Starting phenix.real_space_refine on Fri Mar 6 18:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpp_14860/03_2026/7zpp_14860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpp_14860/03_2026/7zpp_14860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpp_14860/03_2026/7zpp_14860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpp_14860/03_2026/7zpp_14860.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpp_14860/03_2026/7zpp_14860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpp_14860/03_2026/7zpp_14860.cif" } resolution = 4.5 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 122 5.16 5 C 20877 2.51 5 N 5806 2.21 5 O 6288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 33171 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2201 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2075 Classifications: {'peptide': 256} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 244} Chain breaks: 1 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2123 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "D" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2090 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 246} Chain breaks: 1 Chain: "F" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2148 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1657 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Chain: "H" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 205} Chain: "I" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2201 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2075 Classifications: {'peptide': 256} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 244} Chain breaks: 1 Chain: "K" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2123 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "L" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2076 Classifications: {'peptide': 256} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 245} Chain breaks: 1 Chain: "N" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2131 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1657 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Chain: "P" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 205} Chain: "Q" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "R" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "S" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 8.07, per 1000 atoms: 0.24 Number of scatterers: 33171 At special positions: 0 Unit cell: (161.59, 210.21, 92.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 122 16.00 P 78 15.00 O 6288 8.00 N 5806 7.00 C 20877 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: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7254 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 62 sheets defined 52.2% alpha, 18.3% beta 20 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 18 through 27 removed outlier: 3.652A pdb=" N LEU A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 196 through 209 Processing helix chain 'A' and resid 209 through 216 removed outlier: 4.211A pdb=" N GLN A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 146 through 168 removed outlier: 3.714A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 196 through 216 Processing helix chain 'C' and resid 3 through 16 removed outlier: 4.118A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 146 through 168 removed outlier: 3.774A pdb=" N LEU C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 Processing helix chain 'C' and resid 196 through 219 removed outlier: 3.684A pdb=" N ILE C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 125 through 135 Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 173 through 187 Processing helix chain 'D' and resid 196 through 219 Processing helix chain 'E' and resid 1 through 3 No H-bonds generated for 'chain 'E' and resid 1 through 3' Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 95 through 110 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 125 through 136 Processing helix chain 'E' and resid 146 through 168 Processing helix chain 'E' and resid 173 through 187 Processing helix chain 'E' and resid 196 through 219 Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 18 through 27 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 40 through 46 removed outlier: 3.562A pdb=" N GLN F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 109 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 146 through 168 Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 196 through 218 Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'G' and resid 120 through 125 Processing helix chain 'G' and resid 125 through 136 Processing helix chain 'G' and resid 146 through 168 removed outlier: 3.658A pdb=" N LEU G 152 " --> pdb=" O GLN G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 187 Processing helix chain 'G' and resid 196 through 219 removed outlier: 3.722A pdb=" N ILE G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER G 214 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS G 217 " --> pdb=" O GLN G 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 120 through 125 Processing helix chain 'H' and resid 125 through 136 Processing helix chain 'H' and resid 146 through 168 removed outlier: 4.286A pdb=" N LEU H 152 " --> pdb=" O GLN H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 187 Processing helix chain 'H' and resid 196 through 208 Processing helix chain 'H' and resid 209 through 219 removed outlier: 4.444A pdb=" N GLN H 213 " --> pdb=" O ARG H 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 18 through 27 removed outlier: 3.652A pdb=" N LEU I 22 " --> pdb=" O ASP I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 40 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 120 through 125 Processing helix chain 'I' and resid 125 through 135 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 168 Processing helix chain 'I' and resid 169 through 171 No H-bonds generated for 'chain 'I' and resid 169 through 171' Processing helix chain 'I' and resid 173 through 187 Processing helix chain 'I' and resid 196 through 209 Processing helix chain 'I' and resid 209 through 216 removed outlier: 4.211A pdb=" N GLN I 213 " --> pdb=" O ARG I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 219 No H-bonds generated for 'chain 'I' and resid 217 through 219' Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 29 through 40 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 120 through 125 Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 146 through 168 removed outlier: 3.714A pdb=" N LEU J 152 " --> pdb=" O GLN J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 171 No H-bonds generated for 'chain 'J' and resid 169 through 171' Processing helix chain 'J' and resid 173 through 187 Processing helix chain 'J' and resid 196 through 216 Processing helix chain 'K' and resid 3 through 16 removed outlier: 4.118A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 40 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 95 through 110 Processing helix chain 'K' and resid 120 through 125 Processing helix chain 'K' and resid 125 through 136 Processing helix chain 'K' and resid 146 through 168 removed outlier: 3.775A pdb=" N LEU K 152 " --> pdb=" O GLN K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 187 Processing helix chain 'K' and resid 196 through 219 removed outlier: 3.682A pdb=" N ILE K 210 " --> pdb=" O GLU K 206 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 110 Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 125 through 135 Processing helix chain 'L' and resid 146 through 168 Processing helix chain 'L' and resid 173 through 187 Processing helix chain 'L' and resid 196 through 219 Processing helix chain 'M' and resid 4 through 16 Processing helix chain 'M' and resid 18 through 27 Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 95 through 110 Processing helix chain 'M' and resid 120 through 125 Processing helix chain 'M' and resid 125 through 136 Processing helix chain 'M' and resid 146 through 168 Processing helix chain 'M' and resid 173 through 187 Processing helix chain 'M' and resid 196 through 219 Processing helix chain 'M' and resid 267 through 269 No H-bonds generated for 'chain 'M' and resid 267 through 269' Processing helix chain 'N' and resid 5 through 16 Processing helix chain 'N' and resid 18 through 27 Processing helix chain 'N' and resid 29 through 40 Processing helix chain 'N' and resid 40 through 46 removed outlier: 3.562A pdb=" N GLN N 44 " --> pdb=" O CYS N 40 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN N 46 " --> pdb=" O VAL N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 109 Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 125 through 136 Processing helix chain 'N' and resid 146 through 168 Processing helix chain 'N' and resid 169 through 171 No H-bonds generated for 'chain 'N' and resid 169 through 171' Processing helix chain 'N' and resid 173 through 187 Processing helix chain 'N' and resid 196 through 218 Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 18 through 27 Processing helix chain 'O' and resid 29 through 40 Processing helix chain 'O' and resid 40 through 46 Processing helix chain 'O' and resid 95 through 110 Processing helix chain 'O' and resid 120 through 125 Processing helix chain 'O' and resid 125 through 136 Processing helix chain 'O' and resid 146 through 168 removed outlier: 3.658A pdb=" N LEU O 152 " --> pdb=" O GLN O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 187 Processing helix chain 'O' and resid 196 through 219 removed outlier: 3.722A pdb=" N ILE O 210 " --> pdb=" O GLU O 206 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER O 214 " --> pdb=" O ILE O 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER O 216 " --> pdb=" O GLN O 212 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS O 217 " --> pdb=" O GLN O 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 110 Processing helix chain 'P' and resid 120 through 125 Processing helix chain 'P' and resid 125 through 136 Processing helix chain 'P' and resid 146 through 168 removed outlier: 4.286A pdb=" N LEU P 152 " --> pdb=" O GLN P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 187 Processing helix chain 'P' and resid 196 through 208 Processing helix chain 'P' and resid 209 through 219 removed outlier: 4.444A pdb=" N GLN P 213 " --> pdb=" O ARG P 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.756A pdb=" N VAL A 77 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 79 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 64 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP A 63 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 224 removed outlier: 4.581A pdb=" N ARG A 222 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 246 removed outlier: 3.827A pdb=" N TRP A 245 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 264 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 260 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.546A pdb=" N GLU B 89 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 75 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 68 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TRP B 63 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 243 removed outlier: 5.058A pdb=" N GLY B 239 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR B 226 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG B 222 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 223 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 246 removed outlier: 3.775A pdb=" N TRP B 245 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 253 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 260 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 86 through 91 removed outlier: 3.804A pdb=" N ILE C 74 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 77 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP C 63 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 140 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.365A pdb=" N CYS C 224 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 223 " --> pdb=" O ILE C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 229 through 230 Processing sheet with id=AB2, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.605A pdb=" N TRP C 245 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.522A pdb=" N ILE D 74 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.855A pdb=" N VAL D 77 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP D 63 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 241 through 242 removed outlier: 3.544A pdb=" N PHE D 223 " --> pdb=" O ILE D 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 245 through 246 removed outlier: 4.241A pdb=" N TRP D 245 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 252 " --> pdb=" O TRP D 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR E 68 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR E 68 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TRP E 63 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 238 through 242 removed outlier: 6.109A pdb=" N CYS E 224 " --> pdb=" O PRO E 240 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE E 223 " --> pdb=" O ILE E 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 229 through 230 Processing sheet with id=AC2, first strand: chain 'E' and resid 245 through 246 removed outlier: 4.235A pdb=" N TRP E 245 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 68 through 70 removed outlier: 3.753A pdb=" N ILE F 74 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 68 through 70 removed outlier: 6.081A pdb=" N TRP F 63 " --> pdb=" O GLN F 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.800A pdb=" N ARG F 260 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 264 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 251 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS F 254 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL F 243 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 226 " --> pdb=" O GLN F 238 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS F 224 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AC7, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR G 87 " --> pdb=" O TRP G 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 74 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR G 87 " --> pdb=" O TRP G 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR G 68 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL G 77 " --> pdb=" O ASP G 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP G 66 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP G 63 " --> pdb=" O GLN G 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 86 through 87 removed outlier: 3.556A pdb=" N ILE H 74 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 86 through 87 removed outlier: 3.766A pdb=" N THR H 68 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL H 77 " --> pdb=" O ASP H 66 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP H 66 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP H 63 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 115 " --> pdb=" O GLU H 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR H 140 " --> pdb=" O LEU H 115 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 238 through 242 removed outlier: 6.237A pdb=" N CYS H 224 " --> pdb=" O PRO H 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 270 " --> pdb=" O TYR H 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AD4, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.883A pdb=" N TRP H 245 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 252 " --> pdb=" O TRP H 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 86 through 90 removed outlier: 3.757A pdb=" N VAL I 77 " --> pdb=" O ASP I 66 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP I 66 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL I 79 " --> pdb=" O GLN I 64 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN I 64 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP I 63 " --> pdb=" O GLN I 116 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 222 through 224 removed outlier: 4.581A pdb=" N ARG I 222 " --> pdb=" O VAL I 243 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 229 through 230 Processing sheet with id=AD8, first strand: chain 'I' and resid 245 through 246 removed outlier: 3.826A pdb=" N TRP I 245 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE I 264 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG I 260 " --> pdb=" O ASP I 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.547A pdb=" N GLU J 89 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE J 75 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR J 68 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP J 63 " --> pdb=" O GLN J 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 238 through 243 removed outlier: 5.059A pdb=" N GLY J 239 " --> pdb=" O TYR J 226 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N TYR J 226 " --> pdb=" O GLY J 239 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG J 222 " --> pdb=" O VAL J 243 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE J 223 " --> pdb=" O ILE J 272 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 245 through 246 removed outlier: 3.775A pdb=" N TRP J 245 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL J 253 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 260 " --> pdb=" O ASP J 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 86 through 91 removed outlier: 3.802A pdb=" N ILE K 74 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL K 77 " --> pdb=" O ASP K 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP K 63 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR K 140 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 238 through 242 removed outlier: 6.365A pdb=" N CYS K 224 " --> pdb=" O PRO K 240 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE K 223 " --> pdb=" O ILE K 272 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 229 through 230 Processing sheet with id=AE6, first strand: chain 'K' and resid 245 through 246 removed outlier: 3.605A pdb=" N TRP K 245 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.522A pdb=" N ILE L 74 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.854A pdb=" N VAL L 77 " --> pdb=" O ASP L 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP L 63 " --> pdb=" O GLN L 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 241 through 242 removed outlier: 3.545A pdb=" N PHE L 223 " --> pdb=" O ILE L 272 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 245 through 246 removed outlier: 4.241A pdb=" N TRP L 245 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL L 252 " --> pdb=" O TRP L 245 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR M 68 " --> pdb=" O ILE M 75 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR M 68 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP M 63 " --> pdb=" O GLN M 116 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 238 through 242 removed outlier: 6.109A pdb=" N CYS M 224 " --> pdb=" O PRO M 240 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE M 223 " --> pdb=" O ILE M 272 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 229 through 230 Processing sheet with id=AF6, first strand: chain 'M' and resid 245 through 246 removed outlier: 4.235A pdb=" N TRP M 245 " --> pdb=" O VAL M 252 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 68 through 70 removed outlier: 3.752A pdb=" N ILE N 74 " --> pdb=" O VAL N 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 68 through 70 removed outlier: 6.081A pdb=" N TRP N 63 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 260 through 265 removed outlier: 3.800A pdb=" N ARG N 260 " --> pdb=" O ASP N 255 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE N 264 " --> pdb=" O ILE N 251 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE N 251 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS N 254 " --> pdb=" O VAL N 243 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL N 243 " --> pdb=" O LYS N 254 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR N 226 " --> pdb=" O GLN N 238 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS N 224 " --> pdb=" O PRO N 240 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 229 through 230 Processing sheet with id=AG2, first strand: chain 'O' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR O 87 " --> pdb=" O TRP O 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE O 74 " --> pdb=" O VAL O 91 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR O 87 " --> pdb=" O TRP O 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR O 68 " --> pdb=" O ILE O 75 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL O 77 " --> pdb=" O ASP O 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP O 66 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP O 63 " --> pdb=" O GLN O 116 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 86 through 87 removed outlier: 3.556A pdb=" N ILE P 74 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 86 through 87 removed outlier: 3.766A pdb=" N THR P 68 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL P 77 " --> pdb=" O ASP P 66 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP P 66 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TRP P 63 " --> pdb=" O GLN P 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU P 115 " --> pdb=" O GLU P 138 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR P 140 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 238 through 242 removed outlier: 6.237A pdb=" N CYS P 224 " --> pdb=" O PRO P 240 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS P 270 " --> pdb=" O TYR P 225 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 229 through 230 Processing sheet with id=AG8, first strand: chain 'P' and resid 245 through 246 removed outlier: 3.882A pdb=" N TRP P 245 " --> pdb=" O VAL P 252 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL P 252 " --> pdb=" O TRP P 245 " (cutoff:3.500A) 1714 hydrogen bonds defined for protein. 5010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 7.84 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9808 1.34 - 1.46: 5962 1.46 - 1.57: 17989 1.57 - 1.69: 154 1.69 - 1.81: 206 Bond restraints: 34119 Sorted by residual: bond pdb=" CA PRO L 273 " pdb=" C PRO L 273 " ideal model delta sigma weight residual 1.514 1.525 -0.011 5.50e-03 3.31e+04 3.87e+00 bond pdb=" CA PRO D 273 " pdb=" C PRO D 273 " ideal model delta sigma weight residual 1.514 1.525 -0.011 5.50e-03 3.31e+04 3.81e+00 bond pdb=" N GLU E 219 " pdb=" CA GLU E 219 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.44e-02 4.82e+03 3.51e+00 bond pdb=" N GLU M 219 " pdb=" CA GLU M 219 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.44e-02 4.82e+03 3.41e+00 bond pdb=" CA PRO F 273 " pdb=" C PRO F 273 " ideal model delta sigma weight residual 1.514 1.506 0.009 5.50e-03 3.31e+04 2.46e+00 ... (remaining 34114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 46061 2.61 - 5.22: 374 5.22 - 7.84: 64 7.84 - 10.45: 8 10.45 - 13.06: 8 Bond angle restraints: 46515 Sorted by residual: angle pdb=" C GLN E 218 " pdb=" N GLU E 219 " pdb=" CA GLU E 219 " ideal model delta sigma weight residual 122.55 110.04 12.51 2.03e+00 2.43e-01 3.80e+01 angle pdb=" C GLN M 218 " pdb=" N GLU M 219 " pdb=" CA GLU M 219 " ideal model delta sigma weight residual 122.55 110.09 12.46 2.03e+00 2.43e-01 3.77e+01 angle pdb=" CB ARG O 189 " pdb=" CG ARG O 189 " pdb=" CD ARG O 189 " ideal model delta sigma weight residual 111.30 121.95 -10.65 2.30e+00 1.89e-01 2.14e+01 angle pdb=" CB ARG G 189 " pdb=" CG ARG G 189 " pdb=" CD ARG G 189 " ideal model delta sigma weight residual 111.30 121.93 -10.63 2.30e+00 1.89e-01 2.13e+01 angle pdb=" C THR O 103 " pdb=" N MET O 104 " pdb=" CA MET O 104 " ideal model delta sigma weight residual 121.14 113.07 8.07 1.75e+00 3.27e-01 2.13e+01 ... (remaining 46510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 19552 34.44 - 68.88: 495 68.88 - 103.31: 62 103.31 - 137.75: 0 137.75 - 172.19: 4 Dihedral angle restraints: 20113 sinusoidal: 8860 harmonic: 11253 Sorted by residual: dihedral pdb=" CA ILE D 187 " pdb=" C ILE D 187 " pdb=" N LYS D 188 " pdb=" CA LYS D 188 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ILE L 187 " pdb=" C ILE L 187 " pdb=" N LYS L 188 " pdb=" CA LYS L 188 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA TYR B 70 " pdb=" C TYR B 70 " pdb=" N GLU B 71 " pdb=" CA GLU B 71 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 20110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3513 0.038 - 0.075: 960 0.075 - 0.113: 415 0.113 - 0.151: 105 0.151 - 0.188: 13 Chirality restraints: 5006 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CB VAL F 153 " pdb=" CA VAL F 153 " pdb=" CG1 VAL F 153 " pdb=" CG2 VAL F 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CB ILE J 221 " pdb=" CA ILE J 221 " pdb=" CG1 ILE J 221 " pdb=" CG2 ILE J 221 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 5003 not shown) Planarity restraints: 5714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 28 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 29 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 28 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO I 29 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO I 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 29 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 272 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO D 273 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " -0.026 5.00e-02 4.00e+02 ... (remaining 5711 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1270 2.71 - 3.26: 33763 3.26 - 3.81: 56135 3.81 - 4.35: 67169 4.35 - 4.90: 108427 Nonbonded interactions: 266764 Sorted by model distance: nonbonded pdb=" OG1 THR I 95 " pdb=" OE1 GLU I 98 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR A 95 " pdb=" OE1 GLU A 98 " model vdw 2.167 3.040 nonbonded pdb=" O ASP G 18 " pdb=" OG SER G 21 " model vdw 2.170 3.040 nonbonded pdb=" O ASP O 18 " pdb=" OG SER O 21 " model vdw 2.170 3.040 nonbonded pdb=" ND1 HIS M 23 " pdb=" O ILE M 28 " model vdw 2.195 3.120 ... (remaining 266759 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'B' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'C' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'E' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'F' and (resid 4 through 44 or resid 60 through 216 or (resid 217 and (na \ me N or name CA or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'I' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'J' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'K' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'M' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'N' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 through 272)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 60 through 227 or (resid 228 through 231 and (name N or na \ me CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N o \ r name CA or name C or name O or name CB )) or resid 234 through 275)) selection = chain 'L' selection = (chain 'P' and (resid 60 through 227 or (resid 228 through 231 and (name N or na \ me CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N o \ r name CA or name C or name O or name CB )) or resid 234 through 275)) } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 33.350 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.120 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 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 : 0.003 0.043 34119 Z= 0.135 Angle : 0.640 13.062 46515 Z= 0.346 Chirality : 0.044 0.188 5006 Planarity : 0.004 0.056 5714 Dihedral : 15.322 172.189 12859 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: 0.57 (0.14), residues: 3851 helix: 1.52 (0.12), residues: 1868 sheet: -0.21 (0.18), residues: 850 loop : -1.00 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 189 TYR 0.025 0.001 TYR F 134 PHE 0.030 0.002 PHE M 110 TRP 0.025 0.002 TRP I 78 HIS 0.004 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00261 (34119) covalent geometry : angle 0.63975 (46515) hydrogen bonds : bond 0.14599 ( 1746) hydrogen bonds : angle 6.49516 ( 5114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1225 time to evaluate : 1.025 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: 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: 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: A 64 GLN cc_start: 0.6071 (pm20) cc_final: 0.5787 (pm20) REVERT: A 76 LEU cc_start: 0.7544 (mp) cc_final: 0.7318 (mm) REVERT: A 79 VAL cc_start: 0.7454 (t) cc_final: 0.6446 (m) REVERT: A 89 GLU cc_start: 0.8006 (tp30) cc_final: 0.7764 (tp30) REVERT: A 92 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8451 (mtpp) REVERT: A 100 ARG cc_start: 0.7409 (mtt90) cc_final: 0.7030 (mtm-85) REVERT: A 107 TYR cc_start: 0.8475 (t80) cc_final: 0.8182 (t80) REVERT: A 132 MET cc_start: 0.7361 (mmm) cc_final: 0.6964 (mmm) REVERT: A 140 THR cc_start: 0.7935 (p) cc_final: 0.7686 (p) REVERT: A 146 ASN cc_start: 0.7895 (m110) cc_final: 0.6901 (m110) REVERT: A 153 VAL cc_start: 0.8585 (m) cc_final: 0.7424 (m) REVERT: A 155 ARG cc_start: 0.8436 (tpt90) cc_final: 0.7314 (mmm160) REVERT: A 158 GLN cc_start: 0.8689 (tt0) cc_final: 0.8398 (tt0) REVERT: A 161 LYS cc_start: 0.8275 (ttmt) cc_final: 0.8036 (ttmt) REVERT: A 164 LEU cc_start: 0.8109 (mt) cc_final: 0.7749 (mt) REVERT: A 203 PHE cc_start: 0.8106 (t80) cc_final: 0.7824 (t80) REVERT: A 208 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 258 THR cc_start: 0.8571 (p) cc_final: 0.8367 (p) REVERT: A 271 PHE cc_start: 0.5577 (m-80) cc_final: 0.5310 (m-80) REVERT: B 13 ASN cc_start: 0.6506 (m-40) cc_final: 0.6182 (m-40) REVERT: B 70 TYR cc_start: 0.7240 (t80) cc_final: 0.6790 (t80) REVERT: B 73 LYS cc_start: 0.7905 (mttt) cc_final: 0.7321 (mtmt) REVERT: B 75 ILE cc_start: 0.7464 (pt) cc_final: 0.7264 (mp) REVERT: B 98 GLU cc_start: 0.8652 (mp0) cc_final: 0.7992 (mp0) REVERT: B 100 ARG cc_start: 0.8291 (mtt180) cc_final: 0.7737 (mtt-85) REVERT: B 101 VAL cc_start: 0.8907 (t) cc_final: 0.8243 (m) REVERT: B 116 GLN cc_start: 0.6944 (tm-30) cc_final: 0.5121 (tm-30) REVERT: B 129 GLN cc_start: 0.8349 (pt0) cc_final: 0.7631 (pp30) REVERT: B 137 ILE cc_start: 0.8245 (tt) cc_final: 0.7983 (tt) REVERT: B 139 HIS cc_start: 0.7618 (t-170) cc_final: 0.7330 (t70) REVERT: B 164 LEU cc_start: 0.8480 (tp) cc_final: 0.8279 (tp) REVERT: B 165 GLU cc_start: 0.7090 (tp30) cc_final: 0.6858 (tp30) REVERT: B 198 MET cc_start: 0.7968 (tpt) cc_final: 0.7754 (tpp) REVERT: B 201 PHE cc_start: 0.8991 (t80) cc_final: 0.8696 (t80) REVERT: B 205 LYS cc_start: 0.8878 (tptp) cc_final: 0.8228 (tppp) REVERT: C 30 ARG cc_start: 0.8232 (ttt180) cc_final: 0.7579 (ttt180) REVERT: C 132 MET cc_start: 0.7541 (ppp) cc_final: 0.7255 (ppp) REVERT: C 157 HIS cc_start: 0.7254 (m90) cc_final: 0.6933 (m90) REVERT: C 170 MET cc_start: -0.0004 (tpt) cc_final: -0.0917 (ttt) REVERT: D 86 ILE cc_start: 0.6463 (pt) cc_final: 0.6201 (mm) REVERT: D 218 GLN cc_start: 0.8243 (mm110) cc_final: 0.8034 (mm110) REVERT: D 226 TYR cc_start: 0.6293 (p90) cc_final: 0.5997 (p90) REVERT: E 7 LEU cc_start: 0.7762 (tt) cc_final: 0.7497 (tt) REVERT: E 87 TYR cc_start: 0.6387 (t80) cc_final: 0.6105 (t80) REVERT: E 100 ARG cc_start: 0.7666 (mtt90) cc_final: 0.7280 (mtt-85) REVERT: E 127 SER cc_start: 0.7725 (m) cc_final: 0.7371 (p) REVERT: E 159 THR cc_start: 0.8421 (m) cc_final: 0.7836 (p) REVERT: E 199 ASP cc_start: 0.8094 (m-30) cc_final: 0.7128 (m-30) REVERT: F 104 MET cc_start: 0.8067 (ptm) cc_final: 0.7384 (ppp) REVERT: F 183 ILE cc_start: 0.5858 (mt) cc_final: 0.5329 (mt) REVERT: F 198 MET cc_start: 0.7456 (ppp) cc_final: 0.7154 (ppp) REVERT: F 203 PHE cc_start: 0.7120 (t80) cc_final: 0.6483 (t80) REVERT: F 206 GLU cc_start: 0.7161 (pp20) cc_final: 0.6758 (pp20) REVERT: F 207 GLN cc_start: 0.7863 (mp10) cc_final: 0.6959 (mp10) REVERT: F 208 GLN cc_start: 0.7978 (tt0) cc_final: 0.7598 (tt0) REVERT: F 230 LYS cc_start: 0.8581 (mttt) cc_final: 0.8219 (mmmm) REVERT: F 260 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7529 (mtm110) REVERT: F 267 LYS cc_start: 0.8439 (ptmt) cc_final: 0.8218 (ptpt) REVERT: G 48 MET cc_start: 0.0155 (ppp) cc_final: -0.0762 (ppp) REVERT: G 110 PHE cc_start: 0.6705 (m-80) cc_final: 0.6407 (m-80) REVERT: G 132 MET cc_start: 0.7608 (tmm) cc_final: 0.6816 (tmm) REVERT: G 193 LEU cc_start: 0.8661 (mm) cc_final: 0.8443 (mm) REVERT: G 197 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7583 (Cg_endo) REVERT: H 62 HIS cc_start: 0.6698 (t-90) cc_final: 0.6144 (t-170) REVERT: H 100 ARG cc_start: 0.4373 (mtt90) cc_final: 0.4004 (mtm-85) REVERT: H 109 MET cc_start: 0.7789 (tpt) cc_final: 0.7574 (tpt) REVERT: H 132 MET cc_start: 0.4739 (tmm) cc_final: 0.4483 (tmm) REVERT: H 271 PHE cc_start: 0.6126 (p90) cc_final: 0.5574 (p90) REVERT: H 272 ILE cc_start: 0.7351 (mm) cc_final: 0.7010 (mm) REVERT: I 60 ILE cc_start: 0.8447 (mt) cc_final: 0.8091 (mp) REVERT: I 64 GLN cc_start: 0.6439 (pm20) cc_final: 0.6096 (pm20) REVERT: I 79 VAL cc_start: 0.7709 (t) cc_final: 0.7031 (m) REVERT: I 92 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8411 (mtpp) REVERT: I 100 ARG cc_start: 0.7758 (mtt90) cc_final: 0.7442 (mtm180) REVERT: I 101 VAL cc_start: 0.9303 (t) cc_final: 0.8950 (p) REVERT: I 105 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8445 (mtmm) REVERT: I 110 PHE cc_start: 0.8268 (m-80) cc_final: 0.8063 (m-80) REVERT: I 132 MET cc_start: 0.7544 (mmm) cc_final: 0.7058 (mmm) REVERT: I 146 ASN cc_start: 0.7941 (m110) cc_final: 0.7165 (m-40) REVERT: I 153 VAL cc_start: 0.8528 (m) cc_final: 0.7464 (m) REVERT: I 158 GLN cc_start: 0.8796 (tt0) cc_final: 0.7980 (pt0) REVERT: I 164 LEU cc_start: 0.8302 (mt) cc_final: 0.7947 (mt) REVERT: I 184 THR cc_start: 0.8252 (m) cc_final: 0.8001 (m) REVERT: I 203 PHE cc_start: 0.8192 (t80) cc_final: 0.7834 (t80) REVERT: I 208 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7684 (tm-30) REVERT: J 62 HIS cc_start: 0.6749 (t70) cc_final: 0.6143 (t70) REVERT: J 65 VAL cc_start: 0.8463 (t) cc_final: 0.8258 (t) REVERT: J 70 TYR cc_start: 0.7268 (t80) cc_final: 0.6185 (t80) REVERT: J 73 LYS cc_start: 0.8035 (mttt) cc_final: 0.7657 (mmtt) REVERT: J 80 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6918 (tm-30) REVERT: J 82 ASN cc_start: 0.8125 (t0) cc_final: 0.7683 (t0) REVERT: J 86 ILE cc_start: 0.8859 (pt) cc_final: 0.8287 (mm) REVERT: J 98 GLU cc_start: 0.8601 (mp0) cc_final: 0.8330 (mp0) REVERT: J 101 VAL cc_start: 0.8997 (t) cc_final: 0.8526 (m) REVERT: J 104 MET cc_start: 0.7761 (tpp) cc_final: 0.7414 (tpp) REVERT: J 105 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8624 (ttpt) REVERT: J 106 TRP cc_start: 0.8301 (t60) cc_final: 0.8031 (t60) REVERT: J 116 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6654 (tm-30) REVERT: J 117 SER cc_start: 0.8478 (p) cc_final: 0.8242 (t) REVERT: J 127 SER cc_start: 0.8412 (m) cc_final: 0.8166 (t) REVERT: J 129 GLN cc_start: 0.8487 (pt0) cc_final: 0.7881 (pp30) REVERT: J 137 ILE cc_start: 0.7981 (tt) cc_final: 0.7561 (tt) REVERT: J 178 LEU cc_start: 0.8729 (mm) cc_final: 0.8457 (mm) REVERT: J 182 LEU cc_start: 0.8181 (mt) cc_final: 0.7927 (mt) REVERT: J 184 THR cc_start: 0.8867 (p) cc_final: 0.8583 (p) REVERT: J 186 ASN cc_start: 0.7354 (m-40) cc_final: 0.6805 (m110) REVERT: J 189 ARG cc_start: 0.6943 (ttp-170) cc_final: 0.6721 (mtm110) REVERT: J 198 MET cc_start: 0.7858 (tpt) cc_final: 0.7607 (tpp) REVERT: J 205 LYS cc_start: 0.8791 (tptp) cc_final: 0.8364 (tptp) REVERT: K 30 ARG cc_start: 0.7846 (ttt180) cc_final: 0.7155 (ttt180) REVERT: K 110 PHE cc_start: 0.6534 (m-80) cc_final: 0.6068 (m-80) REVERT: K 132 MET cc_start: 0.6292 (ppp) cc_final: 0.5163 (ppp) REVERT: K 163 THR cc_start: 0.7859 (p) cc_final: 0.7651 (p) REVERT: K 244 LEU cc_start: 0.8059 (mm) cc_final: 0.7793 (mm) REVERT: M 7 LEU cc_start: 0.7589 (tt) cc_final: 0.7285 (tt) REVERT: M 12 HIS cc_start: 0.6778 (t-90) cc_final: 0.6404 (t-170) REVERT: M 76 LEU cc_start: 0.5528 (tp) cc_final: 0.4943 (tp) REVERT: M 87 TYR cc_start: 0.6636 (t80) cc_final: 0.6323 (t80) REVERT: M 159 THR cc_start: 0.8464 (m) cc_final: 0.7638 (p) REVERT: M 184 THR cc_start: 0.8958 (p) cc_final: 0.8701 (p) REVERT: M 199 ASP cc_start: 0.8281 (m-30) cc_final: 0.7386 (m-30) REVERT: M 204 ASN cc_start: 0.7590 (t0) cc_final: 0.7380 (t0) REVERT: N 104 MET cc_start: 0.8024 (ptm) cc_final: 0.7553 (ptm) REVERT: N 183 ILE cc_start: 0.5941 (mt) cc_final: 0.5595 (mt) REVERT: N 198 MET cc_start: 0.7182 (ppp) cc_final: 0.6947 (ppp) REVERT: N 208 GLN cc_start: 0.8081 (tt0) cc_final: 0.7582 (tt0) REVERT: N 210 ILE cc_start: 0.8040 (pt) cc_final: 0.7381 (pt) REVERT: N 233 HIS cc_start: 0.7785 (m90) cc_final: 0.7532 (m90) REVERT: N 242 GLN cc_start: 0.7008 (tt0) cc_final: 0.6671 (pp30) REVERT: N 243 VAL cc_start: 0.8087 (t) cc_final: 0.7564 (p) REVERT: N 244 LEU cc_start: 0.7434 (tt) cc_final: 0.7123 (tt) REVERT: N 267 LYS cc_start: 0.8461 (ptmt) cc_final: 0.7536 (mmtt) REVERT: O 18 ASP cc_start: 0.6423 (t70) cc_final: 0.6194 (t70) REVERT: O 48 MET cc_start: -0.2041 (ppp) cc_final: -0.2945 (ppp) REVERT: O 95 THR cc_start: 0.7387 (p) cc_final: 0.6799 (p) REVERT: O 132 MET cc_start: 0.7552 (tmm) cc_final: 0.6998 (tpt) REVERT: O 193 LEU cc_start: 0.8333 (mm) cc_final: 0.8121 (mm) REVERT: P 62 HIS cc_start: 0.6986 (t-90) cc_final: 0.6422 (t-170) REVERT: P 132 MET cc_start: 0.4791 (tmm) cc_final: 0.4547 (tmm) REVERT: P 170 MET cc_start: 0.7179 (mtt) cc_final: 0.6845 (mpp) REVERT: P 272 ILE cc_start: 0.7294 (mm) cc_final: 0.7070 (mm) outliers start: 0 outliers final: 0 residues processed: 1225 average time/residue: 0.2082 time to fit residues: 399.7917 Evaluate side-chains 1048 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1048 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0570 chunk 298 optimal weight: 4.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 16 HIS ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 HIS B 39 GLN B 158 GLN B 211 GLN C 116 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 186 ASN ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS G 148 GLN G 207 GLN G 208 GLN G 211 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 HIS J 16 HIS J 158 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 129 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN L 208 GLN ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN ** M 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 GLN O 69 HIS O 102 GLN O 207 GLN O 208 GLN O 211 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 GLN P 242 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.208861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162746 restraints weight = 72342.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.168737 restraints weight = 46229.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.173030 restraints weight = 32621.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.176146 restraints weight = 24661.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.178391 restraints weight = 19650.452| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34119 Z= 0.148 Angle : 0.669 13.394 46515 Z= 0.353 Chirality : 0.047 0.205 5006 Planarity : 0.005 0.105 5714 Dihedral : 14.346 171.540 5007 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 0.41 % Allowed : 3.87 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: 0.17 (0.13), residues: 3851 helix: 1.29 (0.12), residues: 1870 sheet: -0.41 (0.17), residues: 879 loop : -1.37 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 155 TYR 0.035 0.002 TYR E 70 PHE 0.041 0.002 PHE K 174 TRP 0.034 0.002 TRP H 78 HIS 0.018 0.001 HIS K 157 Details of bonding type rmsd covalent geometry : bond 0.00318 (34119) covalent geometry : angle 0.66945 (46515) hydrogen bonds : bond 0.04159 ( 1746) hydrogen bonds : angle 5.29586 ( 5114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1164 time to evaluate : 1.150 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: 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: 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: A 60 ILE cc_start: 0.8712 (mm) cc_final: 0.8477 (mm) REVERT: A 62 HIS cc_start: 0.7972 (t70) cc_final: 0.7703 (t70) REVERT: A 79 VAL cc_start: 0.7354 (t) cc_final: 0.6848 (m) REVERT: A 92 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8468 (mtpp) REVERT: A 100 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7118 (mtm-85) REVERT: A 107 TYR cc_start: 0.8432 (t80) cc_final: 0.8153 (t80) REVERT: A 118 ASP cc_start: 0.7621 (p0) cc_final: 0.7318 (p0) REVERT: A 132 MET cc_start: 0.7788 (mmm) cc_final: 0.7554 (mmm) REVERT: A 143 ILE cc_start: 0.7836 (pt) cc_final: 0.7398 (pt) REVERT: A 146 ASN cc_start: 0.7940 (m110) cc_final: 0.7394 (m-40) REVERT: A 153 VAL cc_start: 0.8946 (m) cc_final: 0.8739 (m) REVERT: A 155 ARG cc_start: 0.8509 (tpt90) cc_final: 0.7519 (mmm160) REVERT: A 158 GLN cc_start: 0.8905 (tt0) cc_final: 0.8557 (tt0) REVERT: A 164 LEU cc_start: 0.8145 (mt) cc_final: 0.7874 (mt) REVERT: A 203 PHE cc_start: 0.8300 (t80) cc_final: 0.7962 (t80) REVERT: A 208 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 254 LYS cc_start: 0.8375 (pptt) cc_final: 0.7592 (ttpp) REVERT: A 258 THR cc_start: 0.8696 (p) cc_final: 0.8453 (p) REVERT: A 260 ARG cc_start: 0.7308 (ptm160) cc_final: 0.6998 (ptm160) REVERT: B 15 TRP cc_start: 0.7754 (m100) cc_final: 0.7282 (m100) REVERT: B 42 VAL cc_start: 0.3076 (t) cc_final: 0.2725 (t) REVERT: B 63 TRP cc_start: 0.7789 (m100) cc_final: 0.6264 (m100) REVERT: B 64 GLN cc_start: 0.6608 (tp40) cc_final: 0.5879 (mm-40) REVERT: B 65 VAL cc_start: 0.8653 (t) cc_final: 0.8365 (t) REVERT: B 75 ILE cc_start: 0.7754 (pt) cc_final: 0.7466 (mp) REVERT: B 92 LYS cc_start: 0.8718 (tppt) cc_final: 0.8319 (tptp) REVERT: B 101 VAL cc_start: 0.8960 (t) cc_final: 0.8702 (t) REVERT: B 104 MET cc_start: 0.8564 (mmp) cc_final: 0.8264 (mmp) REVERT: B 105 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8783 (mtpp) REVERT: B 116 GLN cc_start: 0.6885 (tm-30) cc_final: 0.6086 (tm-30) REVERT: B 129 GLN cc_start: 0.8516 (pt0) cc_final: 0.8114 (pt0) REVERT: B 131 LEU cc_start: 0.8903 (tt) cc_final: 0.8696 (tt) REVERT: B 132 MET cc_start: 0.8415 (mmp) cc_final: 0.8161 (mmt) REVERT: B 137 ILE cc_start: 0.8512 (tt) cc_final: 0.8190 (tt) REVERT: B 138 GLU cc_start: 0.6211 (tm-30) cc_final: 0.5641 (tm-30) REVERT: B 161 LYS cc_start: 0.9108 (ptpt) cc_final: 0.8901 (ptpt) REVERT: B 164 LEU cc_start: 0.8756 (tp) cc_final: 0.8551 (tp) REVERT: B 165 GLU cc_start: 0.7710 (tp30) cc_final: 0.7388 (tp30) REVERT: B 178 LEU cc_start: 0.8982 (mm) cc_final: 0.8623 (mm) REVERT: B 198 MET cc_start: 0.8108 (tpt) cc_final: 0.7652 (tpp) REVERT: B 204 ASN cc_start: 0.7498 (p0) cc_final: 0.7154 (p0) REVERT: B 208 GLN cc_start: 0.8108 (pt0) cc_final: 0.7862 (pt0) REVERT: C 7 LEU cc_start: 0.8738 (tt) cc_final: 0.8517 (tt) REVERT: C 18 ASP cc_start: 0.8608 (t70) cc_final: 0.8406 (t70) REVERT: C 30 ARG cc_start: 0.9059 (ttt180) cc_final: 0.8697 (ttp80) REVERT: C 106 TRP cc_start: 0.7291 (t60) cc_final: 0.6765 (t60) REVERT: C 110 PHE cc_start: 0.7709 (m-80) cc_final: 0.7087 (m-80) REVERT: C 132 MET cc_start: 0.8232 (ppp) cc_final: 0.7756 (ppp) REVERT: C 161 LYS cc_start: 0.8930 (tmmt) cc_final: 0.8424 (ptpt) REVERT: C 162 ASN cc_start: 0.8733 (m-40) cc_final: 0.8518 (m-40) REVERT: C 186 ASN cc_start: 0.7565 (m-40) cc_final: 0.7279 (m110) REVERT: C 206 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: C 209 ARG cc_start: 0.8375 (ptt90) cc_final: 0.7939 (ptt90) REVERT: D 63 TRP cc_start: 0.5432 (m100) cc_final: 0.5062 (m100) REVERT: D 86 ILE cc_start: 0.6930 (pt) cc_final: 0.6717 (mm) REVERT: D 203 PHE cc_start: 0.7914 (t80) cc_final: 0.7627 (t80) REVERT: D 218 GLN cc_start: 0.8413 (mm110) cc_final: 0.7903 (mm110) REVERT: D 223 PHE cc_start: 0.6265 (p90) cc_final: 0.5799 (p90) REVERT: D 226 TYR cc_start: 0.6513 (p90) cc_final: 0.6075 (p90) REVERT: D 248 ASP cc_start: 0.8119 (p0) cc_final: 0.7910 (p0) REVERT: D 254 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7429 (tppt) REVERT: D 268 ASP cc_start: 0.6883 (t70) cc_final: 0.6500 (t70) REVERT: E 7 LEU cc_start: 0.7814 (tt) cc_final: 0.7525 (tt) REVERT: E 9 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7952 (mm-30) REVERT: E 10 GLU cc_start: 0.8060 (tp30) cc_final: 0.7770 (tp30) REVERT: E 12 HIS cc_start: 0.8175 (t70) cc_final: 0.7561 (t70) REVERT: E 13 ASN cc_start: 0.8762 (m110) cc_final: 0.8502 (m110) REVERT: E 18 ASP cc_start: 0.7410 (t70) cc_final: 0.7179 (t70) REVERT: E 22 LEU cc_start: 0.8071 (pp) cc_final: 0.7844 (pp) REVERT: E 36 ILE cc_start: 0.8235 (mt) cc_final: 0.7814 (tp) REVERT: E 87 TYR cc_start: 0.7103 (t80) cc_final: 0.6886 (t80) REVERT: E 100 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7763 (mtt-85) REVERT: E 110 PHE cc_start: 0.7707 (m-80) cc_final: 0.6977 (m-10) REVERT: E 150 GLN cc_start: 0.7646 (mm110) cc_final: 0.7403 (mm-40) REVERT: E 154 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8662 (mm-30) REVERT: E 159 THR cc_start: 0.8596 (m) cc_final: 0.7979 (p) REVERT: E 199 ASP cc_start: 0.8384 (m-30) cc_final: 0.7602 (m-30) REVERT: E 204 ASN cc_start: 0.8212 (t0) cc_final: 0.8005 (t0) REVERT: E 236 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8480 (mm-30) REVERT: F 14 LYS cc_start: 0.7217 (pttm) cc_final: 0.6926 (pttp) REVERT: F 23 HIS cc_start: 0.7824 (t70) cc_final: 0.7588 (t70) REVERT: F 86 ILE cc_start: 0.6618 (pt) cc_final: 0.5896 (mm) REVERT: F 183 ILE cc_start: 0.5941 (mt) cc_final: 0.5726 (mt) REVERT: F 199 ASP cc_start: 0.8531 (m-30) cc_final: 0.8252 (m-30) REVERT: F 202 ILE cc_start: 0.8297 (mt) cc_final: 0.8003 (mt) REVERT: F 203 PHE cc_start: 0.7647 (t80) cc_final: 0.6822 (t80) REVERT: F 206 GLU cc_start: 0.8002 (pp20) cc_final: 0.7749 (pp20) REVERT: F 208 GLN cc_start: 0.8426 (tt0) cc_final: 0.8125 (tm-30) REVERT: F 233 HIS cc_start: 0.7536 (m90) cc_final: 0.7225 (m90) REVERT: F 236 GLU cc_start: 0.7847 (pm20) cc_final: 0.7533 (mp0) REVERT: F 243 VAL cc_start: 0.8087 (t) cc_final: 0.7481 (m) REVERT: F 244 LEU cc_start: 0.7799 (tt) cc_final: 0.7557 (tt) REVERT: F 256 ARG cc_start: 0.8271 (ttm110) cc_final: 0.7854 (ttm110) REVERT: F 270 LYS cc_start: 0.7850 (mttt) cc_final: 0.7230 (mttt) REVERT: G 10 GLU cc_start: 0.5978 (pt0) cc_final: 0.5666 (pt0) REVERT: G 48 MET cc_start: -0.0461 (ppp) cc_final: -0.1240 (ppp) REVERT: G 85 LEU cc_start: 0.7124 (tp) cc_final: 0.6773 (tp) REVERT: G 110 PHE cc_start: 0.7529 (m-80) cc_final: 0.7096 (m-80) REVERT: G 131 LEU cc_start: 0.9240 (mt) cc_final: 0.8993 (mt) REVERT: G 158 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8828 (pp30) REVERT: G 164 LEU cc_start: 0.8545 (mt) cc_final: 0.8330 (pp) REVERT: G 197 PRO cc_start: 0.8454 (Cg_exo) cc_final: 0.8102 (Cg_endo) REVERT: G 201 PHE cc_start: 0.8731 (t80) cc_final: 0.8207 (t80) REVERT: G 205 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8943 (mmtp) REVERT: H 62 HIS cc_start: 0.7395 (t-90) cc_final: 0.6855 (t-170) REVERT: H 78 TRP cc_start: 0.5965 (m-10) cc_final: 0.5540 (m-10) REVERT: H 87 TYR cc_start: 0.8172 (t80) cc_final: 0.7714 (t80) REVERT: H 101 VAL cc_start: 0.8760 (p) cc_final: 0.8557 (p) REVERT: H 104 MET cc_start: 0.9112 (mmp) cc_final: 0.8510 (mmp) REVERT: H 109 MET cc_start: 0.8129 (tpt) cc_final: 0.7890 (tpt) REVERT: H 110 PHE cc_start: 0.7997 (m-10) cc_final: 0.7527 (m-10) REVERT: H 132 MET cc_start: 0.6168 (tmm) cc_final: 0.5891 (tmm) REVERT: H 164 LEU cc_start: 0.9166 (mm) cc_final: 0.8861 (pp) REVERT: I 60 ILE cc_start: 0.8495 (mt) cc_final: 0.8265 (mp) REVERT: I 64 GLN cc_start: 0.6982 (pm20) cc_final: 0.6574 (pm20) REVERT: I 92 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8507 (mtpp) REVERT: I 100 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7496 (mtm180) REVERT: I 118 ASP cc_start: 0.7852 (p0) cc_final: 0.7565 (p0) REVERT: I 132 MET cc_start: 0.8033 (mmm) cc_final: 0.7766 (mmm) REVERT: I 146 ASN cc_start: 0.7755 (m110) cc_final: 0.6978 (m-40) REVERT: I 158 GLN cc_start: 0.8994 (tt0) cc_final: 0.8670 (tt0) REVERT: I 164 LEU cc_start: 0.8290 (mt) cc_final: 0.7985 (mt) REVERT: I 203 PHE cc_start: 0.8426 (t80) cc_final: 0.7947 (t80) REVERT: I 208 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7736 (tm-30) REVERT: I 222 ARG cc_start: 0.4843 (mtp-110) cc_final: 0.4500 (mtm110) REVERT: J 42 VAL cc_start: 0.4536 (t) cc_final: 0.4283 (t) REVERT: J 64 GLN cc_start: 0.6780 (tp40) cc_final: 0.6290 (mm-40) REVERT: J 65 VAL cc_start: 0.8708 (t) cc_final: 0.8294 (t) REVERT: J 70 TYR cc_start: 0.7316 (t80) cc_final: 0.6517 (t80) REVERT: J 73 LYS cc_start: 0.7830 (mttt) cc_final: 0.7015 (mtmt) REVERT: J 86 ILE cc_start: 0.8663 (pt) cc_final: 0.8060 (mm) REVERT: J 92 LYS cc_start: 0.8758 (tptp) cc_final: 0.8392 (tptp) REVERT: J 101 VAL cc_start: 0.9058 (t) cc_final: 0.8777 (t) REVERT: J 104 MET cc_start: 0.8130 (tpp) cc_final: 0.7550 (tpp) REVERT: J 116 GLN cc_start: 0.7000 (tm-30) cc_final: 0.6550 (tm-30) REVERT: J 131 LEU cc_start: 0.8625 (tt) cc_final: 0.8223 (tt) REVERT: J 138 GLU cc_start: 0.7735 (tp30) cc_final: 0.7478 (tp30) REVERT: J 160 LEU cc_start: 0.8703 (tt) cc_final: 0.8355 (tt) REVERT: J 161 LYS cc_start: 0.9021 (ptpt) cc_final: 0.8624 (ptpt) REVERT: J 162 ASN cc_start: 0.8957 (m110) cc_final: 0.8659 (m-40) REVERT: J 174 PHE cc_start: 0.6951 (t80) cc_final: 0.6662 (t80) REVERT: J 178 LEU cc_start: 0.9006 (mm) cc_final: 0.8806 (mm) REVERT: J 184 THR cc_start: 0.8962 (p) cc_final: 0.8619 (p) REVERT: J 186 ASN cc_start: 0.7613 (m-40) cc_final: 0.7253 (m110) REVERT: J 198 MET cc_start: 0.8020 (tpt) cc_final: 0.7715 (tpp) REVERT: J 201 PHE cc_start: 0.9019 (t80) cc_final: 0.8575 (t80) REVERT: J 204 ASN cc_start: 0.7929 (m110) cc_final: 0.6869 (p0) REVERT: J 205 LYS cc_start: 0.8256 (tptp) cc_final: 0.7597 (tptp) REVERT: K 7 LEU cc_start: 0.8561 (tt) cc_final: 0.8326 (tt) REVERT: K 15 TRP cc_start: 0.7998 (m100) cc_final: 0.7568 (m100) REVERT: K 28 ILE cc_start: 0.8002 (tp) cc_final: 0.7743 (tp) REVERT: K 40 CYS cc_start: 0.8278 (m) cc_final: 0.7876 (p) REVERT: K 109 MET cc_start: 0.8036 (tpp) cc_final: 0.7171 (ptp) REVERT: K 110 PHE cc_start: 0.7476 (m-80) cc_final: 0.7036 (m-80) REVERT: K 132 MET cc_start: 0.7226 (ppp) cc_final: 0.6622 (ppp) REVERT: K 190 LYS cc_start: 0.6073 (mttp) cc_final: 0.5847 (mttm) REVERT: K 206 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: K 245 TRP cc_start: 0.8011 (m100) cc_final: 0.7775 (m100) REVERT: L 63 TRP cc_start: 0.6261 (m100) cc_final: 0.5918 (m100) REVERT: L 226 TYR cc_start: 0.6820 (p90) cc_final: 0.5926 (p90) REVERT: L 248 ASP cc_start: 0.8199 (p0) cc_final: 0.7961 (p0) REVERT: L 259 ASP cc_start: 0.8519 (m-30) cc_final: 0.8116 (m-30) REVERT: L 269 VAL cc_start: 0.7946 (m) cc_final: 0.7722 (m) REVERT: M 7 LEU cc_start: 0.7777 (tt) cc_final: 0.7515 (tt) REVERT: M 12 HIS cc_start: 0.8005 (t-90) cc_final: 0.7440 (t-170) REVERT: M 18 ASP cc_start: 0.7193 (t70) cc_final: 0.6729 (t70) REVERT: M 22 LEU cc_start: 0.7974 (pp) cc_final: 0.7688 (pp) REVERT: M 76 LEU cc_start: 0.7191 (tp) cc_final: 0.6708 (tp) REVERT: M 87 TYR cc_start: 0.7215 (t80) cc_final: 0.6721 (t80) REVERT: M 109 MET cc_start: 0.8461 (tmm) cc_final: 0.8154 (tmm) REVERT: M 154 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8747 (mm-30) REVERT: M 155 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8174 (mtt90) REVERT: M 158 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7379 (tm-30) REVERT: M 159 THR cc_start: 0.8640 (m) cc_final: 0.7886 (p) REVERT: M 162 ASN cc_start: 0.8081 (m-40) cc_final: 0.7818 (m110) REVERT: M 199 ASP cc_start: 0.8557 (m-30) cc_final: 0.7670 (m-30) REVERT: M 202 ILE cc_start: 0.9037 (mm) cc_final: 0.8778 (mm) REVERT: M 204 ASN cc_start: 0.8382 (t0) cc_final: 0.8159 (t0) REVERT: M 205 LYS cc_start: 0.8970 (mttm) cc_final: 0.8737 (mtmm) REVERT: N 23 HIS cc_start: 0.7671 (t70) cc_final: 0.7453 (t70) REVERT: N 65 VAL cc_start: 0.7474 (t) cc_final: 0.7079 (p) REVERT: N 104 MET cc_start: 0.8282 (ptm) cc_final: 0.7920 (ptm) REVERT: N 110 PHE cc_start: 0.8006 (m-80) cc_final: 0.7424 (m-80) REVERT: N 203 PHE cc_start: 0.7699 (t80) cc_final: 0.7324 (t80) REVERT: N 208 GLN cc_start: 0.8415 (tt0) cc_final: 0.8111 (tm-30) REVERT: N 213 GLN cc_start: 0.8876 (mt0) cc_final: 0.8562 (mt0) REVERT: N 230 LYS cc_start: 0.8110 (mttt) cc_final: 0.7811 (tptp) REVERT: N 233 HIS cc_start: 0.7688 (m90) cc_final: 0.7276 (m-70) REVERT: N 237 TRP cc_start: 0.8137 (m100) cc_final: 0.7823 (m100) REVERT: N 242 GLN cc_start: 0.7732 (tt0) cc_final: 0.6995 (pp30) REVERT: N 243 VAL cc_start: 0.8201 (t) cc_final: 0.7365 (m) REVERT: N 244 LEU cc_start: 0.8149 (tt) cc_final: 0.7784 (tt) REVERT: N 256 ARG cc_start: 0.8332 (ttm110) cc_final: 0.7639 (ttm110) REVERT: N 267 LYS cc_start: 0.8694 (ptmt) cc_final: 0.7626 (mmtt) REVERT: N 270 LYS cc_start: 0.7931 (mptt) cc_final: 0.6681 (mptt) REVERT: O 48 MET cc_start: -0.1096 (ppp) cc_final: -0.1946 (ppp) REVERT: O 104 MET cc_start: 0.7988 (pmm) cc_final: 0.7718 (pmm) REVERT: O 110 PHE cc_start: 0.8031 (m-80) cc_final: 0.7623 (m-80) REVERT: O 132 MET cc_start: 0.8198 (tmm) cc_final: 0.7849 (tmm) REVERT: O 175 GLU cc_start: 0.8637 (pm20) cc_final: 0.8309 (mp0) REVERT: O 201 PHE cc_start: 0.8797 (t80) cc_final: 0.7769 (t80) REVERT: O 202 ILE cc_start: 0.8546 (mt) cc_final: 0.8344 (mt) REVERT: O 205 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8846 (mmtp) REVERT: O 208 GLN cc_start: 0.8595 (tm130) cc_final: 0.8286 (tm-30) REVERT: O 209 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8330 (ptm-80) REVERT: O 211 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8201 (tp40) REVERT: P 62 HIS cc_start: 0.7541 (t-90) cc_final: 0.7058 (t-170) REVERT: P 87 TYR cc_start: 0.8410 (t80) cc_final: 0.8188 (t80) REVERT: P 101 VAL cc_start: 0.9164 (p) cc_final: 0.8870 (p) REVERT: P 104 MET cc_start: 0.9147 (mmp) cc_final: 0.8744 (mmp) REVERT: P 132 MET cc_start: 0.5973 (tmm) cc_final: 0.5662 (tmm) REVERT: P 164 LEU cc_start: 0.9293 (mm) cc_final: 0.8897 (pp) REVERT: P 170 MET cc_start: 0.7328 (mtt) cc_final: 0.6911 (mpp) REVERT: P 222 ARG cc_start: 0.5900 (mtp85) cc_final: 0.5572 (mmm-85) REVERT: P 230 LYS cc_start: 0.7156 (mmmt) cc_final: 0.6896 (mmtm) REVERT: P 254 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7959 (tppt) outliers start: 14 outliers final: 4 residues processed: 1172 average time/residue: 0.2094 time to fit residues: 384.5372 Evaluate side-chains 1069 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1063 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 237 optimal weight: 5.9990 chunk 175 optimal weight: 0.0040 chunk 376 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 313 optimal weight: 0.8980 chunk 311 optimal weight: 0.0970 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN B 13 ASN B 102 GLN B 158 GLN B 211 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 204 ASN G 208 GLN G 211 GLN H 102 GLN H 157 HIS ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 HIS J 102 GLN J 158 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 ASN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 GLN ** M 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 208 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.207431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.161332 restraints weight = 71283.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.167318 restraints weight = 45566.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.171534 restraints weight = 32188.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.174618 restraints weight = 24426.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.176835 restraints weight = 19523.086| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34119 Z= 0.139 Angle : 0.643 12.161 46515 Z= 0.339 Chirality : 0.046 0.183 5006 Planarity : 0.005 0.086 5714 Dihedral : 14.485 172.007 5007 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.36 % Rotamer: Outliers : 0.12 % Allowed : 3.93 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: 0.03 (0.13), residues: 3851 helix: 1.17 (0.12), residues: 1866 sheet: -0.50 (0.17), residues: 902 loop : -1.42 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 100 TYR 0.022 0.001 TYR N 134 PHE 0.028 0.002 PHE L 203 TRP 0.033 0.002 TRP P 78 HIS 0.013 0.001 HIS N 62 Details of bonding type rmsd covalent geometry : bond 0.00291 (34119) covalent geometry : angle 0.64258 (46515) hydrogen bonds : bond 0.03889 ( 1746) hydrogen bonds : angle 5.18632 ( 5114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1143 time to evaluate : 1.146 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: 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: 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: A 48 MET cc_start: 0.4878 (mmm) cc_final: 0.4101 (mmm) REVERT: A 60 ILE cc_start: 0.8688 (mm) cc_final: 0.8412 (mm) REVERT: A 62 HIS cc_start: 0.7910 (t70) cc_final: 0.7483 (t70) REVERT: A 64 GLN cc_start: 0.6629 (pm20) cc_final: 0.6218 (pm20) REVERT: A 79 VAL cc_start: 0.7720 (t) cc_final: 0.7148 (p) REVERT: A 92 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8482 (mtpp) REVERT: A 100 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7338 (mtm180) REVERT: A 105 LYS cc_start: 0.9206 (mtpp) cc_final: 0.8993 (mtpp) REVERT: A 107 TYR cc_start: 0.8445 (t80) cc_final: 0.8134 (t80) REVERT: A 113 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7629 (mmmm) REVERT: A 132 MET cc_start: 0.7990 (mmm) cc_final: 0.7751 (mmm) REVERT: A 135 LEU cc_start: 0.8729 (mt) cc_final: 0.8479 (mt) REVERT: A 143 ILE cc_start: 0.7926 (pt) cc_final: 0.7371 (pt) REVERT: A 146 ASN cc_start: 0.7977 (m110) cc_final: 0.7107 (m-40) REVERT: A 155 ARG cc_start: 0.8560 (tpt90) cc_final: 0.7581 (mmm160) REVERT: A 158 GLN cc_start: 0.8953 (tt0) cc_final: 0.8525 (tt0) REVERT: A 182 LEU cc_start: 0.7950 (mt) cc_final: 0.7656 (tp) REVERT: A 201 PHE cc_start: 0.8051 (t80) cc_final: 0.7748 (t80) REVERT: A 203 PHE cc_start: 0.8300 (t80) cc_final: 0.7923 (t80) REVERT: A 208 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7504 (tm-30) REVERT: A 226 TYR cc_start: 0.6015 (p90) cc_final: 0.5518 (p90) REVERT: A 258 THR cc_start: 0.8730 (p) cc_final: 0.8501 (p) REVERT: A 260 ARG cc_start: 0.7405 (ptm160) cc_final: 0.7097 (ptm160) REVERT: B 15 TRP cc_start: 0.7845 (m100) cc_final: 0.7297 (m100) REVERT: B 40 CYS cc_start: 0.7392 (t) cc_final: 0.6880 (p) REVERT: B 63 TRP cc_start: 0.7941 (m100) cc_final: 0.6107 (m100) REVERT: B 64 GLN cc_start: 0.6768 (tp40) cc_final: 0.6026 (mm-40) REVERT: B 65 VAL cc_start: 0.8625 (t) cc_final: 0.8251 (t) REVERT: B 75 ILE cc_start: 0.7832 (pt) cc_final: 0.7525 (mp) REVERT: B 86 ILE cc_start: 0.8595 (pt) cc_final: 0.8083 (mm) REVERT: B 92 LYS cc_start: 0.8717 (tppt) cc_final: 0.8419 (tppp) REVERT: B 100 ARG cc_start: 0.8606 (mtt180) cc_final: 0.8212 (mtt90) REVERT: B 104 MET cc_start: 0.8698 (mmp) cc_final: 0.8309 (mmp) REVERT: B 105 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8760 (mtpp) REVERT: B 116 GLN cc_start: 0.6984 (tm-30) cc_final: 0.6208 (tm-30) REVERT: B 137 ILE cc_start: 0.8492 (tt) cc_final: 0.8107 (tt) REVERT: B 139 HIS cc_start: 0.8082 (t70) cc_final: 0.7839 (t70) REVERT: B 165 GLU cc_start: 0.8035 (tp30) cc_final: 0.7619 (tp30) REVERT: B 170 MET cc_start: 0.8437 (tpt) cc_final: 0.8225 (tpt) REVERT: B 178 LEU cc_start: 0.9058 (mm) cc_final: 0.8730 (mm) REVERT: B 198 MET cc_start: 0.8130 (tpt) cc_final: 0.7729 (tpp) REVERT: B 204 ASN cc_start: 0.7632 (p0) cc_final: 0.7389 (p0) REVERT: B 207 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8344 (mm-40) REVERT: C 7 LEU cc_start: 0.8732 (tt) cc_final: 0.8496 (tt) REVERT: C 28 ILE cc_start: 0.8063 (tp) cc_final: 0.7679 (tp) REVERT: C 35 ASP cc_start: 0.8604 (m-30) cc_final: 0.8393 (m-30) REVERT: C 106 TRP cc_start: 0.7370 (t60) cc_final: 0.6903 (t60) REVERT: C 110 PHE cc_start: 0.7671 (m-80) cc_final: 0.7107 (m-80) REVERT: C 132 MET cc_start: 0.8204 (ppp) cc_final: 0.7783 (ppp) REVERT: C 186 ASN cc_start: 0.7795 (m-40) cc_final: 0.7585 (m110) REVERT: C 209 ARG cc_start: 0.8444 (ptt90) cc_final: 0.7818 (ptt90) REVERT: D 218 GLN cc_start: 0.8429 (mm110) cc_final: 0.7927 (mm110) REVERT: D 223 PHE cc_start: 0.6351 (p90) cc_final: 0.5930 (p90) REVERT: D 226 TYR cc_start: 0.6927 (p90) cc_final: 0.6206 (p90) REVERT: D 244 LEU cc_start: 0.8201 (mt) cc_final: 0.7556 (pp) REVERT: D 248 ASP cc_start: 0.8089 (p0) cc_final: 0.7878 (p0) REVERT: D 254 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7459 (tptt) REVERT: D 268 ASP cc_start: 0.7213 (t70) cc_final: 0.6949 (t70) REVERT: E 10 GLU cc_start: 0.8129 (tp30) cc_final: 0.7678 (tp30) REVERT: E 12 HIS cc_start: 0.8153 (t70) cc_final: 0.7567 (t70) REVERT: E 13 ASN cc_start: 0.8735 (m110) cc_final: 0.8523 (m110) REVERT: E 18 ASP cc_start: 0.7579 (t70) cc_final: 0.7333 (t70) REVERT: E 22 LEU cc_start: 0.8128 (pp) cc_final: 0.7866 (pp) REVERT: E 138 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6981 (tm-30) REVERT: E 150 GLN cc_start: 0.7686 (mm110) cc_final: 0.7433 (mm-40) REVERT: E 158 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7621 (tm-30) REVERT: E 159 THR cc_start: 0.8568 (m) cc_final: 0.7964 (p) REVERT: E 199 ASP cc_start: 0.8391 (m-30) cc_final: 0.7590 (m-30) REVERT: E 205 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8376 (mtpt) REVERT: E 206 GLU cc_start: 0.8609 (pt0) cc_final: 0.7728 (pp20) REVERT: E 208 GLN cc_start: 0.8932 (pp30) cc_final: 0.8651 (pp30) REVERT: E 210 ILE cc_start: 0.9063 (mt) cc_final: 0.8813 (mm) REVERT: F 23 HIS cc_start: 0.7773 (t70) cc_final: 0.7451 (t70) REVERT: F 82 ASN cc_start: 0.8220 (m110) cc_final: 0.7895 (m110) REVERT: F 104 MET cc_start: 0.7989 (ptm) cc_final: 0.7572 (ptm) REVERT: F 150 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7125 (pt0) REVERT: F 158 GLN cc_start: 0.9149 (mt0) cc_final: 0.8472 (pt0) REVERT: F 162 ASN cc_start: 0.8731 (m-40) cc_final: 0.8507 (m110) REVERT: F 199 ASP cc_start: 0.8446 (m-30) cc_final: 0.8233 (m-30) REVERT: F 203 PHE cc_start: 0.7831 (t80) cc_final: 0.7371 (t80) REVERT: F 208 GLN cc_start: 0.8484 (tt0) cc_final: 0.8205 (tm-30) REVERT: F 230 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7761 (mmmm) REVERT: F 233 HIS cc_start: 0.7689 (m90) cc_final: 0.7323 (m90) REVERT: F 236 GLU cc_start: 0.7946 (pm20) cc_final: 0.7674 (pp20) REVERT: F 243 VAL cc_start: 0.8242 (t) cc_final: 0.7537 (m) REVERT: F 244 LEU cc_start: 0.7991 (tt) cc_final: 0.7733 (tt) REVERT: F 256 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7937 (ttm110) REVERT: F 267 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8251 (pttt) REVERT: G 48 MET cc_start: -0.0311 (ppp) cc_final: -0.1180 (ppp) REVERT: G 62 HIS cc_start: 0.7291 (t70) cc_final: 0.6960 (t70) REVERT: G 85 LEU cc_start: 0.7197 (tp) cc_final: 0.6712 (tp) REVERT: G 104 MET cc_start: 0.7873 (pmm) cc_final: 0.7627 (pmm) REVERT: G 110 PHE cc_start: 0.7659 (m-80) cc_final: 0.7190 (m-80) REVERT: G 131 LEU cc_start: 0.9154 (mt) cc_final: 0.8914 (mt) REVERT: G 132 MET cc_start: 0.8276 (tmm) cc_final: 0.7761 (tmm) REVERT: G 155 ARG cc_start: 0.9155 (mtp-110) cc_final: 0.8514 (ptp-110) REVERT: G 164 LEU cc_start: 0.8448 (mt) cc_final: 0.8215 (mt) REVERT: G 171 PHE cc_start: 0.7632 (m-10) cc_final: 0.7403 (m-80) REVERT: G 197 PRO cc_start: 0.8521 (Cg_exo) cc_final: 0.8179 (Cg_endo) REVERT: G 201 PHE cc_start: 0.8870 (t80) cc_final: 0.8345 (t80) REVERT: G 205 LYS cc_start: 0.9232 (mmtm) cc_final: 0.8975 (mmtm) REVERT: G 208 GLN cc_start: 0.8502 (tm130) cc_final: 0.8256 (tm-30) REVERT: H 61 ASP cc_start: 0.7304 (m-30) cc_final: 0.7097 (m-30) REVERT: H 62 HIS cc_start: 0.7495 (t-90) cc_final: 0.6922 (t-170) REVERT: H 78 TRP cc_start: 0.6724 (m-10) cc_final: 0.6212 (m-10) REVERT: H 87 TYR cc_start: 0.8509 (t80) cc_final: 0.7914 (t80) REVERT: H 100 ARG cc_start: 0.5167 (mtt90) cc_final: 0.4940 (mtm-85) REVERT: H 101 VAL cc_start: 0.8824 (p) cc_final: 0.8569 (p) REVERT: H 104 MET cc_start: 0.9079 (mmp) cc_final: 0.8485 (mmp) REVERT: H 106 TRP cc_start: 0.8410 (t60) cc_final: 0.7980 (t60) REVERT: H 110 PHE cc_start: 0.8064 (m-10) cc_final: 0.7698 (m-10) REVERT: H 205 LYS cc_start: 0.7981 (ptpt) cc_final: 0.7549 (ptpp) REVERT: H 207 GLN cc_start: 0.8162 (mm110) cc_final: 0.7757 (mm110) REVERT: H 223 PHE cc_start: 0.7002 (m-80) cc_final: 0.6598 (m-80) REVERT: H 267 LYS cc_start: 0.7137 (ptmm) cc_final: 0.6919 (ptmm) REVERT: H 271 PHE cc_start: 0.6677 (p90) cc_final: 0.6309 (p90) REVERT: H 272 ILE cc_start: 0.7711 (mm) cc_final: 0.7209 (mt) REVERT: I 79 VAL cc_start: 0.7721 (t) cc_final: 0.7246 (p) REVERT: I 92 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8610 (mtpp) REVERT: I 100 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7473 (mtm-85) REVERT: I 132 MET cc_start: 0.8119 (mmm) cc_final: 0.7849 (mmm) REVERT: I 146 ASN cc_start: 0.7827 (m110) cc_final: 0.6948 (m-40) REVERT: I 155 ARG cc_start: 0.8323 (tpt90) cc_final: 0.7854 (mmm160) REVERT: I 178 LEU cc_start: 0.7867 (tp) cc_final: 0.7416 (tp) REVERT: I 184 THR cc_start: 0.8246 (m) cc_final: 0.7847 (p) REVERT: I 201 PHE cc_start: 0.8164 (t80) cc_final: 0.7928 (t80) REVERT: I 203 PHE cc_start: 0.8278 (t80) cc_final: 0.7829 (t80) REVERT: I 208 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7824 (tm-30) REVERT: I 222 ARG cc_start: 0.5370 (mtp-110) cc_final: 0.5017 (mtm110) REVERT: I 254 LYS cc_start: 0.7294 (tptp) cc_final: 0.7066 (tptt) REVERT: I 260 ARG cc_start: 0.7105 (ptm160) cc_final: 0.6833 (ptm160) REVERT: J 40 CYS cc_start: 0.7226 (t) cc_final: 0.6761 (p) REVERT: J 63 TRP cc_start: 0.7798 (m100) cc_final: 0.6087 (m100) REVERT: J 64 GLN cc_start: 0.6886 (tp40) cc_final: 0.6245 (mm-40) REVERT: J 65 VAL cc_start: 0.8663 (t) cc_final: 0.8316 (t) REVERT: J 86 ILE cc_start: 0.8707 (pt) cc_final: 0.7910 (mm) REVERT: J 89 GLU cc_start: 0.7723 (tt0) cc_final: 0.7368 (tt0) REVERT: J 92 LYS cc_start: 0.8765 (tptp) cc_final: 0.8443 (tptp) REVERT: J 101 VAL cc_start: 0.9076 (t) cc_final: 0.8804 (t) REVERT: J 104 MET cc_start: 0.8231 (tpp) cc_final: 0.7483 (tpp) REVERT: J 116 GLN cc_start: 0.6878 (tm-30) cc_final: 0.6596 (tm-30) REVERT: J 131 LEU cc_start: 0.8717 (tt) cc_final: 0.8349 (tt) REVERT: J 137 ILE cc_start: 0.8313 (tt) cc_final: 0.7966 (tt) REVERT: J 138 GLU cc_start: 0.7808 (tp30) cc_final: 0.7495 (tp30) REVERT: J 139 HIS cc_start: 0.8451 (t70) cc_final: 0.8132 (t70) REVERT: J 161 LYS cc_start: 0.8975 (ptpt) cc_final: 0.8772 (ptpt) REVERT: J 162 ASN cc_start: 0.8960 (m110) cc_final: 0.8708 (m-40) REVERT: J 178 LEU cc_start: 0.9011 (mm) cc_final: 0.8734 (mm) REVERT: J 186 ASN cc_start: 0.7660 (m-40) cc_final: 0.7070 (m-40) REVERT: J 198 MET cc_start: 0.8017 (tpt) cc_final: 0.7798 (tpp) REVERT: J 201 PHE cc_start: 0.9017 (t80) cc_final: 0.8541 (t80) REVERT: J 204 ASN cc_start: 0.8173 (m110) cc_final: 0.7163 (p0) REVERT: K 7 LEU cc_start: 0.8588 (tt) cc_final: 0.8381 (tt) REVERT: K 14 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8355 (mmtm) REVERT: K 40 CYS cc_start: 0.8286 (m) cc_final: 0.7646 (p) REVERT: K 244 LEU cc_start: 0.8049 (mm) cc_final: 0.7815 (mm) REVERT: K 245 TRP cc_start: 0.7836 (m100) cc_final: 0.7576 (m100) REVERT: L 63 TRP cc_start: 0.6073 (m100) cc_final: 0.5861 (m100) REVERT: L 223 PHE cc_start: 0.6037 (p90) cc_final: 0.5717 (p90) REVERT: L 226 TYR cc_start: 0.7079 (p90) cc_final: 0.6017 (p90) REVERT: L 238 GLN cc_start: 0.7765 (pp30) cc_final: 0.7310 (pp30) REVERT: L 254 LYS cc_start: 0.7534 (tptt) cc_final: 0.7276 (tptt) REVERT: L 269 VAL cc_start: 0.7752 (m) cc_final: 0.7500 (m) REVERT: M 13 ASN cc_start: 0.8837 (m110) cc_final: 0.8590 (m110) REVERT: M 18 ASP cc_start: 0.7457 (t70) cc_final: 0.7121 (t70) REVERT: M 22 LEU cc_start: 0.8005 (pp) cc_final: 0.7764 (pp) REVERT: M 78 TRP cc_start: 0.5985 (m100) cc_final: 0.5535 (m100) REVERT: M 87 TYR cc_start: 0.7399 (t80) cc_final: 0.6801 (t80) REVERT: M 109 MET cc_start: 0.8439 (tmm) cc_final: 0.8194 (tmm) REVERT: M 154 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8779 (mm-30) REVERT: M 155 ARG cc_start: 0.8561 (ttt180) cc_final: 0.8257 (mtt90) REVERT: M 158 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7449 (tm-30) REVERT: M 159 THR cc_start: 0.8810 (m) cc_final: 0.8251 (p) REVERT: M 162 ASN cc_start: 0.8081 (m-40) cc_final: 0.7835 (m110) REVERT: M 199 ASP cc_start: 0.8551 (m-30) cc_final: 0.7686 (m-30) REVERT: M 205 LYS cc_start: 0.9023 (mttm) cc_final: 0.8756 (mtpp) REVERT: M 209 ARG cc_start: 0.8925 (tmt170) cc_final: 0.8563 (ttp80) REVERT: N 23 HIS cc_start: 0.7665 (t70) cc_final: 0.7394 (t70) REVERT: N 65 VAL cc_start: 0.7539 (t) cc_final: 0.7187 (p) REVERT: N 98 GLU cc_start: 0.7696 (mp0) cc_final: 0.7403 (mp0) REVERT: N 104 MET cc_start: 0.8235 (ptm) cc_final: 0.7922 (ptm) REVERT: N 105 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9154 (mttt) REVERT: N 110 PHE cc_start: 0.8007 (m-80) cc_final: 0.7796 (m-80) REVERT: N 162 ASN cc_start: 0.8539 (m110) cc_final: 0.8308 (m110) REVERT: N 203 PHE cc_start: 0.7837 (t80) cc_final: 0.7382 (t80) REVERT: N 208 GLN cc_start: 0.8458 (tt0) cc_final: 0.8163 (tm-30) REVERT: N 210 ILE cc_start: 0.8321 (pt) cc_final: 0.8065 (pt) REVERT: N 213 GLN cc_start: 0.8750 (mt0) cc_final: 0.8172 (mt0) REVERT: N 233 HIS cc_start: 0.7702 (m90) cc_final: 0.7237 (m-70) REVERT: N 242 GLN cc_start: 0.7822 (tt0) cc_final: 0.7139 (pp30) REVERT: N 243 VAL cc_start: 0.8273 (t) cc_final: 0.7586 (m) REVERT: N 244 LEU cc_start: 0.8249 (tt) cc_final: 0.7943 (tt) REVERT: N 256 ARG cc_start: 0.8404 (ttm110) cc_final: 0.7723 (ttm110) REVERT: N 267 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8449 (ptpt) REVERT: N 270 LYS cc_start: 0.7826 (mptt) cc_final: 0.6979 (mptt) REVERT: O 40 CYS cc_start: 0.5796 (t) cc_final: 0.5537 (t) REVERT: O 48 MET cc_start: -0.1400 (ppp) cc_final: -0.1830 (ppp) REVERT: O 104 MET cc_start: 0.8007 (pmm) cc_final: 0.7762 (pmm) REVERT: O 110 PHE cc_start: 0.8237 (m-80) cc_final: 0.7608 (m-80) REVERT: O 132 MET cc_start: 0.8168 (tmm) cc_final: 0.7669 (tmm) REVERT: O 193 LEU cc_start: 0.8714 (mm) cc_final: 0.8485 (mm) REVERT: O 201 PHE cc_start: 0.8744 (t80) cc_final: 0.7831 (t80) REVERT: O 205 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8846 (mmtp) REVERT: O 208 GLN cc_start: 0.8690 (tm130) cc_final: 0.8421 (tm-30) REVERT: O 209 ARG cc_start: 0.8745 (ptm-80) cc_final: 0.8384 (ptm-80) REVERT: O 211 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8196 (tp40) REVERT: P 62 HIS cc_start: 0.7682 (t-90) cc_final: 0.7201 (t-170) REVERT: P 87 TYR cc_start: 0.8702 (t80) cc_final: 0.8321 (t80) REVERT: P 101 VAL cc_start: 0.9139 (p) cc_final: 0.8907 (p) REVERT: P 104 MET cc_start: 0.9179 (mmp) cc_final: 0.8698 (mmp) REVERT: P 106 TRP cc_start: 0.8470 (t60) cc_final: 0.8145 (t60) REVERT: P 132 MET cc_start: 0.6417 (tmm) cc_final: 0.5848 (tmm) REVERT: P 164 LEU cc_start: 0.9290 (mm) cc_final: 0.8938 (pp) REVERT: P 170 MET cc_start: 0.7338 (mtt) cc_final: 0.6902 (mpp) REVERT: P 172 ASN cc_start: 0.8731 (m-40) cc_final: 0.8361 (p0) REVERT: P 222 ARG cc_start: 0.6023 (mtp85) cc_final: 0.5580 (mtp85) REVERT: P 230 LYS cc_start: 0.7212 (mmmt) cc_final: 0.6969 (mmtm) REVERT: P 236 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7603 (tm-30) outliers start: 4 outliers final: 0 residues processed: 1146 average time/residue: 0.2120 time to fit residues: 380.1178 Evaluate side-chains 1046 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1046 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 374 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 227 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 302 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 338 optimal weight: 0.0970 chunk 207 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN F 242 GLN G 208 GLN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN J 158 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN L 158 GLN M 69 HIS N 158 GLN O 62 HIS O 208 GLN P 157 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.204432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.158089 restraints weight = 71286.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.163919 restraints weight = 45363.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.168075 restraints weight = 32024.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170905 restraints weight = 24300.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.173204 restraints weight = 19637.739| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34119 Z= 0.151 Angle : 0.651 12.610 46515 Z= 0.344 Chirality : 0.047 0.196 5006 Planarity : 0.005 0.080 5714 Dihedral : 14.573 172.196 5007 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.03 (0.13), residues: 3851 helix: 1.12 (0.12), residues: 1863 sheet: -0.52 (0.17), residues: 871 loop : -1.42 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 155 TYR 0.023 0.001 TYR M 70 PHE 0.026 0.002 PHE L 203 TRP 0.041 0.002 TRP L 63 HIS 0.020 0.001 HIS O 62 Details of bonding type rmsd covalent geometry : bond 0.00323 (34119) covalent geometry : angle 0.65125 (46515) hydrogen bonds : bond 0.03878 ( 1746) hydrogen bonds : angle 5.21655 ( 5114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1140 time to evaluate : 1.173 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: 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: 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: A 15 TRP cc_start: 0.6323 (m-10) cc_final: 0.5877 (m100) REVERT: A 60 ILE cc_start: 0.8744 (mm) cc_final: 0.8417 (mm) REVERT: A 62 HIS cc_start: 0.7859 (t70) cc_final: 0.7519 (t70) REVERT: A 64 GLN cc_start: 0.6521 (pm20) cc_final: 0.6185 (pm20) REVERT: A 79 VAL cc_start: 0.7787 (t) cc_final: 0.7254 (p) REVERT: A 92 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8552 (mtpp) REVERT: A 97 GLN cc_start: 0.7429 (pm20) cc_final: 0.6926 (pm20) REVERT: A 100 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7435 (mtm-85) REVERT: A 105 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8964 (mtpp) REVERT: A 107 TYR cc_start: 0.8462 (t80) cc_final: 0.8200 (t80) REVERT: A 113 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7618 (mmmm) REVERT: A 132 MET cc_start: 0.8050 (mmm) cc_final: 0.7679 (mmm) REVERT: A 155 ARG cc_start: 0.8532 (tpt90) cc_final: 0.7541 (mmm160) REVERT: A 158 GLN cc_start: 0.8938 (tt0) cc_final: 0.8523 (tt0) REVERT: A 164 LEU cc_start: 0.8155 (mt) cc_final: 0.7850 (mt) REVERT: A 182 LEU cc_start: 0.7905 (mt) cc_final: 0.7668 (tt) REVERT: A 201 PHE cc_start: 0.8153 (t80) cc_final: 0.7888 (t80) REVERT: A 203 PHE cc_start: 0.8310 (t80) cc_final: 0.7925 (t80) REVERT: A 208 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 226 TYR cc_start: 0.6110 (p90) cc_final: 0.4190 (p90) REVERT: A 254 LYS cc_start: 0.8283 (pptt) cc_final: 0.7870 (pptt) REVERT: A 260 ARG cc_start: 0.7343 (ptm160) cc_final: 0.7083 (ptm160) REVERT: B 15 TRP cc_start: 0.7877 (m100) cc_final: 0.7363 (m100) REVERT: B 40 CYS cc_start: 0.7476 (t) cc_final: 0.6931 (p) REVERT: B 63 TRP cc_start: 0.7976 (m100) cc_final: 0.6298 (m100) REVERT: B 64 GLN cc_start: 0.6922 (tp40) cc_final: 0.6076 (mm-40) REVERT: B 65 VAL cc_start: 0.8575 (t) cc_final: 0.8202 (t) REVERT: B 75 ILE cc_start: 0.7926 (pt) cc_final: 0.7636 (mp) REVERT: B 86 ILE cc_start: 0.8675 (pt) cc_final: 0.8214 (mm) REVERT: B 92 LYS cc_start: 0.8718 (tppt) cc_final: 0.8413 (tppp) REVERT: B 104 MET cc_start: 0.8625 (mmp) cc_final: 0.8343 (mmp) REVERT: B 116 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6453 (tm-30) REVERT: B 132 MET cc_start: 0.8560 (tpp) cc_final: 0.7981 (tpp) REVERT: B 138 GLU cc_start: 0.7966 (tp30) cc_final: 0.7603 (tp30) REVERT: B 139 HIS cc_start: 0.8352 (t70) cc_final: 0.7926 (t70) REVERT: B 157 HIS cc_start: 0.8446 (m-70) cc_final: 0.8205 (m-70) REVERT: B 165 GLU cc_start: 0.7883 (tp30) cc_final: 0.7560 (tp30) REVERT: B 178 LEU cc_start: 0.9070 (mm) cc_final: 0.8821 (mm) REVERT: B 186 ASN cc_start: 0.8299 (m-40) cc_final: 0.7977 (m-40) REVERT: B 198 MET cc_start: 0.8148 (tpt) cc_final: 0.7745 (tpp) REVERT: B 204 ASN cc_start: 0.7807 (p0) cc_final: 0.7515 (p0) REVERT: C 28 ILE cc_start: 0.8065 (tp) cc_final: 0.7674 (tp) REVERT: C 34 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8539 (pp20) REVERT: C 35 ASP cc_start: 0.8576 (m-30) cc_final: 0.7948 (m-30) REVERT: C 110 PHE cc_start: 0.7931 (m-80) cc_final: 0.7334 (m-80) REVERT: C 132 MET cc_start: 0.8266 (ppp) cc_final: 0.7840 (ppp) REVERT: C 199 ASP cc_start: 0.8861 (m-30) cc_final: 0.8615 (m-30) REVERT: C 209 ARG cc_start: 0.8446 (ptt90) cc_final: 0.7943 (ptt90) REVERT: D 223 PHE cc_start: 0.6362 (p90) cc_final: 0.5821 (p90) REVERT: D 226 TYR cc_start: 0.7087 (p90) cc_final: 0.6311 (p90) REVERT: D 254 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7566 (tptm) REVERT: D 262 LEU cc_start: 0.7769 (mp) cc_final: 0.7538 (mp) REVERT: D 263 VAL cc_start: 0.8147 (m) cc_final: 0.7929 (t) REVERT: D 268 ASP cc_start: 0.7121 (t70) cc_final: 0.6853 (t70) REVERT: E 10 GLU cc_start: 0.7972 (tp30) cc_final: 0.7362 (tp30) REVERT: E 12 HIS cc_start: 0.8220 (t70) cc_final: 0.7504 (t70) REVERT: E 15 TRP cc_start: 0.8629 (m-10) cc_final: 0.8342 (m-10) REVERT: E 18 ASP cc_start: 0.7690 (t70) cc_final: 0.7446 (t70) REVERT: E 89 GLU cc_start: 0.7425 (pm20) cc_final: 0.6822 (mp0) REVERT: E 101 VAL cc_start: 0.8669 (t) cc_final: 0.8469 (t) REVERT: E 133 LYS cc_start: 0.9210 (ptpp) cc_final: 0.8065 (pttm) REVERT: E 154 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8673 (mm-30) REVERT: E 159 THR cc_start: 0.8580 (m) cc_final: 0.7945 (p) REVERT: E 178 LEU cc_start: 0.8934 (mt) cc_final: 0.8729 (mt) REVERT: E 199 ASP cc_start: 0.8403 (m-30) cc_final: 0.7573 (m-30) REVERT: E 205 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8301 (mtpt) REVERT: E 208 GLN cc_start: 0.8922 (pp30) cc_final: 0.8650 (pp30) REVERT: E 236 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8453 (mm-30) REVERT: E 242 GLN cc_start: 0.6364 (pp30) cc_final: 0.6017 (pp30) REVERT: E 270 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7882 (mtmt) REVERT: F 23 HIS cc_start: 0.7804 (t70) cc_final: 0.7527 (t70) REVERT: F 104 MET cc_start: 0.7902 (ptm) cc_final: 0.7528 (ptm) REVERT: F 162 ASN cc_start: 0.8815 (m-40) cc_final: 0.8603 (m110) REVERT: F 199 ASP cc_start: 0.8489 (m-30) cc_final: 0.8164 (m-30) REVERT: F 203 PHE cc_start: 0.7738 (t80) cc_final: 0.7222 (t80) REVERT: F 208 GLN cc_start: 0.8483 (tt0) cc_final: 0.8231 (tm-30) REVERT: F 230 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7850 (mmmm) REVERT: F 233 HIS cc_start: 0.7649 (m90) cc_final: 0.7364 (m90) REVERT: F 236 GLU cc_start: 0.7962 (pm20) cc_final: 0.7541 (pm20) REVERT: F 243 VAL cc_start: 0.8346 (t) cc_final: 0.7581 (m) REVERT: F 256 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7903 (ttm110) REVERT: F 267 LYS cc_start: 0.8751 (ptmt) cc_final: 0.8333 (pttt) REVERT: G 48 MET cc_start: -0.0490 (ppp) cc_final: -0.1320 (ppp) REVERT: G 62 HIS cc_start: 0.7281 (t70) cc_final: 0.6860 (t70) REVERT: G 70 TYR cc_start: 0.6755 (t80) cc_final: 0.6433 (t80) REVERT: G 85 LEU cc_start: 0.7129 (tp) cc_final: 0.6622 (tp) REVERT: G 104 MET cc_start: 0.7873 (pmm) cc_final: 0.7634 (pmm) REVERT: G 110 PHE cc_start: 0.7769 (m-80) cc_final: 0.6995 (m-80) REVERT: G 131 LEU cc_start: 0.9264 (mt) cc_final: 0.9030 (mt) REVERT: G 154 GLU cc_start: 0.8505 (pp20) cc_final: 0.7949 (pp20) REVERT: G 155 ARG cc_start: 0.9076 (mtp-110) cc_final: 0.8661 (ptp-110) REVERT: G 158 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8728 (tp-100) REVERT: G 164 LEU cc_start: 0.8592 (mt) cc_final: 0.8359 (pp) REVERT: G 171 PHE cc_start: 0.7679 (m-10) cc_final: 0.7422 (m-80) REVERT: G 183 ILE cc_start: 0.7487 (mt) cc_final: 0.7280 (mt) REVERT: G 197 PRO cc_start: 0.8660 (Cg_exo) cc_final: 0.8357 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8835 (m-30) cc_final: 0.8632 (m-30) REVERT: G 201 PHE cc_start: 0.8836 (t80) cc_final: 0.8307 (t80) REVERT: G 205 LYS cc_start: 0.9235 (mmtm) cc_final: 0.9035 (mmtm) REVERT: H 78 TRP cc_start: 0.6925 (m-10) cc_final: 0.6423 (m-10) REVERT: H 87 TYR cc_start: 0.8563 (t80) cc_final: 0.7986 (t80) REVERT: H 100 ARG cc_start: 0.5224 (mtt90) cc_final: 0.4923 (mtm-85) REVERT: H 101 VAL cc_start: 0.8811 (p) cc_final: 0.8579 (p) REVERT: H 104 MET cc_start: 0.9074 (mmp) cc_final: 0.8472 (mmp) REVERT: H 106 TRP cc_start: 0.8382 (t60) cc_final: 0.7912 (t60) REVERT: H 110 PHE cc_start: 0.8217 (m-10) cc_final: 0.7748 (m-10) REVERT: H 164 LEU cc_start: 0.9004 (pp) cc_final: 0.8378 (pp) REVERT: H 199 ASP cc_start: 0.7987 (m-30) cc_final: 0.7745 (m-30) REVERT: H 205 LYS cc_start: 0.8097 (ptpt) cc_final: 0.7795 (pttm) REVERT: H 207 GLN cc_start: 0.8241 (mm110) cc_final: 0.7758 (mm110) REVERT: I 66 ASP cc_start: 0.7257 (t0) cc_final: 0.7039 (t70) REVERT: I 79 VAL cc_start: 0.7968 (t) cc_final: 0.7487 (p) REVERT: I 90 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7572 (tmm-80) REVERT: I 92 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8474 (mtpp) REVERT: I 97 GLN cc_start: 0.7818 (pm20) cc_final: 0.7277 (pm20) REVERT: I 98 GLU cc_start: 0.8467 (mp0) cc_final: 0.8117 (mp0) REVERT: I 100 ARG cc_start: 0.8009 (mtt90) cc_final: 0.7406 (mtm-85) REVERT: I 146 ASN cc_start: 0.7826 (m110) cc_final: 0.7159 (m110) REVERT: I 155 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7665 (mmm160) REVERT: I 158 GLN cc_start: 0.9075 (tt0) cc_final: 0.8688 (tt0) REVERT: I 160 LEU cc_start: 0.8646 (tt) cc_final: 0.8431 (tt) REVERT: I 164 LEU cc_start: 0.8460 (mt) cc_final: 0.8161 (mt) REVERT: I 184 THR cc_start: 0.8340 (m) cc_final: 0.8068 (p) REVERT: I 190 LYS cc_start: 0.7479 (mttp) cc_final: 0.7216 (mptt) REVERT: I 198 MET cc_start: 0.8424 (ttm) cc_final: 0.8210 (ttm) REVERT: I 203 PHE cc_start: 0.8279 (t80) cc_final: 0.7900 (t80) REVERT: I 208 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7883 (tm-30) REVERT: I 209 ARG cc_start: 0.7287 (tpp80) cc_final: 0.6879 (tpp80) REVERT: I 222 ARG cc_start: 0.5650 (mtp-110) cc_final: 0.5404 (mtm110) REVERT: I 243 VAL cc_start: 0.8705 (t) cc_final: 0.8182 (t) REVERT: I 254 LYS cc_start: 0.7348 (tptp) cc_final: 0.6989 (tptt) REVERT: I 260 ARG cc_start: 0.7055 (ptm160) cc_final: 0.6729 (ptm160) REVERT: I 264 ILE cc_start: 0.7887 (mm) cc_final: 0.7684 (mm) REVERT: J 40 CYS cc_start: 0.7258 (t) cc_final: 0.6794 (p) REVERT: J 63 TRP cc_start: 0.7876 (m100) cc_final: 0.6159 (m100) REVERT: J 64 GLN cc_start: 0.6950 (tp40) cc_final: 0.6249 (mm-40) REVERT: J 65 VAL cc_start: 0.8746 (t) cc_final: 0.8334 (t) REVERT: J 86 ILE cc_start: 0.8842 (pt) cc_final: 0.8045 (mm) REVERT: J 89 GLU cc_start: 0.7594 (tt0) cc_final: 0.7359 (tt0) REVERT: J 92 LYS cc_start: 0.8820 (tptp) cc_final: 0.8442 (tptp) REVERT: J 101 VAL cc_start: 0.9104 (t) cc_final: 0.8815 (t) REVERT: J 104 MET cc_start: 0.8223 (tpp) cc_final: 0.7490 (tpp) REVERT: J 116 GLN cc_start: 0.6900 (tm-30) cc_final: 0.6447 (tm-30) REVERT: J 131 LEU cc_start: 0.8743 (tt) cc_final: 0.8340 (tt) REVERT: J 138 GLU cc_start: 0.7762 (tp30) cc_final: 0.7517 (tp30) REVERT: J 139 HIS cc_start: 0.8482 (t70) cc_final: 0.8103 (t70) REVERT: J 161 LYS cc_start: 0.8916 (ptpt) cc_final: 0.8708 (ptpt) REVERT: J 162 ASN cc_start: 0.8954 (m110) cc_final: 0.8710 (m-40) REVERT: J 186 ASN cc_start: 0.7779 (m-40) cc_final: 0.7214 (m-40) REVERT: J 198 MET cc_start: 0.8079 (tpt) cc_final: 0.7869 (tpp) REVERT: J 201 PHE cc_start: 0.9051 (t80) cc_final: 0.8559 (t80) REVERT: J 204 ASN cc_start: 0.8146 (m110) cc_final: 0.7115 (p0) REVERT: J 205 LYS cc_start: 0.8208 (tptp) cc_final: 0.7647 (tptp) REVERT: J 208 GLN cc_start: 0.8006 (pt0) cc_final: 0.7772 (pt0) REVERT: K 14 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8339 (mmtm) REVERT: K 34 GLU cc_start: 0.8784 (pt0) cc_final: 0.8195 (pp20) REVERT: K 35 ASP cc_start: 0.8696 (m-30) cc_final: 0.8242 (m-30) REVERT: K 40 CYS cc_start: 0.8308 (m) cc_final: 0.7694 (p) REVERT: K 245 TRP cc_start: 0.7911 (m100) cc_final: 0.7625 (m100) REVERT: L 209 ARG cc_start: 0.8730 (mmp-170) cc_final: 0.8446 (mmp-170) REVERT: L 223 PHE cc_start: 0.5969 (p90) cc_final: 0.5682 (p90) REVERT: L 226 TYR cc_start: 0.6470 (p90) cc_final: 0.5826 (p90) REVERT: L 254 LYS cc_start: 0.7569 (tptt) cc_final: 0.7240 (tptt) REVERT: L 263 VAL cc_start: 0.7873 (m) cc_final: 0.7659 (t) REVERT: M 7 LEU cc_start: 0.8152 (tt) cc_final: 0.7730 (tt) REVERT: M 10 GLU cc_start: 0.8076 (tp30) cc_final: 0.7735 (tp30) REVERT: M 18 ASP cc_start: 0.7647 (t70) cc_final: 0.7323 (t70) REVERT: M 155 ARG cc_start: 0.8574 (ttt180) cc_final: 0.8282 (mtt90) REVERT: M 158 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7326 (tm-30) REVERT: M 159 THR cc_start: 0.8825 (m) cc_final: 0.8199 (p) REVERT: M 162 ASN cc_start: 0.8090 (m-40) cc_final: 0.7840 (m110) REVERT: M 174 PHE cc_start: 0.7102 (t80) cc_final: 0.6754 (t80) REVERT: M 178 LEU cc_start: 0.8780 (mt) cc_final: 0.8481 (mt) REVERT: M 199 ASP cc_start: 0.8556 (m-30) cc_final: 0.7683 (m-30) REVERT: M 202 ILE cc_start: 0.8895 (mm) cc_final: 0.8395 (mm) REVERT: M 206 GLU cc_start: 0.8607 (pt0) cc_final: 0.8107 (pt0) REVERT: M 207 GLN cc_start: 0.8388 (mm110) cc_final: 0.8081 (mm110) REVERT: M 209 ARG cc_start: 0.8841 (tmt170) cc_final: 0.8418 (ttp80) REVERT: N 23 HIS cc_start: 0.7729 (t70) cc_final: 0.7485 (t70) REVERT: N 65 VAL cc_start: 0.7543 (t) cc_final: 0.7213 (p) REVERT: N 104 MET cc_start: 0.8009 (ptm) cc_final: 0.7640 (ptm) REVERT: N 110 PHE cc_start: 0.8027 (m-80) cc_final: 0.7782 (m-80) REVERT: N 162 ASN cc_start: 0.8570 (m110) cc_final: 0.8356 (m-40) REVERT: N 203 PHE cc_start: 0.7553 (t80) cc_final: 0.7146 (t80) REVERT: N 208 GLN cc_start: 0.8489 (tt0) cc_final: 0.8240 (tm-30) REVERT: N 210 ILE cc_start: 0.8329 (pt) cc_final: 0.8068 (pt) REVERT: N 213 GLN cc_start: 0.8747 (mt0) cc_final: 0.8143 (mt0) REVERT: N 230 LYS cc_start: 0.8205 (mttt) cc_final: 0.7414 (ttpp) REVERT: N 233 HIS cc_start: 0.7684 (m90) cc_final: 0.7357 (m-70) REVERT: N 242 GLN cc_start: 0.7773 (tt0) cc_final: 0.7132 (pp30) REVERT: N 243 VAL cc_start: 0.8477 (t) cc_final: 0.7469 (m) REVERT: N 244 LEU cc_start: 0.8242 (tt) cc_final: 0.7989 (tt) REVERT: N 256 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7651 (ttm110) REVERT: N 270 LYS cc_start: 0.8075 (mptt) cc_final: 0.7344 (mmtm) REVERT: O 40 CYS cc_start: 0.5741 (t) cc_final: 0.5479 (t) REVERT: O 48 MET cc_start: -0.1442 (ppp) cc_final: -0.1847 (ppp) REVERT: O 62 HIS cc_start: 0.6777 (p-80) cc_final: 0.6336 (p-80) REVERT: O 104 MET cc_start: 0.8024 (pmm) cc_final: 0.7781 (pmm) REVERT: O 110 PHE cc_start: 0.8046 (m-80) cc_final: 0.7725 (m-10) REVERT: O 115 LEU cc_start: 0.8799 (tp) cc_final: 0.8523 (tp) REVERT: O 132 MET cc_start: 0.8150 (tmm) cc_final: 0.7585 (tmm) REVERT: O 193 LEU cc_start: 0.8712 (mm) cc_final: 0.8408 (mm) REVERT: O 201 PHE cc_start: 0.8756 (t80) cc_final: 0.7986 (t80) REVERT: O 205 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8917 (mmtp) REVERT: O 208 GLN cc_start: 0.8732 (tm130) cc_final: 0.8467 (tm-30) REVERT: O 209 ARG cc_start: 0.8776 (ptm-80) cc_final: 0.8458 (ptm-80) REVERT: O 211 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8244 (tp40) REVERT: P 62 HIS cc_start: 0.7789 (t-90) cc_final: 0.7218 (t-170) REVERT: P 87 TYR cc_start: 0.8643 (t80) cc_final: 0.8382 (t80) REVERT: P 101 VAL cc_start: 0.9149 (p) cc_final: 0.8924 (p) REVERT: P 104 MET cc_start: 0.9162 (mmp) cc_final: 0.8677 (mmp) REVERT: P 106 TRP cc_start: 0.8512 (t60) cc_final: 0.8150 (t60) REVERT: P 132 MET cc_start: 0.6362 (tmm) cc_final: 0.5751 (tmm) REVERT: P 137 ILE cc_start: 0.8062 (mm) cc_final: 0.7850 (mm) REVERT: P 170 MET cc_start: 0.7420 (mtt) cc_final: 0.6976 (mpp) REVERT: P 230 LYS cc_start: 0.7390 (mmmt) cc_final: 0.7173 (mmtm) REVERT: P 236 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7515 (tm-30) outliers start: 3 outliers final: 0 residues processed: 1142 average time/residue: 0.2100 time to fit residues: 376.1395 Evaluate side-chains 1068 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1068 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 257 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 300 optimal weight: 8.9990 chunk 201 optimal weight: 0.3980 chunk 311 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 357 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN G 208 GLN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 GLN H 266 ASN I 46 ASN J 102 GLN J 158 GLN J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS N 158 GLN N 186 ASN O 69 HIS O 208 GLN O 211 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 GLN P 242 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.194257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148022 restraints weight = 71031.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.153669 restraints weight = 44347.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.157523 restraints weight = 30899.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160283 restraints weight = 23375.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162177 restraints weight = 18792.542| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 34119 Z= 0.226 Angle : 0.740 13.133 46515 Z= 0.400 Chirality : 0.049 0.330 5006 Planarity : 0.005 0.084 5714 Dihedral : 14.770 174.091 5007 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.42 (0.13), residues: 3851 helix: 0.79 (0.12), residues: 1871 sheet: -0.61 (0.18), residues: 782 loop : -1.65 (0.16), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 260 TYR 0.021 0.002 TYR E 261 PHE 0.027 0.002 PHE D 203 TRP 0.049 0.003 TRP D 63 HIS 0.014 0.002 HIS N 62 Details of bonding type rmsd covalent geometry : bond 0.00468 (34119) covalent geometry : angle 0.74037 (46515) hydrogen bonds : bond 0.04585 ( 1746) hydrogen bonds : angle 5.52772 ( 5114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1206 time to evaluate : 1.039 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: 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: 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: A 60 ILE cc_start: 0.8703 (mm) cc_final: 0.8227 (mm) REVERT: A 62 HIS cc_start: 0.7847 (t70) cc_final: 0.7506 (t70) REVERT: A 64 GLN cc_start: 0.6672 (pm20) cc_final: 0.6350 (pm20) REVERT: A 66 ASP cc_start: 0.7788 (t0) cc_final: 0.7494 (t70) REVERT: A 79 VAL cc_start: 0.8082 (t) cc_final: 0.7568 (p) REVERT: A 80 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6490 (tm-30) REVERT: A 81 THR cc_start: 0.8726 (p) cc_final: 0.8476 (t) REVERT: A 90 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7753 (tmm-80) REVERT: A 91 VAL cc_start: 0.8394 (t) cc_final: 0.8147 (t) REVERT: A 92 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8484 (mtpp) REVERT: A 105 LYS cc_start: 0.9274 (mtpp) cc_final: 0.9051 (mtpp) REVERT: A 107 TYR cc_start: 0.8458 (t80) cc_final: 0.8110 (t80) REVERT: A 113 LYS cc_start: 0.8028 (mmmm) cc_final: 0.7691 (mmmm) REVERT: A 116 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7231 (tm-30) REVERT: A 129 GLN cc_start: 0.7902 (tt0) cc_final: 0.7632 (tt0) REVERT: A 135 LEU cc_start: 0.8925 (mt) cc_final: 0.8652 (mt) REVERT: A 155 ARG cc_start: 0.8537 (tpt90) cc_final: 0.7671 (mmm160) REVERT: A 161 LYS cc_start: 0.8804 (tptt) cc_final: 0.8513 (tptt) REVERT: A 175 GLU cc_start: 0.8331 (pm20) cc_final: 0.8035 (pm20) REVERT: A 184 THR cc_start: 0.8470 (m) cc_final: 0.8217 (p) REVERT: A 190 LYS cc_start: 0.7783 (ptpp) cc_final: 0.7563 (ptpp) REVERT: A 203 PHE cc_start: 0.8538 (t80) cc_final: 0.8105 (t80) REVERT: A 208 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 211 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7868 (tp-100) REVERT: A 226 TYR cc_start: 0.6767 (p90) cc_final: 0.5096 (p90) REVERT: A 253 VAL cc_start: 0.8050 (t) cc_final: 0.7837 (m) REVERT: A 254 LYS cc_start: 0.8206 (pptt) cc_final: 0.7924 (pptt) REVERT: A 256 ARG cc_start: 0.7249 (pmt170) cc_final: 0.6679 (pmt170) REVERT: A 260 ARG cc_start: 0.7432 (ptm160) cc_final: 0.7225 (ptm160) REVERT: B 15 TRP cc_start: 0.7849 (m100) cc_final: 0.7335 (m100) REVERT: B 40 CYS cc_start: 0.7648 (t) cc_final: 0.7031 (p) REVERT: B 64 GLN cc_start: 0.6686 (tp40) cc_final: 0.6019 (mm-40) REVERT: B 73 LYS cc_start: 0.8292 (mttt) cc_final: 0.8066 (mmtm) REVERT: B 86 ILE cc_start: 0.8737 (pt) cc_final: 0.8313 (mm) REVERT: B 87 TYR cc_start: 0.8216 (t80) cc_final: 0.7738 (t80) REVERT: B 89 GLU cc_start: 0.7769 (tt0) cc_final: 0.6935 (tt0) REVERT: B 90 ARG cc_start: 0.8514 (tpt-90) cc_final: 0.8068 (tpp80) REVERT: B 92 LYS cc_start: 0.8882 (tppt) cc_final: 0.8590 (tppp) REVERT: B 102 GLN cc_start: 0.8768 (mp10) cc_final: 0.8373 (mm-40) REVERT: B 104 MET cc_start: 0.8699 (mmp) cc_final: 0.8342 (mmp) REVERT: B 129 GLN cc_start: 0.8492 (pt0) cc_final: 0.8116 (pt0) REVERT: B 131 LEU cc_start: 0.9068 (tt) cc_final: 0.8846 (tt) REVERT: B 132 MET cc_start: 0.8724 (tpp) cc_final: 0.8049 (tpp) REVERT: B 137 ILE cc_start: 0.8444 (tt) cc_final: 0.7881 (tt) REVERT: B 138 GLU cc_start: 0.7919 (tp30) cc_final: 0.7678 (tp30) REVERT: B 139 HIS cc_start: 0.8455 (t70) cc_final: 0.8027 (t70) REVERT: B 165 GLU cc_start: 0.8052 (tp30) cc_final: 0.7737 (tp30) REVERT: B 175 GLU cc_start: 0.8829 (pm20) cc_final: 0.8591 (mp0) REVERT: B 178 LEU cc_start: 0.9146 (mm) cc_final: 0.8819 (mm) REVERT: B 186 ASN cc_start: 0.8381 (m-40) cc_final: 0.8104 (m-40) REVERT: B 198 MET cc_start: 0.8203 (tpt) cc_final: 0.7822 (tpp) REVERT: B 208 GLN cc_start: 0.8139 (pt0) cc_final: 0.7875 (pt0) REVERT: C 11 GLU cc_start: 0.8125 (tp30) cc_final: 0.7374 (tp30) REVERT: C 17 GLN cc_start: 0.7196 (mp10) cc_final: 0.6813 (mp10) REVERT: C 39 GLN cc_start: 0.8516 (tp40) cc_final: 0.7818 (tp40) REVERT: C 62 HIS cc_start: 0.7601 (t70) cc_final: 0.7331 (t70) REVERT: C 106 TRP cc_start: 0.6728 (t60) cc_final: 0.6441 (t60) REVERT: C 110 PHE cc_start: 0.7893 (m-80) cc_final: 0.7287 (m-80) REVERT: C 165 GLU cc_start: 0.7913 (tp30) cc_final: 0.7507 (tp30) REVERT: C 198 MET cc_start: 0.8542 (tpt) cc_final: 0.8203 (tpt) REVERT: C 199 ASP cc_start: 0.8887 (m-30) cc_final: 0.8630 (m-30) REVERT: C 209 ARG cc_start: 0.8575 (ptt90) cc_final: 0.8360 (ptt90) REVERT: C 245 TRP cc_start: 0.8286 (m-90) cc_final: 0.8045 (m-90) REVERT: D 205 LYS cc_start: 0.8226 (mmpt) cc_final: 0.8011 (mmpt) REVERT: D 226 TYR cc_start: 0.7278 (p90) cc_final: 0.6283 (p90) REVERT: D 248 ASP cc_start: 0.8252 (p0) cc_final: 0.7990 (p0) REVERT: D 266 ASN cc_start: 0.8507 (m110) cc_final: 0.8168 (m110) REVERT: E 12 HIS cc_start: 0.8419 (t70) cc_final: 0.7140 (t70) REVERT: E 14 LYS cc_start: 0.8388 (mttp) cc_final: 0.7904 (mtmt) REVERT: E 15 TRP cc_start: 0.8697 (m-10) cc_final: 0.8138 (m-10) REVERT: E 16 HIS cc_start: 0.8032 (m-70) cc_final: 0.6945 (m170) REVERT: E 18 ASP cc_start: 0.7962 (t70) cc_final: 0.7689 (t70) REVERT: E 133 LYS cc_start: 0.9261 (ptpp) cc_final: 0.8454 (pttp) REVERT: E 150 GLN cc_start: 0.7832 (mm110) cc_final: 0.7427 (mm110) REVERT: E 154 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8647 (mm-30) REVERT: E 158 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7659 (tm-30) REVERT: E 159 THR cc_start: 0.8561 (m) cc_final: 0.7930 (p) REVERT: E 178 LEU cc_start: 0.8947 (mt) cc_final: 0.8722 (mt) REVERT: E 224 CYS cc_start: 0.5700 (p) cc_final: 0.5152 (p) REVERT: F 23 HIS cc_start: 0.7868 (t70) cc_final: 0.7503 (t70) REVERT: F 65 VAL cc_start: 0.7441 (t) cc_final: 0.7169 (p) REVERT: F 150 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7318 (pt0) REVERT: F 162 ASN cc_start: 0.9045 (m-40) cc_final: 0.8841 (m-40) REVERT: F 230 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8058 (mmmm) REVERT: F 233 HIS cc_start: 0.7778 (m90) cc_final: 0.7573 (m-70) REVERT: F 236 GLU cc_start: 0.7941 (pm20) cc_final: 0.7556 (pm20) REVERT: F 237 TRP cc_start: 0.8298 (m100) cc_final: 0.7997 (m100) REVERT: F 242 GLN cc_start: 0.7558 (tt0) cc_final: 0.6856 (pp30) REVERT: F 243 VAL cc_start: 0.8561 (t) cc_final: 0.7808 (p) REVERT: F 244 LEU cc_start: 0.8263 (tt) cc_final: 0.7862 (tt) REVERT: F 256 ARG cc_start: 0.8327 (ttm110) cc_final: 0.7964 (ttm110) REVERT: G 48 MET cc_start: -0.0466 (ppp) cc_final: -0.1305 (ppp) REVERT: G 62 HIS cc_start: 0.7760 (t70) cc_final: 0.7191 (t70) REVERT: G 104 MET cc_start: 0.7929 (pmm) cc_final: 0.7648 (pmm) REVERT: G 110 PHE cc_start: 0.7790 (m-80) cc_final: 0.7120 (m-10) REVERT: G 131 LEU cc_start: 0.9244 (mt) cc_final: 0.8962 (mt) REVERT: G 152 LEU cc_start: 0.8781 (tp) cc_final: 0.8556 (tp) REVERT: G 164 LEU cc_start: 0.8643 (mt) cc_final: 0.8358 (mt) REVERT: G 171 PHE cc_start: 0.7667 (m-10) cc_final: 0.7453 (m-80) REVERT: G 199 ASP cc_start: 0.8745 (m-30) cc_final: 0.8537 (m-30) REVERT: H 62 HIS cc_start: 0.7823 (t-90) cc_final: 0.7189 (t-170) REVERT: H 78 TRP cc_start: 0.7313 (m-10) cc_final: 0.6899 (m-10) REVERT: H 87 TYR cc_start: 0.8571 (t80) cc_final: 0.8031 (t80) REVERT: H 101 VAL cc_start: 0.8845 (p) cc_final: 0.8557 (p) REVERT: H 104 MET cc_start: 0.9081 (mmp) cc_final: 0.8442 (mmp) REVERT: H 106 TRP cc_start: 0.8354 (t60) cc_final: 0.7723 (t60) REVERT: H 109 MET cc_start: 0.8276 (tpt) cc_final: 0.7877 (tpp) REVERT: H 110 PHE cc_start: 0.8343 (m-10) cc_final: 0.7776 (m-10) REVERT: H 207 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7877 (mm-40) REVERT: H 223 PHE cc_start: 0.7332 (m-80) cc_final: 0.7005 (m-80) REVERT: I 30 ARG cc_start: 0.7266 (ptp-170) cc_final: 0.6950 (mtm-85) REVERT: I 60 ILE cc_start: 0.8832 (mp) cc_final: 0.8207 (mm) REVERT: I 66 ASP cc_start: 0.8052 (t0) cc_final: 0.7771 (t0) REVERT: I 79 VAL cc_start: 0.8158 (t) cc_final: 0.7564 (p) REVERT: I 86 ILE cc_start: 0.8516 (pt) cc_final: 0.8054 (mp) REVERT: I 92 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8479 (mtpp) REVERT: I 100 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7770 (mtm-85) REVERT: I 135 LEU cc_start: 0.9118 (mt) cc_final: 0.8848 (mm) REVERT: I 146 ASN cc_start: 0.8185 (m110) cc_final: 0.7971 (t0) REVERT: I 152 LEU cc_start: 0.7566 (pt) cc_final: 0.6600 (mp) REVERT: I 155 ARG cc_start: 0.8371 (tpt90) cc_final: 0.7609 (mmm160) REVERT: I 158 GLN cc_start: 0.9019 (tt0) cc_final: 0.8600 (tt0) REVERT: I 159 THR cc_start: 0.8694 (p) cc_final: 0.8374 (m) REVERT: I 164 LEU cc_start: 0.8635 (mt) cc_final: 0.8394 (mt) REVERT: I 190 LYS cc_start: 0.7999 (mttp) cc_final: 0.7372 (mptt) REVERT: I 198 MET cc_start: 0.8708 (ttm) cc_final: 0.8486 (tpp) REVERT: I 203 PHE cc_start: 0.8429 (t80) cc_final: 0.8182 (t80) REVERT: I 208 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8204 (tm-30) REVERT: I 211 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7820 (tp40) REVERT: J 15 TRP cc_start: 0.7977 (m100) cc_final: 0.7486 (m100) REVERT: J 40 CYS cc_start: 0.7391 (t) cc_final: 0.6996 (t) REVERT: J 63 TRP cc_start: 0.7662 (m100) cc_final: 0.5979 (m100) REVERT: J 86 ILE cc_start: 0.8941 (pt) cc_final: 0.8226 (mm) REVERT: J 92 LYS cc_start: 0.8928 (tptp) cc_final: 0.8540 (tptp) REVERT: J 104 MET cc_start: 0.8352 (tpp) cc_final: 0.7888 (tpp) REVERT: J 113 LYS cc_start: 0.7633 (mmmt) cc_final: 0.7431 (mmmt) REVERT: J 131 LEU cc_start: 0.8877 (tt) cc_final: 0.8504 (tt) REVERT: J 137 ILE cc_start: 0.8604 (tt) cc_final: 0.8392 (tt) REVERT: J 139 HIS cc_start: 0.8545 (t70) cc_final: 0.8150 (t70) REVERT: J 162 ASN cc_start: 0.8979 (m110) cc_final: 0.8772 (m110) REVERT: J 170 MET cc_start: 0.8171 (tmm) cc_final: 0.7933 (tmm) REVERT: J 175 GLU cc_start: 0.8819 (pm20) cc_final: 0.8616 (mp0) REVERT: J 178 LEU cc_start: 0.9151 (mm) cc_final: 0.8809 (mm) REVERT: J 198 MET cc_start: 0.8166 (tpt) cc_final: 0.7922 (tpp) REVERT: J 203 PHE cc_start: 0.8489 (t80) cc_final: 0.8100 (t80) REVERT: J 204 ASN cc_start: 0.8422 (m110) cc_final: 0.7856 (m110) REVERT: J 205 LYS cc_start: 0.8383 (tptp) cc_final: 0.7881 (tptp) REVERT: J 207 GLN cc_start: 0.8157 (mp10) cc_final: 0.7880 (mp10) REVERT: J 208 GLN cc_start: 0.8336 (pt0) cc_final: 0.7910 (pt0) REVERT: K 34 GLU cc_start: 0.8785 (pt0) cc_final: 0.8326 (pp20) REVERT: K 35 ASP cc_start: 0.8708 (m-30) cc_final: 0.8393 (m-30) REVERT: K 38 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8115 (tm-30) REVERT: K 190 LYS cc_start: 0.6715 (mttm) cc_final: 0.6273 (mmmt) REVERT: K 222 ARG cc_start: 0.7098 (ttt-90) cc_final: 0.6858 (tmt170) REVERT: K 244 LEU cc_start: 0.8085 (mm) cc_final: 0.7847 (mm) REVERT: K 245 TRP cc_start: 0.8123 (m100) cc_final: 0.7766 (m100) REVERT: L 63 TRP cc_start: 0.6730 (m100) cc_final: 0.6247 (m100) REVERT: L 209 ARG cc_start: 0.8617 (mmp-170) cc_final: 0.8339 (mmp-170) REVERT: L 266 ASN cc_start: 0.8533 (m110) cc_final: 0.8272 (m110) REVERT: L 268 ASP cc_start: 0.7036 (t0) cc_final: 0.6770 (t70) REVERT: L 269 VAL cc_start: 0.7828 (m) cc_final: 0.7528 (m) REVERT: M 7 LEU cc_start: 0.8517 (tt) cc_final: 0.7650 (tt) REVERT: M 11 GLU cc_start: 0.8375 (mp0) cc_final: 0.7943 (mp0) REVERT: M 14 LYS cc_start: 0.8347 (mttp) cc_final: 0.7855 (mtmt) REVERT: M 16 HIS cc_start: 0.7879 (m-70) cc_final: 0.7316 (m170) REVERT: M 18 ASP cc_start: 0.7869 (t70) cc_final: 0.7652 (t70) REVERT: M 25 GLU cc_start: 0.8551 (tt0) cc_final: 0.8075 (tt0) REVERT: M 36 ILE cc_start: 0.8583 (mt) cc_final: 0.8319 (mt) REVERT: M 87 TYR cc_start: 0.6912 (t80) cc_final: 0.6614 (t80) REVERT: M 110 PHE cc_start: 0.8122 (m-80) cc_final: 0.7879 (m-10) REVERT: M 133 LYS cc_start: 0.9069 (ptpp) cc_final: 0.8857 (pttm) REVERT: M 154 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8726 (mm-30) REVERT: M 158 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7802 (tm-30) REVERT: M 159 THR cc_start: 0.8848 (m) cc_final: 0.8293 (p) REVERT: M 195 THR cc_start: 0.8334 (m) cc_final: 0.8065 (p) REVERT: M 201 PHE cc_start: 0.8444 (t80) cc_final: 0.8178 (t80) REVERT: M 205 LYS cc_start: 0.9147 (mttm) cc_final: 0.8800 (mtpp) REVERT: M 207 GLN cc_start: 0.8498 (mm110) cc_final: 0.8160 (mm110) REVERT: M 209 ARG cc_start: 0.8812 (tmt170) cc_final: 0.8478 (ttp80) REVERT: M 241 THR cc_start: 0.6872 (t) cc_final: 0.6540 (t) REVERT: N 23 HIS cc_start: 0.7762 (t70) cc_final: 0.7503 (t70) REVERT: N 65 VAL cc_start: 0.7612 (t) cc_final: 0.7184 (p) REVERT: N 89 GLU cc_start: 0.6997 (tp30) cc_final: 0.6791 (tp30) REVERT: N 99 PHE cc_start: 0.8496 (m-80) cc_final: 0.7513 (m-80) REVERT: N 104 MET cc_start: 0.8172 (ptm) cc_final: 0.7584 (ppp) REVERT: N 105 LYS cc_start: 0.9388 (mtmm) cc_final: 0.9120 (mtmt) REVERT: N 127 SER cc_start: 0.8743 (t) cc_final: 0.8475 (t) REVERT: N 154 GLU cc_start: 0.8358 (mp0) cc_final: 0.8090 (mp0) REVERT: N 170 MET cc_start: 0.7071 (mpp) cc_final: 0.6830 (mpp) REVERT: N 203 PHE cc_start: 0.7978 (t80) cc_final: 0.7615 (t80) REVERT: N 210 ILE cc_start: 0.8363 (pt) cc_final: 0.8051 (pt) REVERT: N 213 GLN cc_start: 0.8752 (mt0) cc_final: 0.8232 (mt0) REVERT: N 233 HIS cc_start: 0.7706 (m90) cc_final: 0.7342 (m-70) REVERT: N 242 GLN cc_start: 0.7790 (tt0) cc_final: 0.7243 (pp30) REVERT: N 243 VAL cc_start: 0.8559 (t) cc_final: 0.7998 (p) REVERT: N 244 LEU cc_start: 0.8403 (tt) cc_final: 0.8100 (tt) REVERT: N 256 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7773 (ttm110) REVERT: N 270 LYS cc_start: 0.8038 (mptt) cc_final: 0.7495 (mptt) REVERT: O 22 LEU cc_start: 0.8546 (mm) cc_final: 0.7766 (mm) REVERT: O 40 CYS cc_start: 0.6077 (t) cc_final: 0.5863 (t) REVERT: O 48 MET cc_start: -0.1450 (ppp) cc_final: -0.1869 (ppp) REVERT: O 98 GLU cc_start: 0.8605 (pt0) cc_final: 0.8291 (pp20) REVERT: O 104 MET cc_start: 0.8122 (pmm) cc_final: 0.7902 (pmm) REVERT: O 106 TRP cc_start: 0.7576 (t60) cc_final: 0.7122 (t60) REVERT: O 110 PHE cc_start: 0.8027 (m-80) cc_final: 0.7457 (m-80) REVERT: O 115 LEU cc_start: 0.8750 (tp) cc_final: 0.8498 (tp) REVERT: O 126 GLU cc_start: 0.8812 (pm20) cc_final: 0.8465 (pm20) REVERT: O 152 LEU cc_start: 0.8839 (tp) cc_final: 0.8619 (tp) REVERT: O 157 HIS cc_start: 0.9065 (m90) cc_final: 0.8844 (m90) REVERT: O 206 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7991 (tm-30) REVERT: O 208 GLN cc_start: 0.8766 (tm130) cc_final: 0.8552 (tm-30) REVERT: O 209 ARG cc_start: 0.8868 (ptm-80) cc_final: 0.8479 (ptm-80) REVERT: P 62 HIS cc_start: 0.7974 (t-90) cc_final: 0.7381 (t-170) REVERT: P 100 ARG cc_start: 0.5482 (mtt90) cc_final: 0.5085 (mtm-85) REVERT: P 104 MET cc_start: 0.9138 (mmp) cc_final: 0.8641 (mmp) REVERT: P 106 TRP cc_start: 0.8545 (t60) cc_final: 0.8041 (t60) REVERT: P 132 MET cc_start: 0.6644 (tmm) cc_final: 0.6162 (tmm) REVERT: P 137 ILE cc_start: 0.8371 (mm) cc_final: 0.8167 (mm) REVERT: P 170 MET cc_start: 0.7728 (mtt) cc_final: 0.7287 (mpp) REVERT: P 207 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8003 (mm-40) REVERT: P 222 ARG cc_start: 0.6384 (mmm-85) cc_final: 0.5889 (mmm160) REVERT: P 223 PHE cc_start: 0.6704 (m-80) cc_final: 0.6441 (m-80) REVERT: P 230 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7571 (mmtm) REVERT: P 233 HIS cc_start: 0.6788 (m-70) cc_final: 0.6573 (m-70) REVERT: P 236 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7539 (pp20) REVERT: P 272 ILE cc_start: 0.8031 (mm) cc_final: 0.7794 (mm) outliers start: 3 outliers final: 0 residues processed: 1208 average time/residue: 0.2079 time to fit residues: 395.0103 Evaluate side-chains 1108 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1108 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 349 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 373 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 209 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 356 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 211 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN E 204 ASN E 218 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN G 211 GLN H 62 HIS H 69 HIS ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** I 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN J 242 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN L 158 GLN L 186 ASN ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS M 238 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 62 HIS O 208 GLN P 62 HIS ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.195916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148971 restraints weight = 71983.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154548 restraints weight = 45143.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.158431 restraints weight = 31644.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161223 restraints weight = 24011.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.163229 restraints weight = 19376.396| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34119 Z= 0.147 Angle : 0.684 13.084 46515 Z= 0.361 Chirality : 0.048 0.239 5006 Planarity : 0.005 0.085 5714 Dihedral : 14.715 173.648 5007 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 0.09 % Allowed : 2.36 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.33 (0.13), residues: 3851 helix: 0.91 (0.12), residues: 1873 sheet: -0.61 (0.18), residues: 816 loop : -1.67 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 155 TYR 0.023 0.001 TYR O 70 PHE 0.042 0.002 PHE H 201 TRP 0.039 0.002 TRP F 15 HIS 0.014 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00315 (34119) covalent geometry : angle 0.68376 (46515) hydrogen bonds : bond 0.03930 ( 1746) hydrogen bonds : angle 5.28860 ( 5114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1182 time to evaluate : 1.149 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: 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: 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: A 60 ILE cc_start: 0.8688 (mm) cc_final: 0.8186 (mm) REVERT: A 62 HIS cc_start: 0.7833 (t70) cc_final: 0.7585 (t70) REVERT: A 64 GLN cc_start: 0.6653 (pm20) cc_final: 0.6415 (pm20) REVERT: A 79 VAL cc_start: 0.8098 (t) cc_final: 0.7685 (p) REVERT: A 90 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7637 (tmm-80) REVERT: A 92 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8441 (mtpp) REVERT: A 100 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7648 (mtm110) REVERT: A 104 MET cc_start: 0.8379 (ttm) cc_final: 0.7752 (ttm) REVERT: A 107 TYR cc_start: 0.8354 (t80) cc_final: 0.8047 (t80) REVERT: A 113 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7672 (mmmm) REVERT: A 118 ASP cc_start: 0.7691 (p0) cc_final: 0.7409 (p0) REVERT: A 129 GLN cc_start: 0.7869 (tt0) cc_final: 0.7595 (tt0) REVERT: A 132 MET cc_start: 0.8268 (mmm) cc_final: 0.8021 (mmm) REVERT: A 135 LEU cc_start: 0.8882 (mt) cc_final: 0.8499 (mt) REVERT: A 146 ASN cc_start: 0.8337 (t0) cc_final: 0.7719 (m-40) REVERT: A 161 LYS cc_start: 0.8753 (tptt) cc_final: 0.8543 (tptt) REVERT: A 164 LEU cc_start: 0.8392 (mt) cc_final: 0.8181 (mt) REVERT: A 190 LYS cc_start: 0.7815 (ptpp) cc_final: 0.7582 (ptpp) REVERT: A 203 PHE cc_start: 0.8479 (t80) cc_final: 0.8022 (t80) REVERT: A 211 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7782 (tp-100) REVERT: A 226 TYR cc_start: 0.6569 (p90) cc_final: 0.4592 (p90) REVERT: A 242 GLN cc_start: 0.7037 (tp-100) cc_final: 0.6774 (tp-100) REVERT: A 254 LYS cc_start: 0.8200 (pptt) cc_final: 0.7916 (pptt) REVERT: A 256 ARG cc_start: 0.7323 (pmt170) cc_final: 0.6759 (pmt170) REVERT: A 260 ARG cc_start: 0.7388 (ptm160) cc_final: 0.7179 (ptm160) REVERT: B 15 TRP cc_start: 0.7807 (m100) cc_final: 0.7252 (m100) REVERT: B 40 CYS cc_start: 0.7554 (t) cc_final: 0.6982 (p) REVERT: B 63 TRP cc_start: 0.7830 (m100) cc_final: 0.6273 (m100) REVERT: B 64 GLN cc_start: 0.6811 (tp40) cc_final: 0.5995 (tp40) REVERT: B 82 ASN cc_start: 0.8106 (p0) cc_final: 0.7875 (p0) REVERT: B 86 ILE cc_start: 0.8737 (pt) cc_final: 0.8228 (mm) REVERT: B 89 GLU cc_start: 0.7757 (tt0) cc_final: 0.7335 (tt0) REVERT: B 92 LYS cc_start: 0.8870 (tppt) cc_final: 0.8251 (tptp) REVERT: B 102 GLN cc_start: 0.8701 (mp10) cc_final: 0.8278 (mm-40) REVERT: B 104 MET cc_start: 0.8528 (mmp) cc_final: 0.8055 (mmp) REVERT: B 129 GLN cc_start: 0.8453 (pt0) cc_final: 0.8080 (pt0) REVERT: B 132 MET cc_start: 0.8706 (tpp) cc_final: 0.8048 (tpp) REVERT: B 137 ILE cc_start: 0.8293 (tt) cc_final: 0.7752 (tt) REVERT: B 138 GLU cc_start: 0.7906 (tp30) cc_final: 0.7653 (tp30) REVERT: B 139 HIS cc_start: 0.8425 (t70) cc_final: 0.7998 (t70) REVERT: B 157 HIS cc_start: 0.8813 (m90) cc_final: 0.8566 (m90) REVERT: B 165 GLU cc_start: 0.7990 (tp30) cc_final: 0.7654 (tp30) REVERT: B 175 GLU cc_start: 0.8791 (pm20) cc_final: 0.8471 (mp0) REVERT: B 178 LEU cc_start: 0.9132 (mm) cc_final: 0.8734 (mm) REVERT: B 186 ASN cc_start: 0.8253 (m-40) cc_final: 0.8053 (m-40) REVERT: B 198 MET cc_start: 0.8058 (tpt) cc_final: 0.7626 (tpp) REVERT: C 5 ILE cc_start: 0.9316 (mt) cc_final: 0.9083 (mt) REVERT: C 11 GLU cc_start: 0.8238 (tp30) cc_final: 0.7361 (tp30) REVERT: C 39 GLN cc_start: 0.8481 (tp40) cc_final: 0.7775 (tp40) REVERT: C 62 HIS cc_start: 0.7582 (t70) cc_final: 0.7302 (t70) REVERT: C 106 TRP cc_start: 0.6732 (t60) cc_final: 0.6479 (t60) REVERT: C 110 PHE cc_start: 0.7892 (m-80) cc_final: 0.7069 (m-80) REVERT: C 132 MET cc_start: 0.8265 (ppp) cc_final: 0.7755 (ppp) REVERT: C 162 ASN cc_start: 0.8832 (m-40) cc_final: 0.8315 (m-40) REVERT: C 190 LYS cc_start: 0.6799 (mttm) cc_final: 0.6389 (mmmt) REVERT: C 198 MET cc_start: 0.8683 (tpt) cc_final: 0.7971 (tpt) REVERT: C 199 ASP cc_start: 0.8907 (m-30) cc_final: 0.8605 (m-30) REVERT: C 202 ILE cc_start: 0.8219 (mt) cc_final: 0.7958 (mt) REVERT: D 205 LYS cc_start: 0.8251 (mmpt) cc_final: 0.8042 (mmpt) REVERT: D 218 GLN cc_start: 0.8453 (mm110) cc_final: 0.7941 (mm110) REVERT: D 223 PHE cc_start: 0.5891 (p90) cc_final: 0.5541 (p90) REVERT: D 224 CYS cc_start: 0.7064 (p) cc_final: 0.6859 (p) REVERT: D 226 TYR cc_start: 0.6628 (p90) cc_final: 0.5748 (p90) REVERT: D 254 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8014 (ttmt) REVERT: D 266 ASN cc_start: 0.8488 (m110) cc_final: 0.8166 (m110) REVERT: E 12 HIS cc_start: 0.8282 (t70) cc_final: 0.7075 (t70) REVERT: E 14 LYS cc_start: 0.8256 (mttp) cc_final: 0.7572 (mtpt) REVERT: E 15 TRP cc_start: 0.8652 (m-10) cc_final: 0.8243 (m-10) REVERT: E 16 HIS cc_start: 0.7945 (m-70) cc_final: 0.6916 (m170) REVERT: E 101 VAL cc_start: 0.8775 (t) cc_final: 0.8545 (t) REVERT: E 138 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7557 (tm-30) REVERT: E 150 GLN cc_start: 0.7796 (mm110) cc_final: 0.7394 (mm110) REVERT: E 154 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8606 (mm-30) REVERT: E 158 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7585 (tm-30) REVERT: E 159 THR cc_start: 0.8529 (m) cc_final: 0.7859 (p) REVERT: E 178 LEU cc_start: 0.8931 (mt) cc_final: 0.8652 (mt) REVERT: E 202 ILE cc_start: 0.8787 (mp) cc_final: 0.8585 (mp) REVERT: E 206 GLU cc_start: 0.8632 (pt0) cc_final: 0.8354 (pt0) REVERT: E 224 CYS cc_start: 0.5816 (p) cc_final: 0.5120 (p) REVERT: E 260 ARG cc_start: 0.7824 (pmt-80) cc_final: 0.7521 (pmt-80) REVERT: F 23 HIS cc_start: 0.7878 (t70) cc_final: 0.7464 (t70) REVERT: F 65 VAL cc_start: 0.7249 (t) cc_final: 0.6806 (p) REVERT: F 104 MET cc_start: 0.7987 (ptm) cc_final: 0.7521 (ppp) REVERT: F 105 LYS cc_start: 0.9245 (mtmm) cc_final: 0.8975 (mttt) REVERT: F 162 ASN cc_start: 0.9014 (m-40) cc_final: 0.8584 (m-40) REVERT: F 164 LEU cc_start: 0.8450 (mt) cc_final: 0.8189 (mt) REVERT: F 207 GLN cc_start: 0.8578 (mp10) cc_final: 0.8285 (mp10) REVERT: F 208 GLN cc_start: 0.8419 (tt0) cc_final: 0.8216 (tt0) REVERT: F 230 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8012 (mmmm) REVERT: F 236 GLU cc_start: 0.7862 (pm20) cc_final: 0.7556 (pm20) REVERT: F 237 TRP cc_start: 0.8258 (m100) cc_final: 0.7971 (m100) REVERT: F 242 GLN cc_start: 0.7453 (tt0) cc_final: 0.6716 (pp30) REVERT: F 243 VAL cc_start: 0.8491 (t) cc_final: 0.7397 (m) REVERT: F 244 LEU cc_start: 0.8252 (tt) cc_final: 0.7782 (tt) REVERT: F 256 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7942 (ttm110) REVERT: G 48 MET cc_start: -0.0431 (ppp) cc_final: -0.1281 (ppp) REVERT: G 62 HIS cc_start: 0.7722 (t70) cc_final: 0.6887 (t70) REVERT: G 70 TYR cc_start: 0.6894 (t80) cc_final: 0.2754 (t80) REVERT: G 104 MET cc_start: 0.8059 (pmm) cc_final: 0.7686 (pmm) REVERT: G 106 TRP cc_start: 0.7008 (t60) cc_final: 0.6802 (t60) REVERT: G 110 PHE cc_start: 0.7666 (m-80) cc_final: 0.7179 (m-10) REVERT: G 131 LEU cc_start: 0.9249 (mt) cc_final: 0.8955 (mt) REVERT: G 157 HIS cc_start: 0.8910 (p-80) cc_final: 0.8625 (p90) REVERT: G 158 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8963 (tp-100) REVERT: G 161 LYS cc_start: 0.9139 (mmpt) cc_final: 0.8847 (tppt) REVERT: G 164 LEU cc_start: 0.8748 (mt) cc_final: 0.8384 (mt) REVERT: G 171 PHE cc_start: 0.7656 (m-10) cc_final: 0.7420 (m-80) REVERT: G 175 GLU cc_start: 0.8584 (mp0) cc_final: 0.8160 (mm-30) REVERT: G 199 ASP cc_start: 0.8699 (m-30) cc_final: 0.8395 (m-30) REVERT: H 62 HIS cc_start: 0.7907 (t70) cc_final: 0.7206 (t70) REVERT: H 78 TRP cc_start: 0.7237 (m-10) cc_final: 0.6492 (m-10) REVERT: H 87 TYR cc_start: 0.8602 (t80) cc_final: 0.8040 (t80) REVERT: H 101 VAL cc_start: 0.8785 (p) cc_final: 0.8563 (p) REVERT: H 104 MET cc_start: 0.9041 (mmp) cc_final: 0.8390 (mmp) REVERT: H 106 TRP cc_start: 0.8301 (t60) cc_final: 0.7248 (t60) REVERT: H 109 MET cc_start: 0.8249 (tpt) cc_final: 0.7849 (tpp) REVERT: H 110 PHE cc_start: 0.8199 (m-10) cc_final: 0.7717 (m-10) REVERT: H 207 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7769 (mm-40) REVERT: H 223 PHE cc_start: 0.7325 (m-80) cc_final: 0.6705 (m-80) REVERT: I 30 ARG cc_start: 0.7255 (ptp-170) cc_final: 0.6858 (mtm-85) REVERT: I 60 ILE cc_start: 0.8845 (mp) cc_final: 0.8324 (mm) REVERT: I 66 ASP cc_start: 0.7946 (t0) cc_final: 0.7744 (t0) REVERT: I 79 VAL cc_start: 0.8203 (t) cc_final: 0.7550 (p) REVERT: I 86 ILE cc_start: 0.8576 (pt) cc_final: 0.8058 (mp) REVERT: I 92 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8402 (mtpp) REVERT: I 98 GLU cc_start: 0.8255 (mp0) cc_final: 0.8049 (mp0) REVERT: I 100 ARG cc_start: 0.8232 (mtt90) cc_final: 0.7467 (mtm-85) REVERT: I 113 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7634 (mmmm) REVERT: I 146 ASN cc_start: 0.8180 (m110) cc_final: 0.7885 (t0) REVERT: I 152 LEU cc_start: 0.7479 (pt) cc_final: 0.6418 (mp) REVERT: I 155 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7548 (mmm160) REVERT: I 158 GLN cc_start: 0.9098 (tt0) cc_final: 0.8615 (tt0) REVERT: I 160 LEU cc_start: 0.8710 (tt) cc_final: 0.8499 (tt) REVERT: I 164 LEU cc_start: 0.8663 (mt) cc_final: 0.8429 (mt) REVERT: I 183 ILE cc_start: 0.8992 (mt) cc_final: 0.8557 (mm) REVERT: I 190 LYS cc_start: 0.7975 (mttp) cc_final: 0.7511 (mptt) REVERT: I 198 MET cc_start: 0.8686 (ttm) cc_final: 0.8406 (tpp) REVERT: I 203 PHE cc_start: 0.8361 (t80) cc_final: 0.8138 (t80) REVERT: I 211 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7754 (tp40) REVERT: I 243 VAL cc_start: 0.8469 (p) cc_final: 0.8217 (p) REVERT: J 7 LEU cc_start: 0.7791 (mt) cc_final: 0.7550 (mt) REVERT: J 13 ASN cc_start: 0.7216 (m-40) cc_final: 0.6823 (m110) REVERT: J 15 TRP cc_start: 0.7928 (m100) cc_final: 0.7434 (m100) REVERT: J 40 CYS cc_start: 0.7255 (t) cc_final: 0.6921 (t) REVERT: J 63 TRP cc_start: 0.7676 (m100) cc_final: 0.6341 (m100) REVERT: J 64 GLN cc_start: 0.7054 (tp40) cc_final: 0.6672 (mp10) REVERT: J 86 ILE cc_start: 0.8919 (pt) cc_final: 0.8266 (mm) REVERT: J 92 LYS cc_start: 0.8951 (tptp) cc_final: 0.8556 (tptp) REVERT: J 104 MET cc_start: 0.8223 (tpp) cc_final: 0.7555 (tpp) REVERT: J 106 TRP cc_start: 0.8543 (t60) cc_final: 0.8295 (t60) REVERT: J 131 LEU cc_start: 0.8737 (tt) cc_final: 0.8371 (tt) REVERT: J 139 HIS cc_start: 0.8582 (t70) cc_final: 0.8069 (t70) REVERT: J 162 ASN cc_start: 0.8941 (m110) cc_final: 0.8736 (m110) REVERT: J 175 GLU cc_start: 0.8678 (pm20) cc_final: 0.8368 (mp0) REVERT: J 178 LEU cc_start: 0.9150 (mm) cc_final: 0.8780 (mm) REVERT: J 198 MET cc_start: 0.8133 (tpt) cc_final: 0.7815 (tpp) REVERT: J 204 ASN cc_start: 0.8564 (m110) cc_final: 0.8137 (m110) REVERT: J 205 LYS cc_start: 0.8505 (tptp) cc_final: 0.8122 (tptp) REVERT: J 208 GLN cc_start: 0.8225 (pt0) cc_final: 0.7934 (pt0) REVERT: K 30 ARG cc_start: 0.9024 (ttt180) cc_final: 0.8451 (ttt180) REVERT: K 35 ASP cc_start: 0.8686 (m-30) cc_final: 0.8474 (m-30) REVERT: K 158 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8205 (tp-100) REVERT: K 205 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8661 (mmmt) REVERT: K 244 LEU cc_start: 0.8138 (mm) cc_final: 0.7924 (mm) REVERT: K 245 TRP cc_start: 0.8110 (m100) cc_final: 0.7776 (m100) REVERT: L 63 TRP cc_start: 0.6750 (m100) cc_final: 0.6155 (m100) REVERT: L 226 TYR cc_start: 0.6637 (p90) cc_final: 0.5609 (p90) REVERT: L 266 ASN cc_start: 0.8458 (m110) cc_final: 0.8188 (m110) REVERT: L 268 ASP cc_start: 0.7027 (t0) cc_final: 0.6741 (t70) REVERT: L 269 VAL cc_start: 0.7822 (m) cc_final: 0.7496 (m) REVERT: M 14 LYS cc_start: 0.8351 (mttp) cc_final: 0.7884 (mtmt) REVERT: M 15 TRP cc_start: 0.8427 (m-10) cc_final: 0.8213 (m-10) REVERT: M 16 HIS cc_start: 0.7770 (m-70) cc_final: 0.7256 (m-70) REVERT: M 18 ASP cc_start: 0.7769 (t70) cc_final: 0.7429 (t70) REVERT: M 25 GLU cc_start: 0.8466 (tt0) cc_final: 0.8052 (tt0) REVERT: M 36 ILE cc_start: 0.8581 (mt) cc_final: 0.8276 (mt) REVERT: M 87 TYR cc_start: 0.6681 (t80) cc_final: 0.6298 (t80) REVERT: M 89 GLU cc_start: 0.6370 (mp0) cc_final: 0.6027 (mp0) REVERT: M 154 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8711 (mm-30) REVERT: M 155 ARG cc_start: 0.8648 (ttt180) cc_final: 0.8376 (mtt90) REVERT: M 158 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7765 (tm-30) REVERT: M 159 THR cc_start: 0.8822 (m) cc_final: 0.8276 (p) REVERT: M 195 THR cc_start: 0.8270 (m) cc_final: 0.7982 (p) REVERT: M 207 GLN cc_start: 0.8452 (mm110) cc_final: 0.8115 (mm110) REVERT: M 209 ARG cc_start: 0.8793 (tmt170) cc_final: 0.8445 (ttp80) REVERT: N 23 HIS cc_start: 0.7829 (t70) cc_final: 0.7555 (t70) REVERT: N 104 MET cc_start: 0.8134 (ptm) cc_final: 0.7538 (ppp) REVERT: N 161 LYS cc_start: 0.8946 (ptpp) cc_final: 0.8596 (ptpp) REVERT: N 165 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7998 (mm-30) REVERT: N 203 PHE cc_start: 0.7826 (t80) cc_final: 0.7475 (t80) REVERT: N 210 ILE cc_start: 0.8410 (pt) cc_final: 0.8070 (pt) REVERT: N 213 GLN cc_start: 0.8740 (mt0) cc_final: 0.8126 (mt0) REVERT: N 233 HIS cc_start: 0.7714 (m90) cc_final: 0.7426 (m-70) REVERT: N 242 GLN cc_start: 0.7728 (tt0) cc_final: 0.7203 (pp30) REVERT: N 243 VAL cc_start: 0.8512 (t) cc_final: 0.8019 (p) REVERT: N 244 LEU cc_start: 0.8327 (tt) cc_final: 0.8033 (tt) REVERT: N 256 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7751 (ttm110) REVERT: N 270 LYS cc_start: 0.8028 (mptt) cc_final: 0.7475 (mptt) REVERT: O 23 HIS cc_start: 0.7426 (t70) cc_final: 0.6839 (t70) REVERT: O 48 MET cc_start: -0.1407 (ppp) cc_final: -0.1828 (ppp) REVERT: O 62 HIS cc_start: 0.7362 (p-80) cc_final: 0.7073 (m-70) REVERT: O 104 MET cc_start: 0.8119 (pmm) cc_final: 0.7834 (pmm) REVERT: O 152 LEU cc_start: 0.8826 (tp) cc_final: 0.8591 (tp) REVERT: O 157 HIS cc_start: 0.8975 (m90) cc_final: 0.8774 (m90) REVERT: O 193 LEU cc_start: 0.8767 (mm) cc_final: 0.8531 (mm) REVERT: O 207 GLN cc_start: 0.8691 (mp10) cc_final: 0.8457 (mp10) REVERT: O 209 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.8449 (ptm-80) REVERT: P 62 HIS cc_start: 0.7829 (t70) cc_final: 0.7275 (t70) REVERT: P 87 TYR cc_start: 0.8563 (t80) cc_final: 0.8355 (t80) REVERT: P 104 MET cc_start: 0.9109 (mmp) cc_final: 0.8585 (mmp) REVERT: P 106 TRP cc_start: 0.8440 (t60) cc_final: 0.7957 (t60) REVERT: P 115 LEU cc_start: 0.4770 (tp) cc_final: 0.4569 (tp) REVERT: P 137 ILE cc_start: 0.8386 (mm) cc_final: 0.8186 (mm) REVERT: P 170 MET cc_start: 0.7688 (mtt) cc_final: 0.7219 (mpp) REVERT: P 172 ASN cc_start: 0.8826 (m-40) cc_final: 0.8531 (p0) REVERT: P 205 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8387 (pttt) REVERT: P 207 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7970 (mm-40) REVERT: P 222 ARG cc_start: 0.6802 (mmm-85) cc_final: 0.6539 (mmm-85) REVERT: P 230 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7483 (mmtm) REVERT: P 236 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7343 (pp20) outliers start: 3 outliers final: 2 residues processed: 1184 average time/residue: 0.2096 time to fit residues: 390.6472 Evaluate side-chains 1106 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1104 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 145 optimal weight: 0.7980 chunk 362 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 170 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN B 242 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN E 204 ASN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN G 208 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN H 157 HIS H 242 GLN ** I 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 GLN J 102 GLN J 157 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 GLN L 158 GLN ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN O 211 GLN P 157 HIS P 242 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.192149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145333 restraints weight = 73331.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.150766 restraints weight = 45454.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154549 restraints weight = 31681.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.157189 restraints weight = 23948.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159062 restraints weight = 19332.348| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34119 Z= 0.177 Angle : 0.727 13.424 46515 Z= 0.388 Chirality : 0.049 0.249 5006 Planarity : 0.005 0.067 5714 Dihedral : 14.792 173.756 5007 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.42 (0.13), residues: 3851 helix: 0.82 (0.12), residues: 1861 sheet: -0.74 (0.18), residues: 827 loop : -1.62 (0.16), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 256 TYR 0.028 0.002 TYR F 225 PHE 0.040 0.002 PHE K 26 TRP 0.045 0.002 TRP B 106 HIS 0.010 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00374 (34119) covalent geometry : angle 0.72662 (46515) hydrogen bonds : bond 0.04222 ( 1746) hydrogen bonds : angle 5.47484 ( 5114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1210 time to evaluate : 1.116 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: 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: 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: A 66 ASP cc_start: 0.7807 (t70) cc_final: 0.7330 (t70) REVERT: A 79 VAL cc_start: 0.8171 (t) cc_final: 0.7780 (p) REVERT: A 80 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6459 (tm-30) REVERT: A 85 LEU cc_start: 0.8130 (tt) cc_final: 0.7862 (tt) REVERT: A 92 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8558 (mtpp) REVERT: A 104 MET cc_start: 0.8417 (ttm) cc_final: 0.7751 (ttm) REVERT: A 107 TYR cc_start: 0.8454 (t80) cc_final: 0.8177 (t80) REVERT: A 113 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7688 (mmmm) REVERT: A 118 ASP cc_start: 0.7724 (p0) cc_final: 0.7447 (p0) REVERT: A 129 GLN cc_start: 0.8119 (tt0) cc_final: 0.7806 (tt0) REVERT: A 135 LEU cc_start: 0.8915 (mt) cc_final: 0.8682 (mt) REVERT: A 155 ARG cc_start: 0.8383 (tpt90) cc_final: 0.7619 (mmm160) REVERT: A 158 GLN cc_start: 0.8636 (tt0) cc_final: 0.8163 (tt0) REVERT: A 161 LYS cc_start: 0.8822 (tptt) cc_final: 0.8574 (tptt) REVERT: A 164 LEU cc_start: 0.8440 (mt) cc_final: 0.8198 (mt) REVERT: A 178 LEU cc_start: 0.8097 (tp) cc_final: 0.7715 (tp) REVERT: A 188 LYS cc_start: 0.7028 (mmtm) cc_final: 0.6802 (mmtm) REVERT: A 190 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7282 (mtpt) REVERT: A 203 PHE cc_start: 0.8544 (t80) cc_final: 0.8135 (t80) REVERT: A 211 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7805 (tp-100) REVERT: A 226 TYR cc_start: 0.6720 (p90) cc_final: 0.5194 (p90) REVERT: A 242 GLN cc_start: 0.6996 (tp-100) cc_final: 0.6672 (tp40) REVERT: A 244 LEU cc_start: 0.8708 (mp) cc_final: 0.8444 (mp) REVERT: A 254 LYS cc_start: 0.8154 (pptt) cc_final: 0.7869 (pptt) REVERT: A 256 ARG cc_start: 0.7263 (pmt170) cc_final: 0.6703 (pmt170) REVERT: A 260 ARG cc_start: 0.7420 (ptm160) cc_final: 0.7157 (ptm160) REVERT: B 15 TRP cc_start: 0.7796 (m100) cc_final: 0.7184 (m100) REVERT: B 40 CYS cc_start: 0.7534 (t) cc_final: 0.6938 (p) REVERT: B 60 ILE cc_start: 0.7368 (mm) cc_final: 0.6977 (mm) REVERT: B 63 TRP cc_start: 0.7845 (m100) cc_final: 0.6229 (m100) REVERT: B 64 GLN cc_start: 0.6775 (tp40) cc_final: 0.6333 (mm-40) REVERT: B 86 ILE cc_start: 0.8786 (pt) cc_final: 0.8366 (mm) REVERT: B 87 TYR cc_start: 0.7977 (t80) cc_final: 0.7759 (t80) REVERT: B 89 GLU cc_start: 0.7866 (tt0) cc_final: 0.7207 (tt0) REVERT: B 92 LYS cc_start: 0.8957 (tppt) cc_final: 0.8725 (tppp) REVERT: B 102 GLN cc_start: 0.8460 (mp10) cc_final: 0.8167 (mp10) REVERT: B 104 MET cc_start: 0.8688 (mmp) cc_final: 0.8323 (mmp) REVERT: B 106 TRP cc_start: 0.8456 (t60) cc_final: 0.8147 (t60) REVERT: B 129 GLN cc_start: 0.8474 (pt0) cc_final: 0.8105 (pt0) REVERT: B 132 MET cc_start: 0.8761 (tpp) cc_final: 0.8070 (tpp) REVERT: B 137 ILE cc_start: 0.8298 (tt) cc_final: 0.7740 (tt) REVERT: B 139 HIS cc_start: 0.8463 (t70) cc_final: 0.7987 (t70) REVERT: B 157 HIS cc_start: 0.8698 (m90) cc_final: 0.8356 (m90) REVERT: B 164 LEU cc_start: 0.8872 (tp) cc_final: 0.8631 (tp) REVERT: B 165 GLU cc_start: 0.8034 (tp30) cc_final: 0.7688 (tp30) REVERT: B 175 GLU cc_start: 0.8752 (pm20) cc_final: 0.8461 (mp0) REVERT: B 178 LEU cc_start: 0.9141 (mm) cc_final: 0.8758 (mm) REVERT: B 186 ASN cc_start: 0.8423 (m-40) cc_final: 0.8090 (m-40) REVERT: B 198 MET cc_start: 0.8074 (tpt) cc_final: 0.7599 (tpp) REVERT: B 204 ASN cc_start: 0.8032 (p0) cc_final: 0.7706 (p0) REVERT: B 208 GLN cc_start: 0.8691 (mt0) cc_final: 0.8263 (mt0) REVERT: C 11 GLU cc_start: 0.8303 (tp30) cc_final: 0.7462 (tp30) REVERT: C 30 ARG cc_start: 0.8874 (ttt90) cc_final: 0.8207 (ttt90) REVERT: C 38 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7670 (tp-100) REVERT: C 39 GLN cc_start: 0.8488 (tp40) cc_final: 0.7911 (tp40) REVERT: C 110 PHE cc_start: 0.7826 (m-80) cc_final: 0.7236 (m-80) REVERT: C 132 MET cc_start: 0.8425 (ppp) cc_final: 0.8194 (ppp) REVERT: C 162 ASN cc_start: 0.8901 (m-40) cc_final: 0.8546 (m-40) REVERT: C 190 LYS cc_start: 0.6773 (mttm) cc_final: 0.6532 (mmmt) REVERT: C 198 MET cc_start: 0.8578 (tpt) cc_final: 0.8084 (tpt) REVERT: C 199 ASP cc_start: 0.8902 (m-30) cc_final: 0.8605 (m-30) REVERT: C 209 ARG cc_start: 0.8633 (ptt90) cc_final: 0.8428 (ptt90) REVERT: C 245 TRP cc_start: 0.8421 (m-90) cc_final: 0.8113 (m-90) REVERT: D 205 LYS cc_start: 0.8226 (mmpt) cc_final: 0.8007 (mmpt) REVERT: D 209 ARG cc_start: 0.8701 (mmp-170) cc_final: 0.8454 (mmp-170) REVERT: D 218 GLN cc_start: 0.8523 (mm110) cc_final: 0.7939 (mm110) REVERT: D 226 TYR cc_start: 0.6905 (p90) cc_final: 0.6007 (p90) REVERT: D 254 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7958 (ttmt) REVERT: D 262 LEU cc_start: 0.8235 (mm) cc_final: 0.7984 (mm) REVERT: D 266 ASN cc_start: 0.8584 (m110) cc_final: 0.8117 (m110) REVERT: D 268 ASP cc_start: 0.6977 (t70) cc_final: 0.6777 (t70) REVERT: E 7 LEU cc_start: 0.8499 (tt) cc_final: 0.7983 (tt) REVERT: E 12 HIS cc_start: 0.8442 (t70) cc_final: 0.7339 (t70) REVERT: E 14 LYS cc_start: 0.8328 (mttp) cc_final: 0.7663 (mtmt) REVERT: E 15 TRP cc_start: 0.8673 (m-10) cc_final: 0.8416 (m-10) REVERT: E 16 HIS cc_start: 0.7659 (m-70) cc_final: 0.6919 (m170) REVERT: E 138 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7661 (tm-30) REVERT: E 150 GLN cc_start: 0.7880 (mm110) cc_final: 0.7369 (mm110) REVERT: E 154 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8583 (mm-30) REVERT: E 158 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7590 (tm-30) REVERT: E 159 THR cc_start: 0.8533 (m) cc_final: 0.7848 (p) REVERT: E 200 ILE cc_start: 0.8764 (mp) cc_final: 0.8553 (mp) REVERT: E 202 ILE cc_start: 0.8844 (mp) cc_final: 0.8598 (mp) REVERT: E 206 GLU cc_start: 0.8539 (pt0) cc_final: 0.8178 (pt0) REVERT: E 209 ARG cc_start: 0.8642 (tmt170) cc_final: 0.8296 (ttp80) REVERT: E 270 LYS cc_start: 0.8435 (mtmt) cc_final: 0.7887 (mtmt) REVERT: F 23 HIS cc_start: 0.7887 (t70) cc_final: 0.7487 (t70) REVERT: F 65 VAL cc_start: 0.7603 (t) cc_final: 0.7259 (p) REVERT: F 89 GLU cc_start: 0.6416 (tp30) cc_final: 0.6058 (tp30) REVERT: F 105 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8986 (mttt) REVERT: F 157 HIS cc_start: 0.7816 (m90) cc_final: 0.7334 (m90) REVERT: F 202 ILE cc_start: 0.8496 (mt) cc_final: 0.8084 (mt) REVERT: F 204 ASN cc_start: 0.8729 (p0) cc_final: 0.8477 (p0) REVERT: F 206 GLU cc_start: 0.8359 (pp20) cc_final: 0.7341 (pp20) REVERT: F 230 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8017 (mmmm) REVERT: F 233 HIS cc_start: 0.7863 (m-70) cc_final: 0.7580 (m-70) REVERT: F 242 GLN cc_start: 0.7580 (tt0) cc_final: 0.7147 (pp30) REVERT: F 243 VAL cc_start: 0.8528 (t) cc_final: 0.7443 (m) REVERT: F 244 LEU cc_start: 0.8297 (tt) cc_final: 0.7961 (tt) REVERT: F 256 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7913 (ttm110) REVERT: G 48 MET cc_start: -0.0476 (ppp) cc_final: -0.1288 (ppp) REVERT: G 62 HIS cc_start: 0.7659 (t70) cc_final: 0.6724 (t70) REVERT: G 70 TYR cc_start: 0.6974 (t80) cc_final: 0.3251 (t80) REVERT: G 85 LEU cc_start: 0.7270 (tp) cc_final: 0.7019 (tp) REVERT: G 110 PHE cc_start: 0.7812 (m-80) cc_final: 0.7389 (m-10) REVERT: G 131 LEU cc_start: 0.9318 (mt) cc_final: 0.9048 (mt) REVERT: G 157 HIS cc_start: 0.8964 (p-80) cc_final: 0.8663 (p90) REVERT: G 158 GLN cc_start: 0.9263 (tp-100) cc_final: 0.8994 (tp40) REVERT: G 161 LYS cc_start: 0.9225 (mmpt) cc_final: 0.8863 (tppt) REVERT: G 164 LEU cc_start: 0.8696 (mt) cc_final: 0.8266 (mt) REVERT: G 171 PHE cc_start: 0.7627 (m-10) cc_final: 0.7391 (m-80) REVERT: G 175 GLU cc_start: 0.8591 (mp0) cc_final: 0.8252 (mm-30) REVERT: G 199 ASP cc_start: 0.8697 (m-30) cc_final: 0.8371 (m-30) REVERT: H 62 HIS cc_start: 0.7962 (t70) cc_final: 0.7265 (t70) REVERT: H 78 TRP cc_start: 0.7465 (m-10) cc_final: 0.6118 (m-10) REVERT: H 87 TYR cc_start: 0.8604 (t80) cc_final: 0.8056 (t80) REVERT: H 101 VAL cc_start: 0.8781 (p) cc_final: 0.8554 (p) REVERT: H 104 MET cc_start: 0.9056 (mmp) cc_final: 0.8392 (mmp) REVERT: H 106 TRP cc_start: 0.8325 (t60) cc_final: 0.7140 (t60) REVERT: H 109 MET cc_start: 0.8299 (tpt) cc_final: 0.7879 (tpp) REVERT: H 110 PHE cc_start: 0.8341 (m-10) cc_final: 0.7650 (m-10) REVERT: H 207 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7797 (mm-40) REVERT: H 256 ARG cc_start: 0.8185 (ppt170) cc_final: 0.7664 (ppt170) REVERT: I 60 ILE cc_start: 0.8769 (mp) cc_final: 0.8304 (mm) REVERT: I 62 HIS cc_start: 0.7915 (t70) cc_final: 0.7573 (t-90) REVERT: I 64 GLN cc_start: 0.6795 (pm20) cc_final: 0.6096 (pm20) REVERT: I 66 ASP cc_start: 0.8085 (t0) cc_final: 0.7648 (t0) REVERT: I 79 VAL cc_start: 0.8177 (t) cc_final: 0.7577 (p) REVERT: I 85 LEU cc_start: 0.7907 (tp) cc_final: 0.7601 (tp) REVERT: I 86 ILE cc_start: 0.8574 (pt) cc_final: 0.8061 (mm) REVERT: I 92 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8475 (mtpp) REVERT: I 98 GLU cc_start: 0.8224 (mp0) cc_final: 0.7930 (mp0) REVERT: I 100 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7573 (mtm-85) REVERT: I 101 VAL cc_start: 0.9375 (p) cc_final: 0.9159 (m) REVERT: I 113 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7684 (mmmm) REVERT: I 143 ILE cc_start: 0.8888 (tp) cc_final: 0.8517 (tp) REVERT: I 145 TRP cc_start: 0.8414 (m-90) cc_final: 0.7765 (m-90) REVERT: I 146 ASN cc_start: 0.8035 (m110) cc_final: 0.7456 (m-40) REVERT: I 152 LEU cc_start: 0.7513 (pt) cc_final: 0.6316 (mp) REVERT: I 153 VAL cc_start: 0.8907 (m) cc_final: 0.7939 (p) REVERT: I 155 ARG cc_start: 0.8291 (tpt90) cc_final: 0.7388 (mmm160) REVERT: I 158 GLN cc_start: 0.9071 (tt0) cc_final: 0.8511 (tt0) REVERT: I 190 LYS cc_start: 0.8104 (mttp) cc_final: 0.7525 (mtpp) REVERT: I 198 MET cc_start: 0.8758 (ttm) cc_final: 0.8499 (tpp) REVERT: I 201 PHE cc_start: 0.8741 (t80) cc_final: 0.8471 (t80) REVERT: I 211 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7677 (tp40) REVERT: I 222 ARG cc_start: 0.6307 (mtp-110) cc_final: 0.5986 (mtp-110) REVERT: I 260 ARG cc_start: 0.7462 (ptm160) cc_final: 0.7180 (ptm160) REVERT: J 13 ASN cc_start: 0.7424 (m-40) cc_final: 0.7217 (m110) REVERT: J 15 TRP cc_start: 0.7988 (m100) cc_final: 0.7419 (m100) REVERT: J 40 CYS cc_start: 0.7265 (t) cc_final: 0.6903 (t) REVERT: J 63 TRP cc_start: 0.7665 (m100) cc_final: 0.6209 (m100) REVERT: J 75 ILE cc_start: 0.7610 (mp) cc_final: 0.7391 (mm) REVERT: J 86 ILE cc_start: 0.8909 (pt) cc_final: 0.8269 (mm) REVERT: J 92 LYS cc_start: 0.8982 (tptp) cc_final: 0.8569 (tptp) REVERT: J 102 GLN cc_start: 0.8503 (mp10) cc_final: 0.8021 (mp10) REVERT: J 104 MET cc_start: 0.8282 (tpp) cc_final: 0.7825 (tpp) REVERT: J 106 TRP cc_start: 0.8503 (t60) cc_final: 0.8228 (t60) REVERT: J 131 LEU cc_start: 0.8800 (tt) cc_final: 0.8403 (tt) REVERT: J 139 HIS cc_start: 0.8204 (t70) cc_final: 0.7867 (t70) REVERT: J 162 ASN cc_start: 0.8947 (m110) cc_final: 0.8740 (m110) REVERT: J 175 GLU cc_start: 0.8640 (pm20) cc_final: 0.8320 (mp0) REVERT: J 178 LEU cc_start: 0.9105 (mm) cc_final: 0.8717 (mm) REVERT: J 182 LEU cc_start: 0.8443 (mt) cc_final: 0.8217 (mt) REVERT: J 198 MET cc_start: 0.8243 (tpt) cc_final: 0.7884 (tpp) REVERT: J 204 ASN cc_start: 0.8555 (m110) cc_final: 0.8299 (m110) REVERT: J 205 LYS cc_start: 0.8517 (tptp) cc_final: 0.8165 (tptp) REVERT: J 207 GLN cc_start: 0.8046 (mp10) cc_final: 0.7806 (mp10) REVERT: K 30 ARG cc_start: 0.8967 (ttt180) cc_final: 0.8372 (ttt180) REVERT: K 39 GLN cc_start: 0.8525 (tp40) cc_final: 0.8040 (tp40) REVERT: K 106 TRP cc_start: 0.7192 (t60) cc_final: 0.6513 (t60) REVERT: K 110 PHE cc_start: 0.7965 (m-80) cc_final: 0.7546 (m-80) REVERT: K 132 MET cc_start: 0.7563 (ppp) cc_final: 0.7032 (ppp) REVERT: K 158 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7968 (tp-100) REVERT: K 245 TRP cc_start: 0.8169 (m100) cc_final: 0.7738 (m100) REVERT: L 63 TRP cc_start: 0.6467 (m100) cc_final: 0.6100 (m100) REVERT: L 266 ASN cc_start: 0.8631 (m110) cc_final: 0.8245 (m-40) REVERT: L 268 ASP cc_start: 0.7075 (t0) cc_final: 0.6785 (t70) REVERT: L 269 VAL cc_start: 0.7738 (m) cc_final: 0.7457 (m) REVERT: M 7 LEU cc_start: 0.8559 (tt) cc_final: 0.8089 (tt) REVERT: M 14 LYS cc_start: 0.8423 (mttp) cc_final: 0.7792 (mtmt) REVERT: M 15 TRP cc_start: 0.8508 (m-10) cc_final: 0.8203 (m-10) REVERT: M 16 HIS cc_start: 0.8072 (m-70) cc_final: 0.6587 (m170) REVERT: M 18 ASP cc_start: 0.7798 (t70) cc_final: 0.7451 (t70) REVERT: M 25 GLU cc_start: 0.8447 (tt0) cc_final: 0.8040 (tt0) REVERT: M 39 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7771 (tm-30) REVERT: M 101 VAL cc_start: 0.9161 (t) cc_final: 0.8935 (t) REVERT: M 109 MET cc_start: 0.8741 (tmm) cc_final: 0.8049 (ttt) REVERT: M 158 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7753 (tm-30) REVERT: M 159 THR cc_start: 0.8640 (m) cc_final: 0.7973 (p) REVERT: M 166 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7869 (ttmm) REVERT: M 195 THR cc_start: 0.8282 (m) cc_final: 0.8019 (p) REVERT: M 207 GLN cc_start: 0.8461 (mm110) cc_final: 0.8111 (mm110) REVERT: M 209 ARG cc_start: 0.8759 (tmt170) cc_final: 0.8439 (ttp80) REVERT: M 224 CYS cc_start: 0.6655 (p) cc_final: 0.6401 (p) REVERT: N 23 HIS cc_start: 0.7826 (t70) cc_final: 0.7524 (t70) REVERT: N 61 ASP cc_start: 0.6346 (t0) cc_final: 0.5730 (t0) REVERT: N 102 GLN cc_start: 0.9017 (mp-120) cc_final: 0.8501 (mp10) REVERT: N 104 MET cc_start: 0.8203 (ptm) cc_final: 0.7537 (ppp) REVERT: N 105 LYS cc_start: 0.9284 (mtmm) cc_final: 0.9013 (mttt) REVERT: N 164 LEU cc_start: 0.8571 (mt) cc_final: 0.8346 (mt) REVERT: N 165 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7985 (mm-30) REVERT: N 203 PHE cc_start: 0.8081 (t80) cc_final: 0.7700 (t80) REVERT: N 205 LYS cc_start: 0.8704 (ptpp) cc_final: 0.8390 (ptpp) REVERT: N 207 GLN cc_start: 0.8379 (mp10) cc_final: 0.7917 (mp10) REVERT: N 210 ILE cc_start: 0.8443 (pt) cc_final: 0.8121 (pt) REVERT: N 213 GLN cc_start: 0.8754 (mt0) cc_final: 0.8117 (mt0) REVERT: N 230 LYS cc_start: 0.8431 (mttt) cc_final: 0.7906 (tptp) REVERT: N 233 HIS cc_start: 0.7762 (m90) cc_final: 0.7440 (m-70) REVERT: N 242 GLN cc_start: 0.7790 (tt0) cc_final: 0.7227 (pp30) REVERT: N 243 VAL cc_start: 0.8560 (t) cc_final: 0.8026 (p) REVERT: N 244 LEU cc_start: 0.8411 (tt) cc_final: 0.8107 (tt) REVERT: N 256 ARG cc_start: 0.8287 (ttm110) cc_final: 0.7764 (ttm110) REVERT: N 267 LYS cc_start: 0.9162 (ptpt) cc_final: 0.8779 (pttt) REVERT: N 270 LYS cc_start: 0.8075 (mptt) cc_final: 0.7514 (mptt) REVERT: O 23 HIS cc_start: 0.7465 (t70) cc_final: 0.6911 (t70) REVERT: O 48 MET cc_start: -0.1660 (ppp) cc_final: -0.2124 (ppp) REVERT: O 98 GLU cc_start: 0.8531 (pt0) cc_final: 0.8241 (pp20) REVERT: O 104 MET cc_start: 0.8204 (pmm) cc_final: 0.7987 (pmm) REVERT: O 110 PHE cc_start: 0.8201 (m-80) cc_final: 0.7939 (m-80) REVERT: O 115 LEU cc_start: 0.8745 (tp) cc_final: 0.8512 (tp) REVERT: O 132 MET cc_start: 0.8213 (tmm) cc_final: 0.7649 (tmm) REVERT: O 152 LEU cc_start: 0.8810 (tp) cc_final: 0.8568 (tp) REVERT: O 193 LEU cc_start: 0.8767 (mm) cc_final: 0.8550 (mm) REVERT: O 206 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8009 (tm-30) REVERT: O 209 ARG cc_start: 0.8876 (ptm-80) cc_final: 0.8615 (ptm-80) REVERT: O 211 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8271 (tp40) REVERT: P 62 HIS cc_start: 0.8016 (t70) cc_final: 0.7380 (t70) REVERT: P 87 TYR cc_start: 0.8595 (t80) cc_final: 0.8369 (t80) REVERT: P 100 ARG cc_start: 0.5490 (mtt90) cc_final: 0.5061 (mtm-85) REVERT: P 104 MET cc_start: 0.9098 (mmp) cc_final: 0.8539 (mmp) REVERT: P 106 TRP cc_start: 0.8427 (t60) cc_final: 0.7980 (t60) REVERT: P 115 LEU cc_start: 0.5094 (tp) cc_final: 0.4768 (tp) REVERT: P 170 MET cc_start: 0.7627 (mtt) cc_final: 0.7146 (mpp) REVERT: P 172 ASN cc_start: 0.8852 (m-40) cc_final: 0.8551 (p0) REVERT: P 205 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8273 (mtmt) REVERT: P 222 ARG cc_start: 0.6853 (mmm-85) cc_final: 0.6118 (mmm160) REVERT: P 223 PHE cc_start: 0.6545 (m-80) cc_final: 0.5939 (m-80) REVERT: P 233 HIS cc_start: 0.6781 (m-70) cc_final: 0.6550 (m-70) REVERT: P 238 GLN cc_start: 0.6730 (mm110) cc_final: 0.6412 (mp10) REVERT: P 272 ILE cc_start: 0.8133 (mp) cc_final: 0.7917 (mp) outliers start: 1 outliers final: 0 residues processed: 1211 average time/residue: 0.2041 time to fit residues: 389.9445 Evaluate side-chains 1117 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1117 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 25 optimal weight: 0.0060 chunk 261 optimal weight: 3.9990 chunk 360 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 385 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS D 213 GLN E 218 GLN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN G 208 GLN H 157 HIS H 242 GLN I 16 HIS ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 GLN I 242 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN L 158 GLN L 213 GLN ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 HIS O 208 GLN P 148 GLN P 157 HIS P 238 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.194472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147335 restraints weight = 71518.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153001 restraints weight = 43947.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.156958 restraints weight = 30489.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159732 restraints weight = 22908.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161690 restraints weight = 18381.799| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34119 Z= 0.163 Angle : 0.732 13.727 46515 Z= 0.390 Chirality : 0.050 0.489 5006 Planarity : 0.005 0.080 5714 Dihedral : 14.797 174.191 5007 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.53 (0.13), residues: 3851 helix: 0.72 (0.12), residues: 1872 sheet: -0.73 (0.17), residues: 849 loop : -1.72 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 100 TYR 0.026 0.001 TYR I 70 PHE 0.031 0.002 PHE N 201 TRP 0.040 0.002 TRP P 78 HIS 0.009 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00341 (34119) covalent geometry : angle 0.73207 (46515) hydrogen bonds : bond 0.04118 ( 1746) hydrogen bonds : angle 5.43796 ( 5114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1192 time to evaluate : 1.055 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: 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: 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: A 11 GLU cc_start: 0.8138 (mp0) cc_final: 0.7917 (mp0) REVERT: A 66 ASP cc_start: 0.7803 (t70) cc_final: 0.7241 (t70) REVERT: A 79 VAL cc_start: 0.8207 (t) cc_final: 0.7755 (p) REVERT: A 80 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6423 (tm-30) REVERT: A 85 LEU cc_start: 0.8053 (tt) cc_final: 0.7804 (tt) REVERT: A 90 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7398 (tmm-80) REVERT: A 92 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8333 (mtpp) REVERT: A 104 MET cc_start: 0.8485 (ttm) cc_final: 0.7801 (ttm) REVERT: A 107 TYR cc_start: 0.8340 (t80) cc_final: 0.8044 (t80) REVERT: A 113 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7626 (mmmm) REVERT: A 116 GLN cc_start: 0.6878 (tm-30) cc_final: 0.6645 (tm-30) REVERT: A 129 GLN cc_start: 0.8203 (tt0) cc_final: 0.7881 (tt0) REVERT: A 135 LEU cc_start: 0.9047 (mt) cc_final: 0.8697 (mt) REVERT: A 155 ARG cc_start: 0.8380 (tpt90) cc_final: 0.7637 (mmm160) REVERT: A 158 GLN cc_start: 0.8652 (tt0) cc_final: 0.8158 (tt0) REVERT: A 161 LYS cc_start: 0.8850 (tptt) cc_final: 0.8621 (tptt) REVERT: A 164 LEU cc_start: 0.8428 (mt) cc_final: 0.8223 (mt) REVERT: A 174 PHE cc_start: 0.6409 (p90) cc_final: 0.5709 (p90) REVERT: A 190 LYS cc_start: 0.8041 (ptpp) cc_final: 0.7369 (mtpt) REVERT: A 200 ILE cc_start: 0.8031 (mm) cc_final: 0.7828 (mm) REVERT: A 203 PHE cc_start: 0.8532 (t80) cc_final: 0.8094 (t80) REVERT: A 242 GLN cc_start: 0.7202 (tp-100) cc_final: 0.6990 (tp40) REVERT: A 244 LEU cc_start: 0.8626 (mp) cc_final: 0.8320 (mt) REVERT: A 253 VAL cc_start: 0.8158 (t) cc_final: 0.7798 (m) REVERT: A 254 LYS cc_start: 0.8176 (pptt) cc_final: 0.7888 (pptt) REVERT: A 256 ARG cc_start: 0.7282 (pmt170) cc_final: 0.6850 (pmt170) REVERT: A 260 ARG cc_start: 0.7344 (ptm160) cc_final: 0.6897 (mtm110) REVERT: B 13 ASN cc_start: 0.7371 (m110) cc_final: 0.7168 (m110) REVERT: B 15 TRP cc_start: 0.7677 (m100) cc_final: 0.7070 (m100) REVERT: B 40 CYS cc_start: 0.7623 (t) cc_final: 0.6978 (p) REVERT: B 60 ILE cc_start: 0.7396 (mm) cc_final: 0.6931 (mm) REVERT: B 63 TRP cc_start: 0.7812 (m100) cc_final: 0.6214 (m100) REVERT: B 64 GLN cc_start: 0.6770 (tp40) cc_final: 0.6319 (mm-40) REVERT: B 82 ASN cc_start: 0.8103 (p0) cc_final: 0.7899 (p0) REVERT: B 86 ILE cc_start: 0.8702 (pt) cc_final: 0.8292 (mm) REVERT: B 87 TYR cc_start: 0.7920 (t80) cc_final: 0.7662 (t80) REVERT: B 89 GLU cc_start: 0.7832 (tt0) cc_final: 0.7186 (tt0) REVERT: B 92 LYS cc_start: 0.9004 (tppt) cc_final: 0.8425 (tptp) REVERT: B 100 ARG cc_start: 0.8784 (ptp90) cc_final: 0.7964 (ptp90) REVERT: B 102 GLN cc_start: 0.8336 (mp10) cc_final: 0.7946 (mp10) REVERT: B 103 THR cc_start: 0.8900 (p) cc_final: 0.8664 (p) REVERT: B 104 MET cc_start: 0.8609 (mmp) cc_final: 0.8117 (mmp) REVERT: B 106 TRP cc_start: 0.8410 (t60) cc_final: 0.8039 (t60) REVERT: B 129 GLN cc_start: 0.8439 (pt0) cc_final: 0.8100 (pt0) REVERT: B 132 MET cc_start: 0.8752 (tpp) cc_final: 0.8048 (tpp) REVERT: B 137 ILE cc_start: 0.8271 (tt) cc_final: 0.7686 (tt) REVERT: B 139 HIS cc_start: 0.8532 (t70) cc_final: 0.7985 (t70) REVERT: B 165 GLU cc_start: 0.8024 (tp30) cc_final: 0.7692 (tp30) REVERT: B 175 GLU cc_start: 0.8632 (pm20) cc_final: 0.8364 (mp0) REVERT: B 178 LEU cc_start: 0.9127 (mm) cc_final: 0.8673 (mm) REVERT: B 186 ASN cc_start: 0.8379 (m-40) cc_final: 0.8111 (m-40) REVERT: B 198 MET cc_start: 0.8076 (tpt) cc_final: 0.7550 (tpp) REVERT: B 204 ASN cc_start: 0.8015 (p0) cc_final: 0.7759 (p0) REVERT: B 208 GLN cc_start: 0.8686 (mt0) cc_final: 0.8264 (mt0) REVERT: C 7 LEU cc_start: 0.8731 (tt) cc_final: 0.8501 (tt) REVERT: C 30 ARG cc_start: 0.8968 (ttt90) cc_final: 0.8289 (ttt90) REVERT: C 34 GLU cc_start: 0.8798 (pt0) cc_final: 0.8442 (pp20) REVERT: C 35 ASP cc_start: 0.8652 (m-30) cc_final: 0.8169 (m-30) REVERT: C 38 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7693 (tp-100) REVERT: C 39 GLN cc_start: 0.8456 (tp40) cc_final: 0.7955 (tp40) REVERT: C 110 PHE cc_start: 0.8138 (m-80) cc_final: 0.7257 (m-80) REVERT: C 132 MET cc_start: 0.8384 (ppp) cc_final: 0.8143 (ppp) REVERT: C 162 ASN cc_start: 0.8828 (m-40) cc_final: 0.8475 (m-40) REVERT: C 198 MET cc_start: 0.8698 (tpt) cc_final: 0.8133 (tpt) REVERT: C 199 ASP cc_start: 0.8897 (m-30) cc_final: 0.8568 (m-30) REVERT: C 245 TRP cc_start: 0.8374 (m-90) cc_final: 0.8067 (m-90) REVERT: D 155 ARG cc_start: 0.8403 (mmm160) cc_final: 0.8095 (mmm160) REVERT: D 209 ARG cc_start: 0.8588 (mmp-170) cc_final: 0.8316 (mmp-170) REVERT: D 223 PHE cc_start: 0.5889 (p90) cc_final: 0.5450 (p90) REVERT: D 224 CYS cc_start: 0.7154 (p) cc_final: 0.6878 (p) REVERT: D 226 TYR cc_start: 0.7122 (p90) cc_final: 0.6143 (p90) REVERT: D 254 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7925 (ttmt) REVERT: D 262 LEU cc_start: 0.8171 (mm) cc_final: 0.7915 (mm) REVERT: D 266 ASN cc_start: 0.8561 (m110) cc_final: 0.8071 (m110) REVERT: E 7 LEU cc_start: 0.8428 (tt) cc_final: 0.7788 (tt) REVERT: E 11 GLU cc_start: 0.8309 (mp0) cc_final: 0.7869 (mp0) REVERT: E 12 HIS cc_start: 0.8458 (t70) cc_final: 0.7617 (t70) REVERT: E 15 TRP cc_start: 0.8690 (m-10) cc_final: 0.8170 (m-10) REVERT: E 18 ASP cc_start: 0.7954 (t70) cc_final: 0.7618 (t70) REVERT: E 89 GLU cc_start: 0.7410 (pm20) cc_final: 0.6864 (mp0) REVERT: E 138 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7576 (tm-30) REVERT: E 150 GLN cc_start: 0.7886 (mm110) cc_final: 0.7367 (mm110) REVERT: E 154 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8550 (mm-30) REVERT: E 158 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7576 (tm-30) REVERT: E 159 THR cc_start: 0.8539 (m) cc_final: 0.7849 (p) REVERT: E 178 LEU cc_start: 0.8837 (mt) cc_final: 0.8637 (mt) REVERT: E 206 GLU cc_start: 0.8405 (pt0) cc_final: 0.8136 (pt0) REVERT: F 11 GLU cc_start: 0.8031 (mp0) cc_final: 0.7367 (mp0) REVERT: F 23 HIS cc_start: 0.8045 (t70) cc_final: 0.7582 (t70) REVERT: F 65 VAL cc_start: 0.7616 (t) cc_final: 0.7183 (p) REVERT: F 89 GLU cc_start: 0.6523 (tp30) cc_final: 0.6229 (tp30) REVERT: F 157 HIS cc_start: 0.7679 (m90) cc_final: 0.7329 (m90) REVERT: F 205 LYS cc_start: 0.8523 (ptpp) cc_final: 0.7971 (mtmt) REVERT: F 207 GLN cc_start: 0.8551 (mp10) cc_final: 0.8156 (mp-120) REVERT: F 208 GLN cc_start: 0.8455 (tt0) cc_final: 0.8179 (tm-30) REVERT: F 230 LYS cc_start: 0.8514 (mmmt) cc_final: 0.7874 (mmmm) REVERT: F 233 HIS cc_start: 0.7885 (m-70) cc_final: 0.7600 (m90) REVERT: F 237 TRP cc_start: 0.8361 (m100) cc_final: 0.8118 (m100) REVERT: F 242 GLN cc_start: 0.7631 (tt0) cc_final: 0.7199 (pp30) REVERT: F 243 VAL cc_start: 0.8519 (t) cc_final: 0.7869 (m) REVERT: F 244 LEU cc_start: 0.8350 (tt) cc_final: 0.8006 (tt) REVERT: F 256 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7928 (ttm110) REVERT: G 48 MET cc_start: -0.0485 (ppp) cc_final: -0.1355 (ppp) REVERT: G 62 HIS cc_start: 0.7734 (t70) cc_final: 0.6732 (t70) REVERT: G 107 TYR cc_start: 0.8343 (t80) cc_final: 0.7678 (t80) REVERT: G 110 PHE cc_start: 0.7906 (m-80) cc_final: 0.7438 (m-10) REVERT: G 131 LEU cc_start: 0.9275 (mt) cc_final: 0.9013 (mt) REVERT: G 157 HIS cc_start: 0.8900 (p-80) cc_final: 0.8585 (p90) REVERT: G 158 GLN cc_start: 0.9252 (tp-100) cc_final: 0.9006 (tp-100) REVERT: G 171 PHE cc_start: 0.7614 (m-10) cc_final: 0.7374 (m-80) REVERT: G 175 GLU cc_start: 0.8636 (mp0) cc_final: 0.8303 (mm-30) REVERT: G 199 ASP cc_start: 0.8663 (m-30) cc_final: 0.8342 (m-30) REVERT: H 62 HIS cc_start: 0.7912 (t70) cc_final: 0.7231 (t70) REVERT: H 78 TRP cc_start: 0.7469 (m-10) cc_final: 0.6044 (m-10) REVERT: H 87 TYR cc_start: 0.8616 (t80) cc_final: 0.8056 (t80) REVERT: H 101 VAL cc_start: 0.8778 (p) cc_final: 0.8554 (p) REVERT: H 104 MET cc_start: 0.9062 (mmp) cc_final: 0.8377 (mmp) REVERT: H 106 TRP cc_start: 0.8328 (t60) cc_final: 0.7161 (t60) REVERT: H 109 MET cc_start: 0.8209 (tpt) cc_final: 0.7773 (tpp) REVERT: H 110 PHE cc_start: 0.8290 (m-10) cc_final: 0.7602 (m-10) REVERT: H 199 ASP cc_start: 0.7972 (m-30) cc_final: 0.7682 (m-30) REVERT: H 207 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7775 (mm-40) REVERT: H 223 PHE cc_start: 0.7329 (m-80) cc_final: 0.7055 (m-80) REVERT: H 256 ARG cc_start: 0.8240 (ppt170) cc_final: 0.7712 (ppt170) REVERT: I 11 GLU cc_start: 0.7930 (mp0) cc_final: 0.7598 (mp0) REVERT: I 30 ARG cc_start: 0.7246 (mtp-110) cc_final: 0.6783 (mtm-85) REVERT: I 60 ILE cc_start: 0.8725 (mp) cc_final: 0.8206 (mm) REVERT: I 79 VAL cc_start: 0.8255 (t) cc_final: 0.7747 (p) REVERT: I 80 GLU cc_start: 0.6544 (tm-30) cc_final: 0.6283 (tm-30) REVERT: I 86 ILE cc_start: 0.8521 (pt) cc_final: 0.7905 (mm) REVERT: I 92 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8500 (mtpp) REVERT: I 101 VAL cc_start: 0.9412 (p) cc_final: 0.9151 (m) REVERT: I 104 MET cc_start: 0.8590 (ttm) cc_final: 0.8091 (ttm) REVERT: I 105 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8647 (mtpp) REVERT: I 113 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7655 (mmmm) REVERT: I 143 ILE cc_start: 0.8950 (tp) cc_final: 0.8556 (tp) REVERT: I 145 TRP cc_start: 0.8385 (m-90) cc_final: 0.8171 (m-90) REVERT: I 146 ASN cc_start: 0.8057 (m110) cc_final: 0.7422 (m-40) REVERT: I 155 ARG cc_start: 0.8263 (tpt90) cc_final: 0.7634 (mmm160) REVERT: I 160 LEU cc_start: 0.8630 (tt) cc_final: 0.8242 (tt) REVERT: I 163 THR cc_start: 0.8453 (m) cc_final: 0.8071 (p) REVERT: I 164 LEU cc_start: 0.8590 (mt) cc_final: 0.8229 (mt) REVERT: I 183 ILE cc_start: 0.9013 (mt) cc_final: 0.8488 (mm) REVERT: I 190 LYS cc_start: 0.8182 (mttp) cc_final: 0.7643 (mtpt) REVERT: I 198 MET cc_start: 0.8656 (ttm) cc_final: 0.8403 (tpp) REVERT: I 201 PHE cc_start: 0.8747 (t80) cc_final: 0.8432 (t80) REVERT: I 222 ARG cc_start: 0.6349 (mtp-110) cc_final: 0.6117 (mtp-110) REVERT: I 238 GLN cc_start: 0.6618 (mt0) cc_final: 0.6296 (mt0) REVERT: J 13 ASN cc_start: 0.7460 (m-40) cc_final: 0.7227 (m110) REVERT: J 15 TRP cc_start: 0.8020 (m100) cc_final: 0.7386 (m100) REVERT: J 40 CYS cc_start: 0.7342 (t) cc_final: 0.7001 (t) REVERT: J 71 GLU cc_start: 0.7970 (pp20) cc_final: 0.7712 (pp20) REVERT: J 75 ILE cc_start: 0.7750 (mp) cc_final: 0.7516 (mm) REVERT: J 86 ILE cc_start: 0.8905 (pt) cc_final: 0.8519 (mm) REVERT: J 92 LYS cc_start: 0.8985 (tptp) cc_final: 0.8572 (tptp) REVERT: J 104 MET cc_start: 0.8271 (tpp) cc_final: 0.7780 (tpp) REVERT: J 106 TRP cc_start: 0.8543 (t60) cc_final: 0.8160 (t60) REVERT: J 131 LEU cc_start: 0.8737 (tt) cc_final: 0.8322 (tt) REVERT: J 139 HIS cc_start: 0.8563 (t70) cc_final: 0.7935 (t70) REVERT: J 162 ASN cc_start: 0.8909 (m110) cc_final: 0.8631 (m110) REVERT: J 170 MET cc_start: 0.8113 (tmm) cc_final: 0.7888 (tmm) REVERT: J 175 GLU cc_start: 0.8695 (pm20) cc_final: 0.8248 (mp0) REVERT: J 178 LEU cc_start: 0.9220 (mm) cc_final: 0.8789 (mm) REVERT: J 198 MET cc_start: 0.8255 (tpt) cc_final: 0.7924 (tpp) REVERT: J 203 PHE cc_start: 0.8629 (t80) cc_final: 0.8359 (t80) REVERT: J 204 ASN cc_start: 0.8597 (m110) cc_final: 0.7698 (m110) REVERT: J 205 LYS cc_start: 0.8874 (tptp) cc_final: 0.8310 (tptp) REVERT: J 208 GLN cc_start: 0.8668 (mt0) cc_final: 0.8223 (mt0) REVERT: K 14 LYS cc_start: 0.8954 (mmtm) cc_final: 0.8741 (mmtm) REVERT: K 30 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8156 (ttt180) REVERT: K 35 ASP cc_start: 0.8644 (m-30) cc_final: 0.8368 (m-30) REVERT: K 39 GLN cc_start: 0.8534 (tp40) cc_final: 0.8057 (tp40) REVERT: K 106 TRP cc_start: 0.7215 (t60) cc_final: 0.6782 (t60) REVERT: K 109 MET cc_start: 0.8207 (tpp) cc_final: 0.7135 (ptp) REVERT: K 110 PHE cc_start: 0.8019 (m-80) cc_final: 0.7015 (m-80) REVERT: K 132 MET cc_start: 0.7702 (ppp) cc_final: 0.7420 (ppp) REVERT: K 208 GLN cc_start: 0.8900 (tt0) cc_final: 0.8538 (tm-30) REVERT: K 245 TRP cc_start: 0.8195 (m100) cc_final: 0.7780 (m100) REVERT: L 63 TRP cc_start: 0.6408 (m100) cc_final: 0.5835 (m100) REVERT: L 209 ARG cc_start: 0.8555 (mmp-170) cc_final: 0.8312 (mmp-170) REVERT: L 226 TYR cc_start: 0.6921 (p90) cc_final: 0.5993 (p90) REVERT: L 268 ASP cc_start: 0.7179 (t0) cc_final: 0.6852 (t70) REVERT: L 269 VAL cc_start: 0.7751 (m) cc_final: 0.7479 (m) REVERT: M 7 LEU cc_start: 0.8468 (tt) cc_final: 0.7745 (tt) REVERT: M 11 GLU cc_start: 0.8385 (mp0) cc_final: 0.7985 (mp0) REVERT: M 14 LYS cc_start: 0.8376 (mttp) cc_final: 0.7725 (mtmt) REVERT: M 15 TRP cc_start: 0.8542 (m-10) cc_final: 0.8281 (m-10) REVERT: M 16 HIS cc_start: 0.7980 (m-70) cc_final: 0.6380 (m90) REVERT: M 18 ASP cc_start: 0.7808 (t70) cc_final: 0.7433 (t70) REVERT: M 25 GLU cc_start: 0.8429 (tt0) cc_final: 0.8045 (tt0) REVERT: M 36 ILE cc_start: 0.8577 (mt) cc_final: 0.8278 (mt) REVERT: M 39 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7833 (tm-30) REVERT: M 87 TYR cc_start: 0.6948 (t80) cc_final: 0.6467 (t80) REVERT: M 101 VAL cc_start: 0.9159 (t) cc_final: 0.8950 (t) REVERT: M 109 MET cc_start: 0.8729 (tmm) cc_final: 0.8474 (tmm) REVERT: M 154 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8698 (mm-30) REVERT: M 158 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7828 (tm-30) REVERT: M 159 THR cc_start: 0.8653 (m) cc_final: 0.8051 (p) REVERT: M 166 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7864 (ttmm) REVERT: M 170 MET cc_start: 0.8278 (pmm) cc_final: 0.8068 (pmm) REVERT: M 185 LEU cc_start: 0.8760 (mm) cc_final: 0.8513 (mm) REVERT: M 195 THR cc_start: 0.8348 (m) cc_final: 0.8066 (p) REVERT: M 207 GLN cc_start: 0.8530 (mm110) cc_final: 0.8283 (mm110) REVERT: M 219 GLU cc_start: 0.7955 (pp20) cc_final: 0.7714 (pp20) REVERT: M 224 CYS cc_start: 0.6590 (p) cc_final: 0.6369 (p) REVERT: N 23 HIS cc_start: 0.7812 (t70) cc_final: 0.7544 (t70) REVERT: N 61 ASP cc_start: 0.6365 (t0) cc_final: 0.6009 (t0) REVERT: N 104 MET cc_start: 0.8227 (ptm) cc_final: 0.7615 (ppp) REVERT: N 157 HIS cc_start: 0.7948 (m90) cc_final: 0.7552 (m90) REVERT: N 164 LEU cc_start: 0.8653 (mt) cc_final: 0.8426 (mt) REVERT: N 165 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8095 (mm-30) REVERT: N 203 PHE cc_start: 0.8092 (t80) cc_final: 0.7781 (t80) REVERT: N 205 LYS cc_start: 0.8749 (ptpp) cc_final: 0.8518 (ptpp) REVERT: N 210 ILE cc_start: 0.8464 (pt) cc_final: 0.8126 (pt) REVERT: N 213 GLN cc_start: 0.8793 (mt0) cc_final: 0.8108 (mt0) REVERT: N 224 CYS cc_start: 0.8145 (p) cc_final: 0.7840 (p) REVERT: N 233 HIS cc_start: 0.7815 (m90) cc_final: 0.7472 (m-70) REVERT: N 243 VAL cc_start: 0.8547 (t) cc_final: 0.7748 (p) REVERT: N 256 ARG cc_start: 0.8360 (ttm110) cc_final: 0.7782 (ttm110) REVERT: N 267 LYS cc_start: 0.9085 (ptmt) cc_final: 0.8823 (pttt) REVERT: N 270 LYS cc_start: 0.8062 (mptt) cc_final: 0.7418 (mptt) REVERT: O 23 HIS cc_start: 0.7443 (t70) cc_final: 0.6906 (t70) REVERT: O 48 MET cc_start: -0.1681 (ppp) cc_final: -0.2142 (ppp) REVERT: O 85 LEU cc_start: 0.7717 (tp) cc_final: 0.7314 (tp) REVERT: O 110 PHE cc_start: 0.8211 (m-80) cc_final: 0.7951 (m-80) REVERT: O 115 LEU cc_start: 0.8735 (tp) cc_final: 0.8367 (tp) REVERT: O 152 LEU cc_start: 0.8858 (tp) cc_final: 0.8608 (tp) REVERT: O 161 LYS cc_start: 0.8910 (ptpp) cc_final: 0.8461 (pttt) REVERT: O 203 PHE cc_start: 0.8395 (t80) cc_final: 0.7974 (t80) REVERT: P 62 HIS cc_start: 0.8017 (t70) cc_final: 0.7372 (t70) REVERT: P 87 TYR cc_start: 0.8507 (t80) cc_final: 0.8265 (t80) REVERT: P 100 ARG cc_start: 0.5547 (mtt90) cc_final: 0.5236 (mtm-85) REVERT: P 104 MET cc_start: 0.9075 (mmp) cc_final: 0.8490 (mmp) REVERT: P 106 TRP cc_start: 0.8388 (t60) cc_final: 0.7984 (t60) REVERT: P 115 LEU cc_start: 0.5245 (tp) cc_final: 0.5043 (tp) REVERT: P 170 MET cc_start: 0.7778 (mtt) cc_final: 0.7262 (mpp) REVERT: P 172 ASN cc_start: 0.8855 (m-40) cc_final: 0.8548 (p0) REVERT: P 207 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7903 (mm-40) REVERT: P 222 ARG cc_start: 0.6905 (mmm-85) cc_final: 0.6164 (mmm160) REVERT: P 223 PHE cc_start: 0.6667 (m-80) cc_final: 0.6027 (m-80) REVERT: P 233 HIS cc_start: 0.6812 (m-70) cc_final: 0.6578 (m-70) REVERT: P 272 ILE cc_start: 0.8132 (mp) cc_final: 0.7899 (mp) outliers start: 1 outliers final: 1 residues processed: 1192 average time/residue: 0.2068 time to fit residues: 387.9333 Evaluate side-chains 1119 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1118 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 186 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 222 optimal weight: 0.0020 chunk 251 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 329 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 157 HIS ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN J 116 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN L 162 ASN ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 GLN ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.192535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.145584 restraints weight = 72385.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151062 restraints weight = 44604.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.154786 restraints weight = 30963.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.157412 restraints weight = 23451.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.159292 restraints weight = 18988.427| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34119 Z= 0.158 Angle : 0.748 14.655 46515 Z= 0.399 Chirality : 0.050 0.393 5006 Planarity : 0.005 0.091 5714 Dihedral : 14.828 174.446 5007 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.59 (0.13), residues: 3851 helix: 0.64 (0.12), residues: 1874 sheet: -0.65 (0.17), residues: 847 loop : -1.79 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 100 TYR 0.040 0.001 TYR B 70 PHE 0.029 0.002 PHE F 201 TRP 0.053 0.002 TRP F 15 HIS 0.014 0.001 HIS O 157 Details of bonding type rmsd covalent geometry : bond 0.00337 (34119) covalent geometry : angle 0.74804 (46515) hydrogen bonds : bond 0.04109 ( 1746) hydrogen bonds : angle 5.44995 ( 5114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1195 time to evaluate : 1.120 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: 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: 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: A 66 ASP cc_start: 0.7786 (t70) cc_final: 0.7227 (t70) REVERT: A 79 VAL cc_start: 0.8190 (t) cc_final: 0.7701 (p) REVERT: A 80 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6399 (tm-30) REVERT: A 85 LEU cc_start: 0.8084 (tt) cc_final: 0.7738 (tt) REVERT: A 90 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7310 (tmm-80) REVERT: A 92 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8465 (mtpp) REVERT: A 97 GLN cc_start: 0.7849 (pm20) cc_final: 0.7636 (pm20) REVERT: A 104 MET cc_start: 0.8480 (ttm) cc_final: 0.7812 (ttm) REVERT: A 107 TYR cc_start: 0.8309 (t80) cc_final: 0.8044 (t80) REVERT: A 113 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7633 (mmmm) REVERT: A 129 GLN cc_start: 0.8207 (tt0) cc_final: 0.7882 (tt0) REVERT: A 135 LEU cc_start: 0.9052 (mt) cc_final: 0.8728 (mt) REVERT: A 155 ARG cc_start: 0.8360 (tpt90) cc_final: 0.7633 (mmm160) REVERT: A 158 GLN cc_start: 0.8637 (tt0) cc_final: 0.8141 (tt0) REVERT: A 161 LYS cc_start: 0.8866 (tptt) cc_final: 0.8649 (tptt) REVERT: A 164 LEU cc_start: 0.8491 (mt) cc_final: 0.8229 (mt) REVERT: A 174 PHE cc_start: 0.6435 (p90) cc_final: 0.5671 (p90) REVERT: A 175 GLU cc_start: 0.8542 (pm20) cc_final: 0.8178 (pm20) REVERT: A 190 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7655 (mtpt) REVERT: A 200 ILE cc_start: 0.8079 (mm) cc_final: 0.7856 (mm) REVERT: A 203 PHE cc_start: 0.8509 (t80) cc_final: 0.8077 (t80) REVERT: A 208 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7948 (tm-30) REVERT: A 253 VAL cc_start: 0.8116 (t) cc_final: 0.7696 (m) REVERT: A 254 LYS cc_start: 0.8128 (pptt) cc_final: 0.7815 (pptt) REVERT: A 256 ARG cc_start: 0.7329 (pmt170) cc_final: 0.6995 (pmt170) REVERT: A 260 ARG cc_start: 0.7342 (ptm160) cc_final: 0.6901 (mtm110) REVERT: B 7 LEU cc_start: 0.8119 (mt) cc_final: 0.7891 (mt) REVERT: B 13 ASN cc_start: 0.7383 (m110) cc_final: 0.6969 (m110) REVERT: B 15 TRP cc_start: 0.7720 (m100) cc_final: 0.7139 (m100) REVERT: B 40 CYS cc_start: 0.7568 (t) cc_final: 0.6914 (p) REVERT: B 60 ILE cc_start: 0.7462 (mm) cc_final: 0.6932 (mm) REVERT: B 63 TRP cc_start: 0.7813 (m100) cc_final: 0.6239 (m100) REVERT: B 64 GLN cc_start: 0.6773 (tp40) cc_final: 0.6341 (mm-40) REVERT: B 82 ASN cc_start: 0.8059 (p0) cc_final: 0.7847 (p0) REVERT: B 86 ILE cc_start: 0.8690 (pt) cc_final: 0.8381 (mm) REVERT: B 87 TYR cc_start: 0.7918 (t80) cc_final: 0.7666 (t80) REVERT: B 89 GLU cc_start: 0.7818 (tt0) cc_final: 0.7200 (tt0) REVERT: B 92 LYS cc_start: 0.8998 (tppt) cc_final: 0.8443 (tptp) REVERT: B 98 GLU cc_start: 0.8363 (pm20) cc_final: 0.8047 (pm20) REVERT: B 100 ARG cc_start: 0.8694 (ptp90) cc_final: 0.7912 (ptp90) REVERT: B 102 GLN cc_start: 0.8319 (mp10) cc_final: 0.7903 (mp10) REVERT: B 103 THR cc_start: 0.8858 (p) cc_final: 0.8621 (p) REVERT: B 104 MET cc_start: 0.8624 (mmp) cc_final: 0.8119 (mmp) REVERT: B 129 GLN cc_start: 0.8431 (pt0) cc_final: 0.8077 (pt0) REVERT: B 132 MET cc_start: 0.8757 (tpp) cc_final: 0.8205 (tpp) REVERT: B 137 ILE cc_start: 0.8267 (tt) cc_final: 0.7797 (mp) REVERT: B 139 HIS cc_start: 0.8136 (t70) cc_final: 0.7924 (t70) REVERT: B 165 GLU cc_start: 0.7873 (tp30) cc_final: 0.7528 (tp30) REVERT: B 175 GLU cc_start: 0.8549 (pm20) cc_final: 0.8141 (mp0) REVERT: B 178 LEU cc_start: 0.9108 (mm) cc_final: 0.8788 (mm) REVERT: B 186 ASN cc_start: 0.8228 (m-40) cc_final: 0.7950 (m-40) REVERT: B 198 MET cc_start: 0.8129 (tpt) cc_final: 0.7604 (tpp) REVERT: B 204 ASN cc_start: 0.8018 (p0) cc_final: 0.7749 (p0) REVERT: B 205 LYS cc_start: 0.8734 (tptp) cc_final: 0.8354 (tppp) REVERT: B 208 GLN cc_start: 0.8643 (mt0) cc_final: 0.8113 (mt0) REVERT: C 16 HIS cc_start: 0.7209 (m-70) cc_final: 0.6151 (m90) REVERT: C 22 LEU cc_start: 0.8220 (mm) cc_final: 0.7866 (mm) REVERT: C 30 ARG cc_start: 0.8958 (ttt90) cc_final: 0.8292 (ttt90) REVERT: C 34 GLU cc_start: 0.8769 (pt0) cc_final: 0.8419 (pp20) REVERT: C 35 ASP cc_start: 0.8650 (m-30) cc_final: 0.8098 (m-30) REVERT: C 38 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7721 (tp-100) REVERT: C 39 GLN cc_start: 0.8538 (tp40) cc_final: 0.8066 (tp40) REVERT: C 110 PHE cc_start: 0.8079 (m-80) cc_final: 0.7323 (m-80) REVERT: C 132 MET cc_start: 0.8327 (ppp) cc_final: 0.8103 (ppp) REVERT: C 162 ASN cc_start: 0.8829 (m-40) cc_final: 0.8483 (m-40) REVERT: C 198 MET cc_start: 0.8649 (tpt) cc_final: 0.8098 (tpt) REVERT: C 201 PHE cc_start: 0.8847 (t80) cc_final: 0.8614 (t80) REVERT: C 244 LEU cc_start: 0.8512 (mm) cc_final: 0.7861 (mm) REVERT: C 245 TRP cc_start: 0.8396 (m-90) cc_final: 0.8178 (m-90) REVERT: D 209 ARG cc_start: 0.8476 (mmp-170) cc_final: 0.8267 (mmp-170) REVERT: D 223 PHE cc_start: 0.5962 (p90) cc_final: 0.5629 (p90) REVERT: D 224 CYS cc_start: 0.7134 (p) cc_final: 0.6910 (p) REVERT: D 226 TYR cc_start: 0.6846 (p90) cc_final: 0.5816 (p90) REVERT: D 254 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7918 (ttmt) REVERT: D 262 LEU cc_start: 0.8198 (mm) cc_final: 0.7922 (mm) REVERT: D 266 ASN cc_start: 0.8633 (m110) cc_final: 0.8088 (m110) REVERT: E 7 LEU cc_start: 0.8451 (tt) cc_final: 0.7725 (tt) REVERT: E 11 GLU cc_start: 0.8286 (mp0) cc_final: 0.7897 (mp0) REVERT: E 12 HIS cc_start: 0.8478 (t70) cc_final: 0.7367 (t70) REVERT: E 15 TRP cc_start: 0.8672 (m-10) cc_final: 0.8285 (m-10) REVERT: E 16 HIS cc_start: 0.8014 (m170) cc_final: 0.6457 (m170) REVERT: E 22 LEU cc_start: 0.8466 (pp) cc_final: 0.8253 (pp) REVERT: E 89 GLU cc_start: 0.7422 (pm20) cc_final: 0.6950 (mp0) REVERT: E 97 GLN cc_start: 0.7989 (pm20) cc_final: 0.7665 (pm20) REVERT: E 100 ARG cc_start: 0.8737 (ptp90) cc_final: 0.8204 (ptp90) REVERT: E 133 LYS cc_start: 0.9212 (ptpp) cc_final: 0.8980 (pttm) REVERT: E 138 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7491 (tm-30) REVERT: E 150 GLN cc_start: 0.7883 (mm110) cc_final: 0.7350 (mm110) REVERT: E 154 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8540 (mm-30) REVERT: E 158 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 159 THR cc_start: 0.8349 (m) cc_final: 0.7621 (p) REVERT: E 174 PHE cc_start: 0.7635 (t80) cc_final: 0.7359 (t80) REVERT: E 178 LEU cc_start: 0.8851 (mt) cc_final: 0.8261 (mt) REVERT: E 206 GLU cc_start: 0.8412 (pt0) cc_final: 0.8136 (pt0) REVERT: E 242 GLN cc_start: 0.5291 (pp30) cc_final: 0.5041 (pp30) REVERT: F 11 GLU cc_start: 0.7988 (mp0) cc_final: 0.7439 (mp0) REVERT: F 23 HIS cc_start: 0.7906 (t70) cc_final: 0.7468 (t70) REVERT: F 65 VAL cc_start: 0.7094 (t) cc_final: 0.6582 (p) REVERT: F 89 GLU cc_start: 0.6640 (tp30) cc_final: 0.6359 (tp30) REVERT: F 157 HIS cc_start: 0.7682 (m90) cc_final: 0.7193 (m90) REVERT: F 158 GLN cc_start: 0.9194 (mp10) cc_final: 0.8743 (mp10) REVERT: F 170 MET cc_start: 0.7856 (mpp) cc_final: 0.7534 (mpp) REVERT: F 199 ASP cc_start: 0.8265 (m-30) cc_final: 0.8040 (m-30) REVERT: F 206 GLU cc_start: 0.8208 (pp20) cc_final: 0.7714 (pp20) REVERT: F 230 LYS cc_start: 0.8506 (mmmt) cc_final: 0.7905 (mmmm) REVERT: F 233 HIS cc_start: 0.7879 (m-70) cc_final: 0.7595 (m90) REVERT: F 237 TRP cc_start: 0.8334 (m100) cc_final: 0.8133 (m100) REVERT: F 242 GLN cc_start: 0.7761 (tt0) cc_final: 0.7477 (tm-30) REVERT: F 243 VAL cc_start: 0.8547 (t) cc_final: 0.7518 (m) REVERT: F 267 LYS cc_start: 0.8764 (ptmt) cc_final: 0.8208 (pttt) REVERT: G 48 MET cc_start: -0.0510 (ppp) cc_final: -0.1355 (ppp) REVERT: G 62 HIS cc_start: 0.7835 (t70) cc_final: 0.6815 (t70) REVERT: G 107 TYR cc_start: 0.8355 (t80) cc_final: 0.7683 (t80) REVERT: G 110 PHE cc_start: 0.7822 (m-80) cc_final: 0.7449 (m-10) REVERT: G 131 LEU cc_start: 0.9282 (mt) cc_final: 0.9015 (mt) REVERT: G 158 GLN cc_start: 0.9289 (tp-100) cc_final: 0.8918 (tp-100) REVERT: G 164 LEU cc_start: 0.8718 (mt) cc_final: 0.8485 (mt) REVERT: G 171 PHE cc_start: 0.7621 (m-10) cc_final: 0.7377 (m-80) REVERT: G 175 GLU cc_start: 0.8650 (mp0) cc_final: 0.8312 (mm-30) REVERT: G 199 ASP cc_start: 0.8584 (m-30) cc_final: 0.8267 (m-30) REVERT: H 62 HIS cc_start: 0.7896 (t70) cc_final: 0.7208 (t70) REVERT: H 78 TRP cc_start: 0.7528 (m-10) cc_final: 0.6077 (m-10) REVERT: H 87 TYR cc_start: 0.8615 (t80) cc_final: 0.8049 (t80) REVERT: H 101 VAL cc_start: 0.8773 (p) cc_final: 0.8499 (p) REVERT: H 104 MET cc_start: 0.9056 (mmp) cc_final: 0.8372 (mmp) REVERT: H 106 TRP cc_start: 0.8335 (t60) cc_final: 0.7163 (t60) REVERT: H 109 MET cc_start: 0.8210 (tpt) cc_final: 0.7790 (tpp) REVERT: H 110 PHE cc_start: 0.8298 (m-10) cc_final: 0.7624 (m-10) REVERT: H 199 ASP cc_start: 0.7956 (m-30) cc_final: 0.7647 (m-30) REVERT: H 207 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7764 (mm-40) REVERT: H 223 PHE cc_start: 0.7366 (m-80) cc_final: 0.7041 (m-80) REVERT: H 256 ARG cc_start: 0.8230 (ppt170) cc_final: 0.7750 (ppt170) REVERT: H 270 LYS cc_start: 0.7398 (mptt) cc_final: 0.7073 (mmtm) REVERT: I 60 ILE cc_start: 0.8694 (mp) cc_final: 0.8172 (mm) REVERT: I 79 VAL cc_start: 0.8281 (t) cc_final: 0.7681 (p) REVERT: I 80 GLU cc_start: 0.6525 (tm-30) cc_final: 0.6317 (tm-30) REVERT: I 85 LEU cc_start: 0.7847 (tp) cc_final: 0.7561 (tp) REVERT: I 86 ILE cc_start: 0.8493 (pt) cc_final: 0.8042 (mm) REVERT: I 92 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8526 (mtpp) REVERT: I 104 MET cc_start: 0.8549 (ttm) cc_final: 0.8252 (ttm) REVERT: I 105 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8667 (mtpp) REVERT: I 113 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7649 (mmmm) REVERT: I 135 LEU cc_start: 0.9124 (mt) cc_final: 0.8854 (mt) REVERT: I 143 ILE cc_start: 0.8970 (tp) cc_final: 0.8579 (tp) REVERT: I 146 ASN cc_start: 0.8034 (m110) cc_final: 0.7373 (m-40) REVERT: I 152 LEU cc_start: 0.7152 (pt) cc_final: 0.5936 (mp) REVERT: I 158 GLN cc_start: 0.8626 (tt0) cc_final: 0.7659 (pt0) REVERT: I 160 LEU cc_start: 0.8611 (tt) cc_final: 0.8233 (tt) REVERT: I 163 THR cc_start: 0.8325 (m) cc_final: 0.7821 (p) REVERT: I 164 LEU cc_start: 0.8537 (mt) cc_final: 0.8269 (mt) REVERT: I 190 LYS cc_start: 0.8254 (mttp) cc_final: 0.7735 (mtpt) REVERT: I 198 MET cc_start: 0.8668 (ttm) cc_final: 0.8390 (tpp) REVERT: I 201 PHE cc_start: 0.8758 (t80) cc_final: 0.8413 (t80) REVERT: I 238 GLN cc_start: 0.6763 (mt0) cc_final: 0.6474 (mt0) REVERT: I 244 LEU cc_start: 0.8376 (mt) cc_final: 0.8045 (mt) REVERT: I 260 ARG cc_start: 0.7479 (ptp-170) cc_final: 0.7245 (ptp-170) REVERT: I 262 LEU cc_start: 0.8300 (tt) cc_final: 0.8077 (tt) REVERT: J 15 TRP cc_start: 0.7913 (m100) cc_final: 0.7249 (m100) REVERT: J 40 CYS cc_start: 0.7301 (t) cc_final: 0.6955 (t) REVERT: J 63 TRP cc_start: 0.7613 (m100) cc_final: 0.5925 (m100) REVERT: J 71 GLU cc_start: 0.8017 (pp20) cc_final: 0.7661 (pp20) REVERT: J 75 ILE cc_start: 0.7767 (mp) cc_final: 0.7545 (mm) REVERT: J 86 ILE cc_start: 0.8887 (pt) cc_final: 0.8414 (mm) REVERT: J 92 LYS cc_start: 0.9039 (tptp) cc_final: 0.8633 (tptp) REVERT: J 98 GLU cc_start: 0.8262 (pm20) cc_final: 0.7946 (pm20) REVERT: J 104 MET cc_start: 0.8253 (tpp) cc_final: 0.7779 (tpp) REVERT: J 106 TRP cc_start: 0.8544 (t60) cc_final: 0.8148 (t60) REVERT: J 131 LEU cc_start: 0.8737 (tt) cc_final: 0.8334 (tt) REVERT: J 139 HIS cc_start: 0.8252 (t70) cc_final: 0.7920 (t70) REVERT: J 158 GLN cc_start: 0.8386 (mp-120) cc_final: 0.8058 (mp-120) REVERT: J 162 ASN cc_start: 0.8889 (m110) cc_final: 0.8578 (m-40) REVERT: J 165 GLU cc_start: 0.8149 (tp30) cc_final: 0.7932 (tp30) REVERT: J 174 PHE cc_start: 0.7804 (t80) cc_final: 0.7239 (t80) REVERT: J 178 LEU cc_start: 0.9219 (mm) cc_final: 0.8836 (mm) REVERT: J 198 MET cc_start: 0.8326 (tpt) cc_final: 0.7931 (tpp) REVERT: J 204 ASN cc_start: 0.8622 (m110) cc_final: 0.7840 (m110) REVERT: J 205 LYS cc_start: 0.8849 (tptp) cc_final: 0.8334 (tptp) REVERT: J 208 GLN cc_start: 0.8669 (mt0) cc_final: 0.8246 (mt0) REVERT: K 14 LYS cc_start: 0.8959 (mmtm) cc_final: 0.8709 (mmtt) REVERT: K 18 ASP cc_start: 0.8905 (t0) cc_final: 0.8692 (t70) REVERT: K 30 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8371 (ttt180) REVERT: K 106 TRP cc_start: 0.7212 (t60) cc_final: 0.6570 (t60) REVERT: K 110 PHE cc_start: 0.8004 (m-80) cc_final: 0.7465 (m-80) REVERT: K 132 MET cc_start: 0.7702 (ppp) cc_final: 0.7423 (ppp) REVERT: K 161 LYS cc_start: 0.9038 (pptt) cc_final: 0.8567 (pttp) REVERT: K 245 TRP cc_start: 0.8131 (m100) cc_final: 0.7662 (m100) REVERT: K 255 ASP cc_start: 0.6944 (t0) cc_final: 0.6738 (t0) REVERT: L 63 TRP cc_start: 0.6511 (m100) cc_final: 0.5749 (m100) REVERT: L 209 ARG cc_start: 0.8473 (mmp-170) cc_final: 0.8206 (mmm160) REVERT: L 226 TYR cc_start: 0.6952 (p90) cc_final: 0.6052 (p90) REVERT: L 268 ASP cc_start: 0.7211 (t0) cc_final: 0.6909 (t70) REVERT: L 269 VAL cc_start: 0.7712 (m) cc_final: 0.7450 (m) REVERT: M 7 LEU cc_start: 0.8508 (tt) cc_final: 0.7728 (tt) REVERT: M 11 GLU cc_start: 0.8357 (mp0) cc_final: 0.7951 (mp0) REVERT: M 14 LYS cc_start: 0.8366 (mttp) cc_final: 0.8043 (mtpt) REVERT: M 15 TRP cc_start: 0.8541 (m-10) cc_final: 0.8117 (m-10) REVERT: M 16 HIS cc_start: 0.7958 (m-70) cc_final: 0.6267 (m170) REVERT: M 18 ASP cc_start: 0.7799 (t70) cc_final: 0.7441 (t70) REVERT: M 25 GLU cc_start: 0.8456 (tt0) cc_final: 0.8106 (tt0) REVERT: M 36 ILE cc_start: 0.8781 (mt) cc_final: 0.8466 (mt) REVERT: M 39 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7840 (tm-30) REVERT: M 69 HIS cc_start: 0.6835 (t-90) cc_final: 0.6468 (t70) REVERT: M 78 TRP cc_start: 0.6855 (m-90) cc_final: 0.6309 (m-90) REVERT: M 109 MET cc_start: 0.8756 (tmm) cc_final: 0.7904 (tmm) REVERT: M 154 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8697 (mm-30) REVERT: M 158 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7800 (tm-30) REVERT: M 159 THR cc_start: 0.8643 (m) cc_final: 0.8024 (p) REVERT: M 166 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7880 (ttmm) REVERT: M 195 THR cc_start: 0.8280 (m) cc_final: 0.8043 (p) REVERT: M 205 LYS cc_start: 0.9143 (mttm) cc_final: 0.8730 (mttt) REVERT: M 207 GLN cc_start: 0.8553 (mm110) cc_final: 0.8190 (mm110) REVERT: M 209 ARG cc_start: 0.8787 (tmt170) cc_final: 0.8459 (ttp80) REVERT: M 224 CYS cc_start: 0.6814 (p) cc_final: 0.6532 (p) REVERT: N 23 HIS cc_start: 0.7814 (t70) cc_final: 0.7519 (t70) REVERT: N 61 ASP cc_start: 0.6400 (t0) cc_final: 0.6020 (t0) REVERT: N 102 GLN cc_start: 0.8767 (mp10) cc_final: 0.8316 (mp10) REVERT: N 104 MET cc_start: 0.8133 (ptm) cc_final: 0.7557 (ppp) REVERT: N 105 LYS cc_start: 0.9339 (mtmm) cc_final: 0.9071 (mttt) REVERT: N 161 LYS cc_start: 0.8968 (ptpp) cc_final: 0.8480 (ptpp) REVERT: N 164 LEU cc_start: 0.8653 (mt) cc_final: 0.8420 (mt) REVERT: N 165 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7962 (mm-30) REVERT: N 203 PHE cc_start: 0.8122 (t80) cc_final: 0.7799 (t80) REVERT: N 205 LYS cc_start: 0.8741 (ptpp) cc_final: 0.8540 (ptpp) REVERT: N 210 ILE cc_start: 0.8427 (pt) cc_final: 0.8119 (pt) REVERT: N 213 GLN cc_start: 0.8822 (mt0) cc_final: 0.8128 (mt0) REVERT: N 224 CYS cc_start: 0.8163 (p) cc_final: 0.7799 (p) REVERT: N 233 HIS cc_start: 0.7803 (m90) cc_final: 0.7348 (m90) REVERT: N 243 VAL cc_start: 0.8115 (t) cc_final: 0.7900 (p) REVERT: N 256 ARG cc_start: 0.8431 (ttm110) cc_final: 0.7835 (ttm110) REVERT: N 266 ASN cc_start: 0.8341 (p0) cc_final: 0.8139 (m-40) REVERT: N 267 LYS cc_start: 0.8948 (ptmt) cc_final: 0.8520 (pttt) REVERT: O 23 HIS cc_start: 0.7466 (t70) cc_final: 0.6914 (t70) REVERT: O 48 MET cc_start: -0.1632 (ppp) cc_final: -0.2117 (ppp) REVERT: O 62 HIS cc_start: 0.6795 (m-70) cc_final: 0.6421 (m-70) REVERT: O 104 MET cc_start: 0.8282 (pmm) cc_final: 0.8030 (pmm) REVERT: O 110 PHE cc_start: 0.8074 (m-80) cc_final: 0.7824 (m-80) REVERT: O 115 LEU cc_start: 0.8575 (tp) cc_final: 0.8370 (tp) REVERT: O 157 HIS cc_start: 0.9046 (p-80) cc_final: 0.8798 (p90) REVERT: O 161 LYS cc_start: 0.8798 (ptpp) cc_final: 0.8511 (pttt) REVERT: O 193 LEU cc_start: 0.8770 (mm) cc_final: 0.8560 (mm) REVERT: O 203 PHE cc_start: 0.8379 (t80) cc_final: 0.7965 (t80) REVERT: O 205 LYS cc_start: 0.9270 (mmtm) cc_final: 0.8973 (mmtm) REVERT: P 62 HIS cc_start: 0.8016 (t70) cc_final: 0.7370 (t70) REVERT: P 87 TYR cc_start: 0.8523 (t80) cc_final: 0.8238 (t80) REVERT: P 100 ARG cc_start: 0.5604 (mtt90) cc_final: 0.5348 (mtm-85) REVERT: P 104 MET cc_start: 0.9065 (mmp) cc_final: 0.8465 (mmp) REVERT: P 106 TRP cc_start: 0.8406 (t60) cc_final: 0.8024 (t60) REVERT: P 170 MET cc_start: 0.7695 (mtt) cc_final: 0.7055 (mpp) REVERT: P 172 ASN cc_start: 0.8894 (m-40) cc_final: 0.8585 (p0) REVERT: P 207 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7971 (mm-40) REVERT: P 222 ARG cc_start: 0.6920 (mmm-85) cc_final: 0.6184 (mmm160) REVERT: P 223 PHE cc_start: 0.6687 (m-80) cc_final: 0.6056 (m-80) REVERT: P 233 HIS cc_start: 0.6889 (m-70) cc_final: 0.6615 (m-70) REVERT: P 238 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6677 (mp10) outliers start: 2 outliers final: 0 residues processed: 1196 average time/residue: 0.2062 time to fit residues: 388.0158 Evaluate side-chains 1109 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1109 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 202 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 280 optimal weight: 0.4980 chunk 380 optimal weight: 0.0970 chunk 105 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 356 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN E 23 HIS F 62 HIS ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN N 242 GLN ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN P 157 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.193771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147128 restraints weight = 70707.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152743 restraints weight = 43497.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.156697 restraints weight = 30168.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159475 restraints weight = 22646.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.161378 restraints weight = 18164.256| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34119 Z= 0.156 Angle : 0.758 13.445 46515 Z= 0.405 Chirality : 0.050 0.254 5006 Planarity : 0.005 0.069 5714 Dihedral : 14.821 174.602 5007 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.33 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.60 (0.13), residues: 3851 helix: 0.63 (0.12), residues: 1866 sheet: -0.60 (0.17), residues: 869 loop : -1.84 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 100 TYR 0.037 0.001 TYR B 70 PHE 0.023 0.002 PHE N 201 TRP 0.046 0.002 TRP P 78 HIS 0.029 0.001 HIS E 16 Details of bonding type rmsd covalent geometry : bond 0.00331 (34119) covalent geometry : angle 0.75760 (46515) hydrogen bonds : bond 0.04157 ( 1746) hydrogen bonds : angle 5.45501 ( 5114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1178 time to evaluate : 1.056 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: 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: 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: A 66 ASP cc_start: 0.7754 (t70) cc_final: 0.7151 (t70) REVERT: A 79 VAL cc_start: 0.8174 (t) cc_final: 0.7642 (p) REVERT: A 80 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6361 (tm-30) REVERT: A 85 LEU cc_start: 0.7955 (tt) cc_final: 0.7590 (tt) REVERT: A 90 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7284 (tmm-80) REVERT: A 92 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8441 (mtpp) REVERT: A 97 GLN cc_start: 0.7825 (pm20) cc_final: 0.7524 (pm20) REVERT: A 104 MET cc_start: 0.8506 (ttm) cc_final: 0.7808 (ttm) REVERT: A 107 TYR cc_start: 0.8280 (t80) cc_final: 0.7904 (t80) REVERT: A 113 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7660 (mmmm) REVERT: A 129 GLN cc_start: 0.8213 (tt0) cc_final: 0.7930 (tt0) REVERT: A 135 LEU cc_start: 0.9068 (mt) cc_final: 0.8520 (mt) REVERT: A 152 LEU cc_start: 0.7368 (pt) cc_final: 0.6401 (mp) REVERT: A 155 ARG cc_start: 0.8372 (tpt90) cc_final: 0.7631 (mmm160) REVERT: A 158 GLN cc_start: 0.8644 (tt0) cc_final: 0.8153 (tt0) REVERT: A 160 LEU cc_start: 0.8531 (tt) cc_final: 0.8280 (tt) REVERT: A 161 LYS cc_start: 0.8880 (tptt) cc_final: 0.8625 (tptt) REVERT: A 164 LEU cc_start: 0.8480 (mt) cc_final: 0.8194 (mt) REVERT: A 174 PHE cc_start: 0.6382 (p90) cc_final: 0.5908 (p90) REVERT: A 190 LYS cc_start: 0.8192 (ptpp) cc_final: 0.7762 (mtpt) REVERT: A 203 PHE cc_start: 0.8547 (t80) cc_final: 0.8081 (t80) REVERT: A 238 GLN cc_start: 0.6442 (mt0) cc_final: 0.6031 (mt0) REVERT: A 254 LYS cc_start: 0.8079 (pptt) cc_final: 0.7828 (pptt) REVERT: A 256 ARG cc_start: 0.7401 (pmt170) cc_final: 0.7033 (pmt170) REVERT: A 260 ARG cc_start: 0.7299 (ptm160) cc_final: 0.6899 (mtm110) REVERT: B 15 TRP cc_start: 0.7631 (m100) cc_final: 0.7063 (m100) REVERT: B 40 CYS cc_start: 0.7506 (t) cc_final: 0.6884 (p) REVERT: B 60 ILE cc_start: 0.7437 (mm) cc_final: 0.6928 (mm) REVERT: B 63 TRP cc_start: 0.7794 (m100) cc_final: 0.6233 (m100) REVERT: B 64 GLN cc_start: 0.6790 (tp40) cc_final: 0.6275 (mm-40) REVERT: B 82 ASN cc_start: 0.8105 (p0) cc_final: 0.7895 (p0) REVERT: B 86 ILE cc_start: 0.8658 (pt) cc_final: 0.8323 (mm) REVERT: B 89 GLU cc_start: 0.7850 (tt0) cc_final: 0.7094 (tt0) REVERT: B 92 LYS cc_start: 0.9053 (tppt) cc_final: 0.8821 (tppt) REVERT: B 100 ARG cc_start: 0.8699 (ptp90) cc_final: 0.7737 (ptp90) REVERT: B 103 THR cc_start: 0.8871 (p) cc_final: 0.8530 (p) REVERT: B 104 MET cc_start: 0.8717 (mmp) cc_final: 0.8104 (mmp) REVERT: B 129 GLN cc_start: 0.8526 (pt0) cc_final: 0.8212 (pt0) REVERT: B 132 MET cc_start: 0.8811 (tpp) cc_final: 0.8199 (tpp) REVERT: B 137 ILE cc_start: 0.8184 (tt) cc_final: 0.7813 (mp) REVERT: B 139 HIS cc_start: 0.8496 (t70) cc_final: 0.7836 (t70) REVERT: B 165 GLU cc_start: 0.7838 (tp30) cc_final: 0.7536 (tp30) REVERT: B 175 GLU cc_start: 0.8546 (pm20) cc_final: 0.8234 (mp0) REVERT: B 178 LEU cc_start: 0.9124 (mm) cc_final: 0.8782 (mm) REVERT: B 198 MET cc_start: 0.8205 (tpt) cc_final: 0.7627 (tpp) REVERT: B 204 ASN cc_start: 0.8080 (p0) cc_final: 0.7846 (p0) REVERT: B 205 LYS cc_start: 0.8748 (tptp) cc_final: 0.8349 (tppp) REVERT: B 208 GLN cc_start: 0.8623 (mt0) cc_final: 0.8097 (mt0) REVERT: C 11 GLU cc_start: 0.8444 (tp30) cc_final: 0.8165 (tp30) REVERT: C 30 ARG cc_start: 0.8970 (ttt90) cc_final: 0.8301 (ttt90) REVERT: C 34 GLU cc_start: 0.8790 (pt0) cc_final: 0.8438 (pp20) REVERT: C 35 ASP cc_start: 0.8631 (m-30) cc_final: 0.8098 (m-30) REVERT: C 38 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7737 (tp-100) REVERT: C 39 GLN cc_start: 0.8494 (tp40) cc_final: 0.8074 (tp40) REVERT: C 110 PHE cc_start: 0.8123 (m-80) cc_final: 0.7330 (m-80) REVERT: C 132 MET cc_start: 0.8344 (ppp) cc_final: 0.8116 (ppp) REVERT: C 186 ASN cc_start: 0.8278 (m-40) cc_final: 0.8066 (m110) REVERT: C 198 MET cc_start: 0.8513 (tpt) cc_final: 0.7844 (tpt) REVERT: C 201 PHE cc_start: 0.8854 (t80) cc_final: 0.8588 (t80) REVERT: C 244 LEU cc_start: 0.8461 (mm) cc_final: 0.7880 (mm) REVERT: C 245 TRP cc_start: 0.8380 (m-90) cc_final: 0.8121 (m-90) REVERT: D 154 GLU cc_start: 0.6673 (pm20) cc_final: 0.6079 (mp0) REVERT: D 158 GLN cc_start: 0.8376 (mp10) cc_final: 0.8082 (tm-30) REVERT: D 209 ARG cc_start: 0.8463 (mmp-170) cc_final: 0.8260 (mmm160) REVERT: D 226 TYR cc_start: 0.6866 (p90) cc_final: 0.5891 (p90) REVERT: D 254 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7904 (ttmt) REVERT: D 262 LEU cc_start: 0.8216 (mm) cc_final: 0.7932 (mm) REVERT: D 266 ASN cc_start: 0.8606 (m110) cc_final: 0.8045 (m110) REVERT: E 9 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7759 (mm-30) REVERT: E 10 GLU cc_start: 0.8217 (tp30) cc_final: 0.8011 (tp30) REVERT: E 89 GLU cc_start: 0.7491 (pm20) cc_final: 0.7027 (mp0) REVERT: E 97 GLN cc_start: 0.8023 (pm20) cc_final: 0.7732 (pm20) REVERT: E 100 ARG cc_start: 0.8737 (ptp90) cc_final: 0.8423 (ptt-90) REVERT: E 133 LYS cc_start: 0.9208 (ptpp) cc_final: 0.9002 (pttm) REVERT: E 138 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7513 (tm-30) REVERT: E 150 GLN cc_start: 0.7927 (mm110) cc_final: 0.7405 (mm110) REVERT: E 154 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8587 (mm-30) REVERT: E 158 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7525 (tm-30) REVERT: E 159 THR cc_start: 0.8323 (m) cc_final: 0.7603 (p) REVERT: E 174 PHE cc_start: 0.7712 (t80) cc_final: 0.7366 (t80) REVERT: E 178 LEU cc_start: 0.8837 (mt) cc_final: 0.8261 (mt) REVERT: E 206 GLU cc_start: 0.8395 (pt0) cc_final: 0.8053 (pt0) REVERT: E 236 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8426 (mm-30) REVERT: E 242 GLN cc_start: 0.5040 (pp30) cc_final: 0.4814 (pp30) REVERT: F 11 GLU cc_start: 0.8092 (mp0) cc_final: 0.7452 (mp0) REVERT: F 23 HIS cc_start: 0.7882 (t70) cc_final: 0.7453 (t70) REVERT: F 65 VAL cc_start: 0.7053 (t) cc_final: 0.6716 (p) REVERT: F 102 GLN cc_start: 0.8528 (mp10) cc_final: 0.8322 (mp10) REVERT: F 105 LYS cc_start: 0.9212 (ptpp) cc_final: 0.9006 (pttm) REVERT: F 107 TYR cc_start: 0.8338 (t80) cc_final: 0.7633 (t80) REVERT: F 129 GLN cc_start: 0.8242 (mt0) cc_final: 0.7945 (mt0) REVERT: F 158 GLN cc_start: 0.9022 (mp10) cc_final: 0.8704 (mp10) REVERT: F 170 MET cc_start: 0.7664 (mpp) cc_final: 0.7407 (mpp) REVERT: F 199 ASP cc_start: 0.8117 (m-30) cc_final: 0.7916 (m-30) REVERT: F 205 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8446 (mtmm) REVERT: F 206 GLU cc_start: 0.8124 (pp20) cc_final: 0.7689 (pp20) REVERT: F 230 LYS cc_start: 0.8527 (mmmt) cc_final: 0.7920 (mmmm) REVERT: F 233 HIS cc_start: 0.7859 (m-70) cc_final: 0.7578 (m90) REVERT: F 237 TRP cc_start: 0.8317 (m100) cc_final: 0.7951 (m100) REVERT: F 242 GLN cc_start: 0.7841 (tt0) cc_final: 0.7523 (tm-30) REVERT: F 243 VAL cc_start: 0.8538 (t) cc_final: 0.7521 (m) REVERT: F 267 LYS cc_start: 0.8793 (ptmt) cc_final: 0.8373 (pttt) REVERT: F 270 LYS cc_start: 0.8176 (mttt) cc_final: 0.6341 (mttt) REVERT: G 23 HIS cc_start: 0.7700 (t70) cc_final: 0.7147 (t70) REVERT: G 48 MET cc_start: -0.0550 (ppp) cc_final: -0.1355 (ppp) REVERT: G 106 TRP cc_start: 0.7441 (t60) cc_final: 0.7126 (t60) REVERT: G 107 TYR cc_start: 0.8349 (t80) cc_final: 0.7682 (t80) REVERT: G 110 PHE cc_start: 0.7776 (m-80) cc_final: 0.7361 (m-10) REVERT: G 131 LEU cc_start: 0.9375 (mt) cc_final: 0.9102 (mt) REVERT: G 150 GLN cc_start: 0.8458 (pp30) cc_final: 0.8199 (pp30) REVERT: G 171 PHE cc_start: 0.7591 (m-10) cc_final: 0.7350 (m-80) REVERT: G 175 GLU cc_start: 0.8659 (mp0) cc_final: 0.8376 (mm-30) REVERT: H 62 HIS cc_start: 0.7873 (t70) cc_final: 0.7159 (t70) REVERT: H 78 TRP cc_start: 0.7481 (m-10) cc_final: 0.6044 (m-10) REVERT: H 87 TYR cc_start: 0.8623 (t80) cc_final: 0.8065 (t80) REVERT: H 101 VAL cc_start: 0.8771 (p) cc_final: 0.8538 (p) REVERT: H 104 MET cc_start: 0.9062 (mmp) cc_final: 0.8372 (mmp) REVERT: H 106 TRP cc_start: 0.8330 (t60) cc_final: 0.7155 (t60) REVERT: H 109 MET cc_start: 0.8230 (tpt) cc_final: 0.7801 (tpp) REVERT: H 110 PHE cc_start: 0.8316 (m-10) cc_final: 0.7773 (m-10) REVERT: H 172 ASN cc_start: 0.8776 (m-40) cc_final: 0.8416 (p0) REVERT: H 207 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7806 (mm-40) REVERT: H 223 PHE cc_start: 0.7343 (m-80) cc_final: 0.7011 (m-80) REVERT: H 256 ARG cc_start: 0.8232 (ppt170) cc_final: 0.7747 (ppt170) REVERT: H 270 LYS cc_start: 0.7502 (mptt) cc_final: 0.7202 (mmtm) REVERT: I 60 ILE cc_start: 0.8669 (mp) cc_final: 0.8124 (mm) REVERT: I 79 VAL cc_start: 0.8287 (t) cc_final: 0.7787 (p) REVERT: I 85 LEU cc_start: 0.8022 (tp) cc_final: 0.7265 (tp) REVERT: I 86 ILE cc_start: 0.8468 (pt) cc_final: 0.8005 (mm) REVERT: I 89 GLU cc_start: 0.7999 (tp30) cc_final: 0.7776 (tp30) REVERT: I 92 LYS cc_start: 0.9017 (mtmm) cc_final: 0.8508 (mtpp) REVERT: I 100 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8190 (mtm110) REVERT: I 101 VAL cc_start: 0.9198 (m) cc_final: 0.8945 (p) REVERT: I 104 MET cc_start: 0.8525 (ttm) cc_final: 0.8161 (ttm) REVERT: I 105 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8527 (mtpp) REVERT: I 113 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7663 (mmmm) REVERT: I 131 LEU cc_start: 0.8871 (mt) cc_final: 0.8649 (mt) REVERT: I 152 LEU cc_start: 0.7134 (pt) cc_final: 0.6092 (mp) REVERT: I 158 GLN cc_start: 0.8590 (tt0) cc_final: 0.7645 (pt0) REVERT: I 160 LEU cc_start: 0.8642 (tt) cc_final: 0.8235 (tt) REVERT: I 163 THR cc_start: 0.8263 (m) cc_final: 0.7762 (p) REVERT: I 164 LEU cc_start: 0.8543 (mt) cc_final: 0.8262 (mt) REVERT: I 183 ILE cc_start: 0.8960 (mt) cc_final: 0.8723 (mt) REVERT: I 190 LYS cc_start: 0.8279 (mttp) cc_final: 0.7756 (mtpt) REVERT: I 198 MET cc_start: 0.8663 (ttm) cc_final: 0.8397 (tpp) REVERT: I 201 PHE cc_start: 0.8779 (t80) cc_final: 0.8445 (t80) REVERT: I 238 GLN cc_start: 0.6893 (mt0) cc_final: 0.6633 (mt0) REVERT: I 244 LEU cc_start: 0.8322 (mt) cc_final: 0.7966 (mt) REVERT: I 260 ARG cc_start: 0.7495 (ptp-170) cc_final: 0.7244 (ptp-170) REVERT: J 15 TRP cc_start: 0.7814 (m100) cc_final: 0.7202 (m100) REVERT: J 40 CYS cc_start: 0.7255 (t) cc_final: 0.6975 (t) REVERT: J 64 GLN cc_start: 0.7425 (tp40) cc_final: 0.7080 (tp40) REVERT: J 71 GLU cc_start: 0.7948 (pp20) cc_final: 0.7724 (pp20) REVERT: J 75 ILE cc_start: 0.7792 (mp) cc_final: 0.7566 (mm) REVERT: J 86 ILE cc_start: 0.8858 (pt) cc_final: 0.8503 (mm) REVERT: J 89 GLU cc_start: 0.7802 (tt0) cc_final: 0.7525 (tt0) REVERT: J 92 LYS cc_start: 0.9050 (tptp) cc_final: 0.8612 (tptp) REVERT: J 101 VAL cc_start: 0.8910 (t) cc_final: 0.8706 (t) REVERT: J 104 MET cc_start: 0.8293 (tpp) cc_final: 0.7655 (tpp) REVERT: J 106 TRP cc_start: 0.8583 (t60) cc_final: 0.8088 (t60) REVERT: J 131 LEU cc_start: 0.8739 (tt) cc_final: 0.8397 (tt) REVERT: J 139 HIS cc_start: 0.8561 (t70) cc_final: 0.7860 (t70) REVERT: J 162 ASN cc_start: 0.8884 (m110) cc_final: 0.8608 (m110) REVERT: J 174 PHE cc_start: 0.7882 (t80) cc_final: 0.7607 (t80) REVERT: J 178 LEU cc_start: 0.9200 (mm) cc_final: 0.8799 (mm) REVERT: J 198 MET cc_start: 0.8364 (tpt) cc_final: 0.8095 (tpp) REVERT: J 204 ASN cc_start: 0.8484 (m110) cc_final: 0.7924 (m110) REVERT: J 205 LYS cc_start: 0.8873 (tptp) cc_final: 0.8332 (tptp) REVERT: J 208 GLN cc_start: 0.8492 (mt0) cc_final: 0.7825 (mt0) REVERT: K 14 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8640 (mmtm) REVERT: K 15 TRP cc_start: 0.8489 (m100) cc_final: 0.8050 (m-10) REVERT: K 18 ASP cc_start: 0.8890 (t0) cc_final: 0.8658 (t70) REVERT: K 34 GLU cc_start: 0.8362 (pp20) cc_final: 0.8129 (pp20) REVERT: K 106 TRP cc_start: 0.7069 (t60) cc_final: 0.6734 (t60) REVERT: K 109 MET cc_start: 0.8220 (tpp) cc_final: 0.7142 (ptp) REVERT: K 110 PHE cc_start: 0.7999 (m-80) cc_final: 0.6857 (m-80) REVERT: K 132 MET cc_start: 0.7817 (ppp) cc_final: 0.7549 (ppp) REVERT: K 161 LYS cc_start: 0.9013 (pptt) cc_final: 0.8691 (pttp) REVERT: K 205 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8617 (mmmt) REVERT: K 245 TRP cc_start: 0.8120 (m100) cc_final: 0.7846 (m100) REVERT: L 63 TRP cc_start: 0.6497 (m100) cc_final: 0.5831 (m100) REVERT: L 226 TYR cc_start: 0.6970 (p90) cc_final: 0.5836 (p90) REVERT: L 268 ASP cc_start: 0.7212 (t0) cc_final: 0.6880 (t70) REVERT: L 269 VAL cc_start: 0.7686 (m) cc_final: 0.7414 (m) REVERT: M 7 LEU cc_start: 0.8509 (tt) cc_final: 0.7683 (tt) REVERT: M 11 GLU cc_start: 0.8377 (mp0) cc_final: 0.7957 (mp0) REVERT: M 14 LYS cc_start: 0.8327 (mttp) cc_final: 0.8037 (mtpt) REVERT: M 15 TRP cc_start: 0.8584 (m-10) cc_final: 0.8194 (m-10) REVERT: M 16 HIS cc_start: 0.7933 (m-70) cc_final: 0.6379 (m170) REVERT: M 18 ASP cc_start: 0.7815 (t70) cc_final: 0.7438 (t70) REVERT: M 25 GLU cc_start: 0.8443 (tt0) cc_final: 0.7950 (tt0) REVERT: M 36 ILE cc_start: 0.8756 (mt) cc_final: 0.8450 (mt) REVERT: M 39 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7805 (tm-30) REVERT: M 87 TYR cc_start: 0.6823 (t80) cc_final: 0.6588 (t80) REVERT: M 109 MET cc_start: 0.8681 (tmm) cc_final: 0.7940 (tmm) REVERT: M 152 LEU cc_start: 0.8786 (mm) cc_final: 0.7656 (mm) REVERT: M 154 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8735 (mm-30) REVERT: M 155 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8391 (mtt90) REVERT: M 158 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7806 (tm-30) REVERT: M 159 THR cc_start: 0.8639 (m) cc_final: 0.8022 (p) REVERT: M 166 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7843 (ttmm) REVERT: M 178 LEU cc_start: 0.8790 (mt) cc_final: 0.8519 (mt) REVERT: M 185 LEU cc_start: 0.8768 (mm) cc_final: 0.8547 (mm) REVERT: M 195 THR cc_start: 0.8227 (m) cc_final: 0.8016 (p) REVERT: M 205 LYS cc_start: 0.9064 (mttm) cc_final: 0.8717 (mttt) REVERT: M 207 GLN cc_start: 0.8461 (mm110) cc_final: 0.8079 (mm110) REVERT: M 209 ARG cc_start: 0.8753 (tmt170) cc_final: 0.8443 (ttp80) REVERT: M 224 CYS cc_start: 0.7094 (p) cc_final: 0.6868 (p) REVERT: N 23 HIS cc_start: 0.7767 (t70) cc_final: 0.7471 (t70) REVERT: N 61 ASP cc_start: 0.6284 (t0) cc_final: 0.5925 (t0) REVERT: N 86 ILE cc_start: 0.7824 (pt) cc_final: 0.7473 (tp) REVERT: N 102 GLN cc_start: 0.8768 (mp10) cc_final: 0.8281 (mp-120) REVERT: N 104 MET cc_start: 0.8145 (ptm) cc_final: 0.7529 (ppp) REVERT: N 105 LYS cc_start: 0.9331 (mtmm) cc_final: 0.9057 (mttt) REVERT: N 150 GLN cc_start: 0.7895 (mt0) cc_final: 0.7677 (mt0) REVERT: N 157 HIS cc_start: 0.8074 (m90) cc_final: 0.7852 (m90) REVERT: N 158 GLN cc_start: 0.8955 (mp10) cc_final: 0.8721 (mp10) REVERT: N 164 LEU cc_start: 0.8672 (mt) cc_final: 0.8442 (mt) REVERT: N 165 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7719 (mm-30) REVERT: N 205 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8057 (ptpp) REVERT: N 208 GLN cc_start: 0.8243 (tm-30) cc_final: 0.8038 (tm-30) REVERT: N 210 ILE cc_start: 0.8470 (pt) cc_final: 0.8096 (pt) REVERT: N 213 GLN cc_start: 0.8822 (mt0) cc_final: 0.8126 (mt0) REVERT: N 224 CYS cc_start: 0.7991 (p) cc_final: 0.7737 (p) REVERT: N 233 HIS cc_start: 0.7698 (m90) cc_final: 0.7245 (m90) REVERT: N 243 VAL cc_start: 0.8095 (t) cc_final: 0.7789 (m) REVERT: N 256 ARG cc_start: 0.8422 (ttm110) cc_final: 0.7824 (ttm110) REVERT: N 267 LYS cc_start: 0.8921 (ptmt) cc_final: 0.8516 (pttt) REVERT: O 23 HIS cc_start: 0.7445 (t70) cc_final: 0.6886 (t70) REVERT: O 48 MET cc_start: -0.1712 (ppp) cc_final: -0.2161 (ppp) REVERT: O 62 HIS cc_start: 0.7094 (m-70) cc_final: 0.6630 (m-70) REVERT: O 104 MET cc_start: 0.8338 (pmm) cc_final: 0.8072 (pmm) REVERT: O 110 PHE cc_start: 0.8033 (m-80) cc_final: 0.7805 (m-80) REVERT: O 115 LEU cc_start: 0.8541 (tp) cc_final: 0.8322 (tp) REVERT: O 152 LEU cc_start: 0.8913 (tp) cc_final: 0.8658 (tp) REVERT: O 157 HIS cc_start: 0.8960 (p-80) cc_final: 0.8745 (p90) REVERT: O 161 LYS cc_start: 0.8807 (ptpp) cc_final: 0.8534 (pttt) REVERT: O 193 LEU cc_start: 0.8762 (mm) cc_final: 0.8510 (mm) REVERT: O 203 PHE cc_start: 0.8373 (t80) cc_final: 0.7942 (t80) REVERT: O 205 LYS cc_start: 0.9246 (mmtm) cc_final: 0.8967 (mmtm) REVERT: P 62 HIS cc_start: 0.8012 (t70) cc_final: 0.7355 (t70) REVERT: P 87 TYR cc_start: 0.8518 (t80) cc_final: 0.8228 (t80) REVERT: P 104 MET cc_start: 0.9066 (mmp) cc_final: 0.8468 (mmp) REVERT: P 106 TRP cc_start: 0.8331 (t60) cc_final: 0.7947 (t60) REVERT: P 170 MET cc_start: 0.7737 (mtt) cc_final: 0.7127 (mpp) REVERT: P 172 ASN cc_start: 0.8889 (m-40) cc_final: 0.8576 (p0) REVERT: P 201 PHE cc_start: 0.7914 (t80) cc_final: 0.7626 (t80) REVERT: P 222 ARG cc_start: 0.6974 (mmm-85) cc_final: 0.6257 (mmm160) REVERT: P 223 PHE cc_start: 0.6750 (m-80) cc_final: 0.6148 (m-80) REVERT: P 233 HIS cc_start: 0.6769 (m-70) cc_final: 0.6473 (m-70) outliers start: 2 outliers final: 1 residues processed: 1179 average time/residue: 0.2121 time to fit residues: 395.1063 Evaluate side-chains 1098 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1097 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 177 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 262 optimal weight: 0.5980 chunk 193 optimal weight: 0.6980 chunk 300 optimal weight: 9.9990 chunk 248 optimal weight: 0.3980 chunk 221 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 HIS F 150 GLN H 157 HIS ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 GLN ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN L 158 GLN M 23 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 GLN ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN O 211 GLN P 157 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.192974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146284 restraints weight = 70294.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151909 restraints weight = 43047.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.155790 restraints weight = 29788.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.158507 restraints weight = 22402.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.160367 restraints weight = 18009.049| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34119 Z= 0.164 Angle : 0.762 14.383 46515 Z= 0.406 Chirality : 0.050 0.258 5006 Planarity : 0.005 0.061 5714 Dihedral : 14.836 174.939 5007 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.66 (0.13), residues: 3851 helix: 0.56 (0.12), residues: 1874 sheet: -0.60 (0.17), residues: 851 loop : -1.85 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 30 TYR 0.026 0.001 TYR I 70 PHE 0.022 0.002 PHE N 201 TRP 0.055 0.002 TRP M 63 HIS 0.026 0.001 HIS E 16 Details of bonding type rmsd covalent geometry : bond 0.00345 (34119) covalent geometry : angle 0.76160 (46515) hydrogen bonds : bond 0.04277 ( 1746) hydrogen bonds : angle 5.47310 ( 5114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8155.90 seconds wall clock time: 140 minutes 52.91 seconds (8452.91 seconds total)