final: 0.8700 (mp10) REVERT: G 290 LYS cc_start: 0.9575 (ptpt) cc_final: 0.9275 (ptpp) REVERT: M 53 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8504 (ppp) REVERT: Q 53 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8434 (ppp) REVERT: Q 142 MET cc_start: 0.8697 (ptt) cc_final: 0.7889 (ppp) REVERT: P 9 PHE cc_start: 0.8466 (m-80) cc_final: 0.7994 (m-80) REVERT: O 9 PHE cc_start: 0.8716 (m-80) cc_final: 0.7982 (m-80) REVERT: O 158 PHE cc_start: 0.8498 (t80) cc_final: 0.8082 (m-80) REVERT: N 53 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8369 (ppp) REVERT: N 142 MET cc_start: 0.8939 (ptp) cc_final: 0.8586 (ptp) outliers start: 79 outliers final: 41 residues processed: 342 average time/residue: 0.1930 time to fit residues: 104.5725 Evaluate side-chains 328 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 184 VAL Chi-restraints excluded: chain L residue 285 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 187 TRP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 158 PHE Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 36 TYR Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain P residue 159 TYR Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain N residue 159 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 57 optimal weight: 0.0870 chunk 176 optimal weight: 20.0000 chunk 296 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 212 optimal weight: 0.5980 chunk 364 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 45 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 overall best weight: 2.1368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 261 GLN ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 ASN ** I 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 GLN R 164 ASN P 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.084629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.061807 restraints weight = 171423.080| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 6.69 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31932 Z= 0.143 Angle : 0.670 10.986 43152 Z= 0.339 Chirality : 0.045 0.263 4500 Planarity : 0.004 0.050 5622 Dihedral : 4.461 23.970 4224 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.58 % Allowed : 19.65 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 3762 helix: 1.43 (0.14), residues: 1380 sheet: -1.54 (0.20), residues: 702 loop : -3.27 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 294 TYR 0.018 0.001 TYR K 298 PHE 0.010 0.001 PHE D 57 TRP 0.008 0.001 TRP H 187 HIS 0.003 0.001 HIS I 266 Details of bonding type rmsd covalent geometry : bond 0.00318 (31932) covalent geometry : angle 0.66953 (43152) hydrogen bonds : bond 0.03158 ( 1209) hydrogen bonds : angle 4.35329 ( 3513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 306 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.6368 (pmm) cc_final: 0.5952 (pmm) REVERT: D 257 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8950 (tp30) REVERT: D 287 ARG cc_start: 0.9531 (tmm-80) cc_final: 0.8981 (tmm-80) REVERT: B 249 ASP cc_start: 0.9317 (m-30) cc_final: 0.9016 (m-30) REVERT: B 256 LYS cc_start: 0.9498 (ttmt) cc_final: 0.9029 (ttpp) REVERT: B 269 MET cc_start: 0.5220 (mmp) cc_final: 0.4814 (mmp) REVERT: B 280 GLN cc_start: 0.8454 (mp10) cc_final: 0.8191 (mp10) REVERT: B 295 GLU cc_start: 0.9291 (tp30) cc_final: 0.8874 (tm-30) REVERT: L 12 LEU cc_start: 0.9561 (mm) cc_final: 0.9339 (mt) REVERT: L 256 LYS cc_start: 0.9541 (ttmt) cc_final: 0.9143 (ttpp) REVERT: L 289 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8680 (mm-30) REVERT: J 12 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9131 (mm) REVERT: J 154 MET cc_start: 0.6292 (pmm) cc_final: 0.5890 (pmm) REVERT: J 249 ASP cc_start: 0.9286 (m-30) cc_final: 0.8985 (m-30) REVERT: J 256 LYS cc_start: 0.9550 (ttmm) cc_final: 0.9283 (ttmt) REVERT: J 270 MET cc_start: 0.5951 (mtt) cc_final: 0.5591 (ptp) REVERT: J 295 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8773 (tm-30) REVERT: F 249 ASP cc_start: 0.9295 (m-30) cc_final: 0.8992 (m-30) REVERT: F 256 LYS cc_start: 0.9580 (ttmm) cc_final: 0.9325 (ttmm) REVERT: F 289 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8632 (mt-10) REVERT: F 294 ARG cc_start: 0.9443 (mmm-85) cc_final: 0.9171 (mmm-85) REVERT: F 295 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8792 (tm-30) REVERT: H 154 MET cc_start: 0.5766 (pmm) cc_final: 0.5378 (pmm) REVERT: H 249 ASP cc_start: 0.9342 (m-30) cc_final: 0.8978 (m-30) REVERT: H 256 LYS cc_start: 0.9571 (ttmm) cc_final: 0.9236 (ttmm) REVERT: H 289 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8794 (pt0) REVERT: C 114 MET cc_start: 0.6073 (ptp) cc_final: 0.5839 (ppp) REVERT: C 177 GLN cc_start: 0.7894 (pm20) cc_final: 0.7612 (pm20) REVERT: C 256 LYS cc_start: 0.9492 (ttmm) cc_final: 0.9198 (ptmm) REVERT: C 284 GLU cc_start: 0.9412 (pp20) cc_final: 0.9030 (pp20) REVERT: C 287 ARG cc_start: 0.9637 (ttp80) cc_final: 0.9355 (ttp80) REVERT: A 92 ILE cc_start: 0.3647 (OUTLIER) cc_final: 0.3381 (pt) REVERT: A 114 MET cc_start: 0.4008 (ppp) cc_final: 0.3527 (pmm) REVERT: A 173 MET cc_start: 0.7666 (mmm) cc_final: 0.7405 (mmm) REVERT: A 284 GLU cc_start: 0.9098 (pp20) cc_final: 0.8779 (pp20) REVERT: A 285 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8700 (mt-10) REVERT: A 287 ARG cc_start: 0.9658 (tmm-80) cc_final: 0.9224 (tmm-80) REVERT: A 290 LYS cc_start: 0.9605 (ptpt) cc_final: 0.9266 (ptpp) REVERT: K 8 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8374 (p0) REVERT: K 114 MET cc_start: 0.5987 (ptp) cc_final: 0.5581 (ppp) REVERT: K 280 GLN cc_start: 0.9035 (mp10) cc_final: 0.8830 (mp10) REVERT: K 284 GLU cc_start: 0.9154 (pp20) cc_final: 0.8442 (pp20) REVERT: K 287 ARG cc_start: 0.9621 (ttp80) cc_final: 0.8961 (tmm-80) REVERT: I 48 TYR cc_start: 0.8697 (t80) cc_final: 0.8428 (t80) REVERT: I 177 GLN cc_start: 0.8302 (pm20) cc_final: 0.8068 (pm20) REVERT: I 178 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8561 (mmmm) REVERT: I 191 TYR cc_start: 0.7732 (t80) cc_final: 0.7505 (t80) REVERT: I 249 ASP cc_start: 0.9405 (m-30) cc_final: 0.9122 (m-30) REVERT: I 254 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9438 (tp) REVERT: I 256 LYS cc_start: 0.9542 (ttmm) cc_final: 0.9093 (ttpp) REVERT: I 257 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9002 (tp30) REVERT: I 284 GLU cc_start: 0.9331 (pp20) cc_final: 0.9020 (pp20) REVERT: I 287 ARG cc_start: 0.9633 (ttp80) cc_final: 0.9086 (ttp80) REVERT: E 62 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7683 (m) REVERT: E 114 MET cc_start: 0.6089 (ptp) cc_final: 0.5772 (ppp) REVERT: E 150 MET cc_start: 0.8779 (ptp) cc_final: 0.8436 (pmm) REVERT: E 256 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8900 (ttpp) REVERT: E 280 GLN cc_start: 0.9059 (mp10) cc_final: 0.8822 (mp10) REVERT: G 92 ILE cc_start: 0.3560 (OUTLIER) cc_final: 0.3293 (pt) REVERT: G 178 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8677 (mmmm) REVERT: G 280 GLN cc_start: 0.9024 (mp10) cc_final: 0.8710 (mp10) REVERT: R 158 PHE cc_start: 0.8061 (t80) cc_final: 0.7585 (t80) REVERT: Q 142 MET cc_start: 0.8659 (ptt) cc_final: 0.7849 (pmm) REVERT: Q 158 PHE cc_start: 0.8199 (t80) cc_final: 0.7751 (m-80) REVERT: P 9 PHE cc_start: 0.8423 (m-80) cc_final: 0.7941 (m-80) REVERT: O 9 PHE cc_start: 0.8573 (m-80) cc_final: 0.7924 (m-80) REVERT: O 53 MET cc_start: 0.8487 (ppp) cc_final: 0.8143 (ppp) REVERT: O 158 PHE cc_start: 0.8315 (t80) cc_final: 0.7782 (m-80) REVERT: N 53 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8359 (ppp) REVERT: N 136 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: N 142 MET cc_start: 0.8934 (ptp) cc_final: 0.8527 (ptp) outliers start: 52 outliers final: 34 residues processed: 342 average time/residue: 0.1960 time to fit residues: 106.2483 Evaluate side-chains 335 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 184 VAL Chi-restraints excluded: chain L residue 285 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain M residue 158 PHE Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain P residue 159 TYR Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain N residue 159 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 10 optimal weight: 40.0000 chunk 315 optimal weight: 6.9990 chunk 58 optimal weight: 40.0000 chunk 23 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 322 optimal weight: 9.9990 chunk 82 optimal weight: 40.0000 chunk 52 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.081415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.058680 restraints weight = 175132.436| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 6.64 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.8073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31932 Z= 0.187 Angle : 0.719 12.023 43152 Z= 0.362 Chirality : 0.046 0.209 4500 Planarity : 0.005 0.052 5622 Dihedral : 4.577 24.017 4224 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 1.71 % Allowed : 19.50 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 3762 helix: 1.36 (0.14), residues: 1380 sheet: -1.57 (0.20), residues: 702 loop : -3.18 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 294 TYR 0.023 0.001 TYR E 191 PHE 0.019 0.001 PHE L 57 TRP 0.010 0.001 TRP J 246 HIS 0.004 0.001 HIS I 266 Details of bonding type rmsd covalent geometry : bond 0.00404 (31932) covalent geometry : angle 0.71894 (43152) hydrogen bonds : bond 0.03328 ( 1209) hydrogen bonds : angle 4.39596 ( 3513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 291 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.6379 (pmm) cc_final: 0.5977 (pmm) REVERT: D 257 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.8955 (tp30) REVERT: D 270 MET cc_start: 0.5440 (mtt) cc_final: 0.4912 (ptp) REVERT: D 287 ARG cc_start: 0.9510 (tmm-80) cc_final: 0.8942 (tmm-80) REVERT: B 249 ASP cc_start: 0.9333 (m-30) cc_final: 0.9039 (m-30) REVERT: B 256 LYS cc_start: 0.9484 (ttmt) cc_final: 0.9009 (ttpp) REVERT: B 269 MET cc_start: 0.5771 (mmp) cc_final: 0.5472 (mmp) REVERT: B 270 MET cc_start: 0.6721 (mtt) cc_final: 0.6372 (ptp) REVERT: B 280 GLN cc_start: 0.8459 (mp10) cc_final: 0.8159 (mp10) REVERT: B 295 GLU cc_start: 0.9315 (tp30) cc_final: 0.8876 (tp30) REVERT: L 12 LEU cc_start: 0.9561 (mm) cc_final: 0.9301 (mm) REVERT: J 12 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9151 (mm) REVERT: J 154 MET cc_start: 0.6359 (pmm) cc_final: 0.5968 (pmm) REVERT: J 249 ASP cc_start: 0.9289 (m-30) cc_final: 0.8984 (m-30) REVERT: J 256 LYS cc_start: 0.9567 (ttmm) cc_final: 0.9279 (ttmt) REVERT: J 270 MET cc_start: 0.6184 (mtt) cc_final: 0.5672 (ptp) REVERT: J 295 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8795 (tm-30) REVERT: F 249 ASP cc_start: 0.9290 (m-30) cc_final: 0.8988 (m-30) REVERT: F 289 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8718 (mt-10) REVERT: F 295 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8787 (tm-30) REVERT: H 151 MET cc_start: 0.3069 (OUTLIER) cc_final: 0.2650 (ttp) REVERT: H 154 MET cc_start: 0.5908 (pmm) cc_final: 0.5538 (pmm) REVERT: H 249 ASP cc_start: 0.9325 (m-30) cc_final: 0.8950 (m-30) REVERT: C 114 MET cc_start: 0.6146 (ptp) cc_final: 0.5864 (ppp) REVERT: C 256 LYS cc_start: 0.9487 (ttmm) cc_final: 0.9194 (ptmm) REVERT: C 284 GLU cc_start: 0.9436 (pp20) cc_final: 0.9075 (pp20) REVERT: C 288 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.8968 (mm) REVERT: C 294 ARG cc_start: 0.9389 (mmm-85) cc_final: 0.9076 (mmm-85) REVERT: A 92 ILE cc_start: 0.3988 (OUTLIER) cc_final: 0.3738 (pt) REVERT: A 284 GLU cc_start: 0.9138 (pp20) cc_final: 0.8840 (pp20) REVERT: A 285 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8782 (mt-10) REVERT: A 287 ARG cc_start: 0.9682 (tmm-80) cc_final: 0.9256 (tmm-80) REVERT: A 290 LYS cc_start: 0.9582 (ptpt) cc_final: 0.9269 (ptpp) REVERT: K 114 MET cc_start: 0.5950 (ptp) cc_final: 0.5548 (ppp) REVERT: K 287 ARG cc_start: 0.9642 (ttp80) cc_final: 0.9081 (tmm-80) REVERT: K 294 ARG cc_start: 0.9606 (mtp180) cc_final: 0.9384 (mmm-85) REVERT: I 48 TYR cc_start: 0.8730 (t80) cc_final: 0.8467 (t80) REVERT: I 177 GLN cc_start: 0.8370 (pm20) cc_final: 0.8122 (pm20) REVERT: I 178 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8667 (mmmm) REVERT: I 191 TYR cc_start: 0.7645 (t80) cc_final: 0.7374 (t80) REVERT: I 249 ASP cc_start: 0.9395 (m-30) cc_final: 0.9124 (m-30) REVERT: I 254 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9367 (tp) REVERT: I 256 LYS cc_start: 0.9541 (ttmm) cc_final: 0.9110 (ttpp) REVERT: I 257 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.9048 (tm-30) REVERT: I 284 GLU cc_start: 0.9336 (pp20) cc_final: 0.9026 (pp20) REVERT: I 287 ARG cc_start: 0.9623 (ttp80) cc_final: 0.9107 (ttp80) REVERT: I 294 ARG cc_start: 0.9510 (mtp180) cc_final: 0.9196 (mmm-85) REVERT: E 62 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7755 (m) REVERT: E 114 MET cc_start: 0.6145 (ptp) cc_final: 0.5820 (ppp) REVERT: E 256 LYS cc_start: 0.9227 (ttmt) cc_final: 0.8943 (ttpp) REVERT: G 280 GLN cc_start: 0.9013 (mp10) cc_final: 0.8718 (mp10) REVERT: R 53 MET cc_start: 0.8469 (ppp) cc_final: 0.8026 (ppp) REVERT: R 158 PHE cc_start: 0.8235 (t80) cc_final: 0.7670 (t80) REVERT: Q 142 MET cc_start: 0.8685 (ptt) cc_final: 0.7862 (pmm) REVERT: Q 158 PHE cc_start: 0.8304 (t80) cc_final: 0.7874 (m-80) REVERT: P 9 PHE cc_start: 0.8378 (m-80) cc_final: 0.7818 (m-80) REVERT: O 9 PHE cc_start: 0.8593 (m-80) cc_final: 0.7850 (m-80) REVERT: O 53 MET cc_start: 0.8562 (ppp) cc_final: 0.8222 (ppp) REVERT: O 158 PHE cc_start: 0.8464 (t80) cc_final: 0.8002 (m-80) REVERT: N 53 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8338 (ppp) REVERT: N 142 MET cc_start: 0.8945 (ptp) cc_final: 0.8575 (ptp) outliers start: 56 outliers final: 38 residues processed: 333 average time/residue: 0.1829 time to fit residues: 97.8737 Evaluate side-chains 327 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 184 VAL Chi-restraints excluded: chain L residue 285 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 187 TRP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 159 TYR Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain N residue 159 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 157 optimal weight: 7.9990 chunk 80 optimal weight: 40.0000 chunk 72 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 279 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 324 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 353 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 HIS ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 HIS ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 HIS ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 ASN ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.082698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.059770 restraints weight = 170394.054| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 6.76 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.8121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31932 Z= 0.154 Angle : 0.710 14.220 43152 Z= 0.354 Chirality : 0.046 0.235 4500 Planarity : 0.005 0.053 5622 Dihedral : 4.531 24.285 4224 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.49 % Allowed : 19.77 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.13), residues: 3762 helix: 1.39 (0.14), residues: 1380 sheet: -1.54 (0.19), residues: 702 loop : -3.13 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 287 TYR 0.024 0.001 TYR F 4 PHE 0.019 0.001 PHE F 57 TRP 0.009 0.001 TRP F 187 HIS 0.003 0.001 HIS I 266 Details of bonding type rmsd covalent geometry : bond 0.00343 (31932) covalent geometry : angle 0.70992 (43152) hydrogen bonds : bond 0.03182 ( 1209) hydrogen bonds : angle 4.36364 ( 3513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.6285 (pmm) cc_final: 0.5874 (pmm) REVERT: D 257 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8954 (tp30) REVERT: D 287 ARG cc_start: 0.9521 (tmm-80) cc_final: 0.8928 (tmm-80) REVERT: B 249 ASP cc_start: 0.9320 (m-30) cc_final: 0.9016 (m-30) REVERT: B 256 LYS cc_start: 0.9502 (ttmt) cc_final: 0.9025 (ttpp) REVERT: B 269 MET cc_start: 0.5705 (mmp) cc_final: 0.5214 (mmp) REVERT: B 280 GLN cc_start: 0.8517 (mp10) cc_final: 0.8221 (mp10) REVERT: B 295 GLU cc_start: 0.9303 (tp30) cc_final: 0.8866 (tm-30) REVERT: L 12 LEU cc_start: 0.9559 (mm) cc_final: 0.9339 (mt) REVERT: J 12 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9129 (mm) REVERT: J 154 MET cc_start: 0.6407 (pmm) cc_final: 0.6013 (pmm) REVERT: J 249 ASP cc_start: 0.9284 (m-30) cc_final: 0.8972 (m-30) REVERT: J 256 LYS cc_start: 0.9545 (ttmm) cc_final: 0.9286 (ttmt) REVERT: J 270 MET cc_start: 0.6018 (mtt) cc_final: 0.5617 (ptp) REVERT: J 295 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8773 (tm-30) REVERT: F 249 ASP cc_start: 0.9285 (m-30) cc_final: 0.8990 (m-30) REVERT: F 289 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8751 (mt-10) REVERT: F 295 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8785 (tm-30) REVERT: H 154 MET cc_start: 0.5830 (pmm) cc_final: 0.5623 (pmm) REVERT: H 249 ASP cc_start: 0.9317 (m-30) cc_final: 0.8969 (m-30) REVERT: C 114 MET cc_start: 0.6207 (ptp) cc_final: 0.5918 (ppp) REVERT: C 256 LYS cc_start: 0.9504 (ttmm) cc_final: 0.9205 (ptmm) REVERT: C 284 GLU cc_start: 0.9429 (pp20) cc_final: 0.9089 (pp20) REVERT: C 288 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.8950 (mm) REVERT: C 294 ARG cc_start: 0.9366 (mmm-85) cc_final: 0.9038 (mmm-85) REVERT: A 92 ILE cc_start: 0.3446 (OUTLIER) cc_final: 0.3213 (pt) REVERT: A 114 MET cc_start: 0.3428 (ppp) cc_final: 0.3223 (pmm) REVERT: A 284 GLU cc_start: 0.9117 (pp20) cc_final: 0.8824 (pp20) REVERT: A 285 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8732 (mt-10) REVERT: A 287 ARG cc_start: 0.9677 (tmm-80) cc_final: 0.9238 (tmm-80) REVERT: A 290 LYS cc_start: 0.9574 (ptpt) cc_final: 0.9245 (ptpp) REVERT: K 114 MET cc_start: 0.6069 (ptp) cc_final: 0.5737 (ppp) REVERT: K 284 GLU cc_start: 0.9139 (pp20) cc_final: 0.8521 (pp20) REVERT: K 287 ARG cc_start: 0.9654 (ttp80) cc_final: 0.8997 (tmm-80) REVERT: K 294 ARG cc_start: 0.9591 (mtp180) cc_final: 0.9356 (mmm-85) REVERT: I 8 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8518 (p0) REVERT: I 48 TYR cc_start: 0.8726 (t80) cc_final: 0.8362 (t80) REVERT: I 177 GLN cc_start: 0.8398 (pm20) cc_final: 0.8053 (pm20) REVERT: I 178 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8613 (mmmm) REVERT: I 191 TYR cc_start: 0.7650 (t80) cc_final: 0.7383 (t80) REVERT: I 249 ASP cc_start: 0.9399 (m-30) cc_final: 0.9113 (m-30) REVERT: I 254 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9333 (tp) REVERT: I 256 LYS cc_start: 0.9552 (ttmm) cc_final: 0.9112 (ttpp) REVERT: I 257 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.9028 (tm-30) REVERT: I 284 GLU cc_start: 0.9357 (pp20) cc_final: 0.9051 (pp20) REVERT: I 287 ARG cc_start: 0.9621 (ttp80) cc_final: 0.9072 (ttp80) REVERT: E 62 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7870 (m) REVERT: E 114 MET cc_start: 0.6158 (ptp) cc_final: 0.5765 (ppp) REVERT: E 256 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8920 (ttpp) REVERT: E 280 GLN cc_start: 0.9068 (mp10) cc_final: 0.8823 (mp10) REVERT: G 114 MET cc_start: 0.6322 (pmm) cc_final: 0.5596 (ppp) REVERT: G 177 GLN cc_start: 0.8332 (pm20) cc_final: 0.7924 (pm20) REVERT: G 280 GLN cc_start: 0.9027 (mp10) cc_final: 0.8710 (mp10) REVERT: R 53 MET cc_start: 0.8537 (ppp) cc_final: 0.8121 (ppp) REVERT: R 158 PHE cc_start: 0.8146 (t80) cc_final: 0.7610 (t80) REVERT: Q 136 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: Q 142 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7873 (pmm) REVERT: P 9 PHE cc_start: 0.8343 (m-80) cc_final: 0.7989 (m-80) REVERT: P 136 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6980 (m-30) REVERT: O 9 PHE cc_start: 0.8462 (m-80) cc_final: 0.7801 (m-80) REVERT: O 53 MET cc_start: 0.8502 (ppp) cc_final: 0.8164 (ppp) REVERT: O 158 PHE cc_start: 0.8365 (t80) cc_final: 0.7886 (m-80) REVERT: N 53 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8222 (ppp) REVERT: N 136 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: N 142 MET cc_start: 0.8933 (ptp) cc_final: 0.8575 (ptp) outliers start: 49 outliers final: 33 residues processed: 321 average time/residue: 0.1894 time to fit residues: 97.0110 Evaluate side-chains 328 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 184 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 285 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 187 TRP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain R residue 159 TYR Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 159 TYR Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain N residue 159 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 270 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 342 optimal weight: 0.0010 chunk 324 optimal weight: 0.0770 chunk 104 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 overall best weight: 0.7946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.083737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.060676 restraints weight = 170930.302| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 6.79 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.8135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 31932 Z= 0.150 Angle : 0.805 59.164 43152 Z= 0.418 Chirality : 0.046 0.518 4500 Planarity : 0.005 0.063 5622 Dihedral : 4.547 24.340 4224 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.46 % Allowed : 19.80 % Favored : 78.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.13), residues: 3762 helix: 1.39 (0.14), residues: 1380 sheet: -1.53 (0.19), residues: 702 loop : -3.12 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG Q 54 TYR 0.017 0.001 TYR E 298 PHE 0.023 0.001 PHE M 158 TRP 0.008 0.001 TRP F 187 HIS 0.003 0.001 HIS I 266 Details of bonding type rmsd covalent geometry : bond 0.00340 (31932) covalent geometry : angle 0.80489 (43152) hydrogen bonds : bond 0.03221 ( 1209) hydrogen bonds : angle 4.36042 ( 3513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6031.86 seconds wall clock time: 104 minutes 40.94 seconds (6280.94 seconds total)