Starting phenix.real_space_refine on Mon Jul 6 05:48:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpp_14860/07_2026/7zpp_14860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpp_14860/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zpp_14860/07_2026/7zpp_14860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpp_14860/07_2026/7zpp_14860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zpp_14860/07_2026/7zpp_14860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpp_14860/07_2026/7zpp_14860.map" } 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-6108/lib/python3.11/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: 7.90, 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: 2.78 Conformation dependent library (CDL) restraints added in 1.5 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: 4.34 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: 9.06 Time building geometry restraints manager: 3.80 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=" C3' DG T 10 " pdb=" C2' DG T 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG Q 8 " pdb=" C2' DG Q 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG R 10 " pdb=" C2' DG R 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG S 8 " pdb=" C2' DG S 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.64e+00 bond pdb=" C3' DG Q 4 " pdb=" C2' DG Q 4 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.19e+00 ... (remaining 34114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 46060 2.61 - 5.22: 375 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: 3406 0.038 - 0.075: 1017 0.075 - 0.113: 463 0.113 - 0.151: 107 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 36.550 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5274 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 0.037 34119 Z= 0.205 Angle : 0.657 13.062 46515 Z= 0.386 Chirality : 0.045 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/Z covalent geometry : bond 0.00295 / 0.21 (34119) covalent geometry : angle 0.65708 / 0.39 (46515) hydrogen bonds : bond 0.14599 / 9.87 ( 1746) hydrogen bonds : angle 6.49516 / 4.63 ( 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 : 1.018 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: 0.2208 time to fit residues: 423.7879 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 : 1.082 ------------------------------------------------------------------------------- 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... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 157 HIS ** 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 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 HIS J 16 HIS J 158 GLN J 211 GLN ** 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 N 213 GLN O 69 HIS 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.209061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162959 restraints weight = 72572.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.168977 restraints weight = 46464.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.173246 restraints weight = 32764.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.176372 restraints weight = 24811.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.178654 restraints weight = 19772.127| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34119 Z= 0.159 Angle : 0.698 12.793 46515 Z= 0.372 Chirality : 0.049 0.297 5006 Planarity : 0.005 0.091 5714 Dihedral : 14.425 168.340 5007 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 0.35 % Allowed : 3.58 % Favored : 96.07 % 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: 0.11 (0.13), residues: 3851 helix: 1.23 (0.12), residues: 1871 sheet: -0.50 (0.17), residues: 894 loop : -1.34 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 256 TYR 0.042 0.002 TYR E 70 PHE 0.042 0.002 PHE K 174 TRP 0.033 0.002 TRP P 78 HIS 0.023 0.002 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (34119) covalent geometry : angle 0.69784 / 0.37 (46515) hydrogen bonds : bond 0.04556 / 3.06 ( 1746) hydrogen bonds : angle 5.44606 / 3.91 ( 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 1167 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1155 time to evaluate : 1.140 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8735 (mm) cc_final: 0.8505 (mm) REVERT: A 62 HIS cc_start: 0.7927 (t70) cc_final: 0.7642 (t70) REVERT: A 64 GLN cc_start: 0.6600 (pm20) cc_final: 0.6307 (pm20) REVERT: A 76 LEU cc_start: 0.7494 (mp) cc_final: 0.7249 (mm) REVERT: A 79 VAL cc_start: 0.7348 (t) cc_final: 0.6815 (m) REVERT: A 92 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8482 (mtpp) REVERT: A 100 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7459 (mtm180) REVERT: A 107 TYR cc_start: 0.8440 (t80) cc_final: 0.8156 (t80) REVERT: A 118 ASP cc_start: 0.7635 (p0) cc_final: 0.7282 (p0) REVERT: A 132 MET cc_start: 0.7779 (mmm) cc_final: 0.7518 (mmm) REVERT: A 143 ILE cc_start: 0.7771 (pt) cc_final: 0.7306 (pt) REVERT: A 146 ASN cc_start: 0.8009 (m110) cc_final: 0.7451 (m-40) REVERT: A 153 VAL cc_start: 0.8996 (m) cc_final: 0.8793 (m) REVERT: A 155 ARG cc_start: 0.8511 (tpt90) cc_final: 0.7495 (mmm160) REVERT: A 158 GLN cc_start: 0.8869 (tt0) cc_final: 0.8537 (tt0) REVERT: A 161 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7895 (tppt) REVERT: A 203 PHE cc_start: 0.8293 (t80) cc_final: 0.7970 (t80) REVERT: A 208 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 254 LYS cc_start: 0.8289 (pptt) cc_final: 0.7447 (ttpp) REVERT: A 260 ARG cc_start: 0.7332 (ptm160) cc_final: 0.7053 (ptm160) REVERT: B 15 TRP cc_start: 0.7781 (m100) cc_final: 0.7402 (m100) REVERT: B 42 VAL cc_start: 0.3063 (t) cc_final: 0.2730 (t) REVERT: B 63 TRP cc_start: 0.7790 (m100) cc_final: 0.6302 (m100) REVERT: B 64 GLN cc_start: 0.6569 (tp40) cc_final: 0.5841 (tp40) REVERT: B 65 VAL cc_start: 0.8682 (t) cc_final: 0.8460 (t) REVERT: B 75 ILE cc_start: 0.7735 (pt) cc_final: 0.7424 (mp) REVERT: B 92 LYS cc_start: 0.8709 (tppt) cc_final: 0.8256 (tptp) REVERT: B 101 VAL cc_start: 0.9010 (t) cc_final: 0.8784 (t) REVERT: B 104 MET cc_start: 0.8470 (mmp) cc_final: 0.8159 (mmp) REVERT: B 129 GLN cc_start: 0.8479 (pt0) cc_final: 0.8071 (pt0) REVERT: B 131 LEU cc_start: 0.8887 (tt) cc_final: 0.8667 (tt) REVERT: B 137 ILE cc_start: 0.8475 (tt) cc_final: 0.8204 (tt) REVERT: B 161 LYS cc_start: 0.9098 (ptpt) cc_final: 0.8895 (ptpt) REVERT: B 164 LEU cc_start: 0.8747 (tp) cc_final: 0.8497 (tp) REVERT: B 165 GLU cc_start: 0.7668 (tp30) cc_final: 0.7384 (tp30) REVERT: B 178 LEU cc_start: 0.8961 (mm) cc_final: 0.8540 (mm) REVERT: B 198 MET cc_start: 0.8093 (tpt) cc_final: 0.7651 (tpp) REVERT: B 204 ASN cc_start: 0.7407 (p0) cc_final: 0.7041 (p0) REVERT: B 208 GLN cc_start: 0.8036 (pt0) cc_final: 0.7784 (pt0) REVERT: C 7 LEU cc_start: 0.8731 (tt) cc_final: 0.8512 (tt) REVERT: C 18 ASP cc_start: 0.8735 (t70) cc_final: 0.8487 (t70) REVERT: C 30 ARG cc_start: 0.9045 (ttt180) cc_final: 0.8724 (ttp80) REVERT: C 110 PHE cc_start: 0.7688 (m-80) cc_final: 0.7394 (m-80) REVERT: C 132 MET cc_start: 0.8183 (ppp) cc_final: 0.7652 (ppp) REVERT: C 206 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: C 209 ARG cc_start: 0.8422 (ptt90) cc_final: 0.7961 (ptt90) REVERT: D 63 TRP cc_start: 0.5085 (m100) cc_final: 0.4730 (m100) REVERT: D 86 ILE cc_start: 0.6863 (pt) cc_final: 0.6604 (mm) REVERT: D 203 PHE cc_start: 0.7851 (t80) cc_final: 0.7591 (t80) REVERT: D 218 GLN cc_start: 0.8404 (mm110) cc_final: 0.7901 (mm110) REVERT: D 223 PHE cc_start: 0.6342 (p90) cc_final: 0.5836 (p90) REVERT: D 226 TYR cc_start: 0.6611 (p90) cc_final: 0.6077 (p90) REVERT: D 254 LYS cc_start: 0.7707 (ttmm) cc_final: 0.7436 (tppt) REVERT: E 7 LEU cc_start: 0.7712 (tt) cc_final: 0.7461 (tt) REVERT: E 9 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7963 (mm-30) REVERT: E 10 GLU cc_start: 0.8094 (tp30) cc_final: 0.7809 (tp30) REVERT: E 13 ASN cc_start: 0.8769 (m110) cc_final: 0.8476 (m110) REVERT: E 18 ASP cc_start: 0.7363 (t70) cc_final: 0.7160 (t70) REVERT: E 36 ILE cc_start: 0.8137 (mt) cc_final: 0.7719 (tp) REVERT: E 87 TYR cc_start: 0.7103 (t80) cc_final: 0.6580 (t80) REVERT: E 110 PHE cc_start: 0.7708 (m-80) cc_final: 0.6922 (m-10) REVERT: E 150 GLN cc_start: 0.7597 (mm110) cc_final: 0.7290 (mm-40) REVERT: E 159 THR cc_start: 0.8596 (m) cc_final: 0.7974 (p) REVERT: E 199 ASP cc_start: 0.8390 (m-30) cc_final: 0.7608 (m-30) REVERT: E 236 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8469 (mm-30) REVERT: F 23 HIS cc_start: 0.7759 (t70) cc_final: 0.7480 (t70) REVERT: F 86 ILE cc_start: 0.6655 (pt) cc_final: 0.5922 (mm) REVERT: F 183 ILE cc_start: 0.5948 (mt) cc_final: 0.5736 (mt) REVERT: F 199 ASP cc_start: 0.8526 (m-30) cc_final: 0.8275 (m-30) REVERT: F 202 ILE cc_start: 0.8323 (mt) cc_final: 0.7965 (mt) REVERT: F 203 PHE cc_start: 0.7649 (t80) cc_final: 0.6863 (t80) REVERT: F 206 GLU cc_start: 0.7993 (pp20) cc_final: 0.7742 (pp20) REVERT: F 208 GLN cc_start: 0.8556 (tt0) cc_final: 0.8137 (tm-30) REVERT: F 233 HIS cc_start: 0.7549 (m90) cc_final: 0.7247 (m90) REVERT: F 236 GLU cc_start: 0.7839 (pm20) cc_final: 0.7523 (mp0) REVERT: F 243 VAL cc_start: 0.8047 (t) cc_final: 0.7420 (m) REVERT: F 244 LEU cc_start: 0.7767 (tt) cc_final: 0.7524 (tt) REVERT: F 256 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7893 (ttm110) REVERT: F 260 ARG cc_start: 0.7115 (mtm110) cc_final: 0.6853 (mtm110) REVERT: F 270 LYS cc_start: 0.7868 (mttt) cc_final: 0.7295 (mttt) REVERT: G 10 GLU cc_start: 0.5638 (pt0) cc_final: 0.5297 (pt0) REVERT: G 48 MET cc_start: -0.0469 (ppp) cc_final: -0.1243 (ppp) REVERT: G 85 LEU cc_start: 0.7170 (tp) cc_final: 0.6786 (tp) REVERT: G 110 PHE cc_start: 0.7512 (m-80) cc_final: 0.7098 (m-80) REVERT: G 131 LEU cc_start: 0.9218 (mt) cc_final: 0.9000 (mt) REVERT: G 160 LEU cc_start: 0.8392 (pp) cc_final: 0.8177 (pp) REVERT: G 197 PRO cc_start: 0.8142 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: G 201 PHE cc_start: 0.8775 (t80) cc_final: 0.8266 (t80) REVERT: G 205 LYS cc_start: 0.9197 (mmtm) cc_final: 0.8954 (mmtp) REVERT: G 208 GLN cc_start: 0.8440 (tm130) cc_final: 0.8074 (tm-30) REVERT: H 62 HIS cc_start: 0.7434 (t-90) cc_final: 0.6896 (t-170) REVERT: H 78 TRP cc_start: 0.5843 (m-10) cc_final: 0.5316 (m-10) REVERT: H 87 TYR cc_start: 0.8025 (t80) cc_final: 0.7648 (t80) REVERT: H 101 VAL cc_start: 0.8763 (p) cc_final: 0.8542 (p) REVERT: H 104 MET cc_start: 0.9125 (mmp) cc_final: 0.8530 (mmp) REVERT: H 109 MET cc_start: 0.8104 (tpt) cc_final: 0.7873 (tpt) REVERT: H 110 PHE cc_start: 0.7984 (m-10) cc_final: 0.7498 (m-10) REVERT: H 132 MET cc_start: 0.6109 (tmm) cc_final: 0.5790 (tmm) REVERT: H 164 LEU cc_start: 0.9170 (mm) cc_final: 0.8933 (pp) REVERT: I 60 ILE cc_start: 0.8501 (mt) cc_final: 0.8286 (mp) REVERT: I 79 VAL cc_start: 0.7579 (t) cc_final: 0.7124 (p) REVERT: I 92 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8457 (mtpp) REVERT: I 100 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7601 (mtm-85) REVERT: I 101 VAL cc_start: 0.9299 (t) cc_final: 0.9069 (p) REVERT: I 105 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8323 (mtmm) REVERT: I 118 ASP cc_start: 0.7886 (p0) cc_final: 0.7577 (p0) REVERT: I 132 MET cc_start: 0.7982 (mmm) cc_final: 0.7673 (mmm) REVERT: I 146 ASN cc_start: 0.7931 (m110) cc_final: 0.7136 (m-40) REVERT: I 158 GLN cc_start: 0.8970 (tt0) cc_final: 0.8685 (tt0) REVERT: I 164 LEU cc_start: 0.8311 (mt) cc_final: 0.8066 (mt) REVERT: I 203 PHE cc_start: 0.8426 (t80) cc_final: 0.7979 (t80) REVERT: I 208 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7769 (tm-30) REVERT: I 222 ARG cc_start: 0.4674 (mtp-110) cc_final: 0.4275 (mtm110) REVERT: J 42 VAL cc_start: 0.4508 (t) cc_final: 0.4264 (t) REVERT: J 63 TRP cc_start: 0.7745 (m100) cc_final: 0.6486 (m100) REVERT: J 64 GLN cc_start: 0.6763 (tp40) cc_final: 0.5963 (tp40) REVERT: J 70 TYR cc_start: 0.7245 (t80) cc_final: 0.6482 (t80) REVERT: J 73 LYS cc_start: 0.7873 (mttt) cc_final: 0.7047 (mtmt) REVERT: J 86 ILE cc_start: 0.8657 (pt) cc_final: 0.7915 (mm) REVERT: J 92 LYS cc_start: 0.8790 (tptp) cc_final: 0.8447 (tptp) REVERT: J 101 VAL cc_start: 0.9082 (t) cc_final: 0.8831 (t) REVERT: J 104 MET cc_start: 0.8229 (tpp) cc_final: 0.7611 (tpp) REVERT: J 131 LEU cc_start: 0.8623 (tt) cc_final: 0.8281 (tt) REVERT: J 137 ILE cc_start: 0.8206 (tt) cc_final: 0.7973 (tt) REVERT: J 138 GLU cc_start: 0.7726 (tp30) cc_final: 0.7455 (tp30) REVERT: J 160 LEU cc_start: 0.8687 (tt) cc_final: 0.8339 (tt) REVERT: J 161 LYS cc_start: 0.9027 (ptpt) cc_final: 0.8621 (ptpt) REVERT: J 162 ASN cc_start: 0.8944 (m110) cc_final: 0.8662 (m-40) REVERT: J 174 PHE cc_start: 0.6803 (t80) cc_final: 0.6382 (t80) REVERT: J 178 LEU cc_start: 0.8995 (mm) cc_final: 0.8742 (mm) REVERT: J 184 THR cc_start: 0.8969 (p) cc_final: 0.8510 (p) REVERT: J 186 ASN cc_start: 0.7595 (m-40) cc_final: 0.7007 (m110) REVERT: J 189 ARG cc_start: 0.6633 (ttp-170) cc_final: 0.6275 (mtm110) REVERT: J 198 MET cc_start: 0.8034 (tpt) cc_final: 0.7746 (tpp) REVERT: J 204 ASN cc_start: 0.7889 (m110) cc_final: 0.7265 (m110) REVERT: J 205 LYS cc_start: 0.8254 (tptp) cc_final: 0.7771 (tptp) REVERT: J 208 GLN cc_start: 0.7950 (pt0) cc_final: 0.7644 (pt0) REVERT: K 7 LEU cc_start: 0.8625 (tt) cc_final: 0.8406 (tt) REVERT: K 15 TRP cc_start: 0.8000 (m100) cc_final: 0.7608 (m100) REVERT: K 18 ASP cc_start: 0.8779 (t70) cc_final: 0.8576 (t70) REVERT: K 40 CYS cc_start: 0.8287 (m) cc_final: 0.7683 (p) REVERT: K 109 MET cc_start: 0.7998 (tpp) cc_final: 0.7142 (ptp) REVERT: K 110 PHE cc_start: 0.7420 (m-80) cc_final: 0.6966 (m-80) REVERT: K 132 MET cc_start: 0.7212 (ppp) cc_final: 0.6581 (ppp) REVERT: K 193 LEU cc_start: 0.7595 (mt) cc_final: 0.7013 (mm) REVERT: K 206 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7756 (pm20) REVERT: K 245 TRP cc_start: 0.8093 (m100) cc_final: 0.7877 (m100) REVERT: L 63 TRP cc_start: 0.6213 (m100) cc_final: 0.5897 (m100) REVERT: L 86 ILE cc_start: 0.6307 (pt) cc_final: 0.6068 (mm) REVERT: L 226 TYR cc_start: 0.6875 (p90) cc_final: 0.6056 (p90) REVERT: L 248 ASP cc_start: 0.8135 (p0) cc_final: 0.7903 (p0) REVERT: L 259 ASP cc_start: 0.8522 (m-30) cc_final: 0.8143 (m-30) REVERT: M 7 LEU cc_start: 0.7706 (tt) cc_final: 0.7466 (tt) REVERT: M 12 HIS cc_start: 0.7983 (t-90) cc_final: 0.7408 (t-170) REVERT: M 18 ASP cc_start: 0.7225 (t70) cc_final: 0.6815 (t70) REVERT: M 22 LEU cc_start: 0.7958 (pp) cc_final: 0.7667 (pp) REVERT: M 76 LEU cc_start: 0.7230 (tp) cc_final: 0.6233 (tp) REVERT: M 87 TYR cc_start: 0.7203 (t80) cc_final: 0.6644 (t80) REVERT: M 109 MET cc_start: 0.8429 (tmm) cc_final: 0.8139 (tmm) REVERT: M 158 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7344 (tm-30) REVERT: M 159 THR cc_start: 0.8642 (m) cc_final: 0.7841 (p) REVERT: M 162 ASN cc_start: 0.8085 (m-40) cc_final: 0.7820 (m110) REVERT: M 199 ASP cc_start: 0.8561 (m-30) cc_final: 0.7660 (m-30) REVERT: M 202 ILE cc_start: 0.9019 (mm) cc_final: 0.8657 (mm) REVERT: N 14 LYS cc_start: 0.7336 (pttm) cc_final: 0.7134 (ptmt) REVERT: N 23 HIS cc_start: 0.7618 (t70) cc_final: 0.7405 (t70) REVERT: N 65 VAL cc_start: 0.7271 (t) cc_final: 0.6920 (p) REVERT: N 104 MET cc_start: 0.8277 (ptm) cc_final: 0.7932 (ptm) REVERT: N 110 PHE cc_start: 0.8030 (m-80) cc_final: 0.7204 (m-10) REVERT: N 154 GLU cc_start: 0.8152 (tp30) cc_final: 0.7949 (mm-30) REVERT: N 162 ASN cc_start: 0.8168 (m110) cc_final: 0.7949 (m110) REVERT: N 203 PHE cc_start: 0.7651 (t80) cc_final: 0.6795 (t80) REVERT: N 205 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7709 (mtmm) REVERT: N 206 GLU cc_start: 0.7741 (pp20) cc_final: 0.7472 (pp20) REVERT: N 208 GLN cc_start: 0.8410 (tt0) cc_final: 0.8092 (tm-30) REVERT: N 213 GLN cc_start: 0.8772 (mt0) cc_final: 0.8440 (mt0) REVERT: N 230 LYS cc_start: 0.8123 (mttt) cc_final: 0.7836 (tptp) REVERT: N 233 HIS cc_start: 0.7705 (m90) cc_final: 0.7308 (m-70) REVERT: N 242 GLN cc_start: 0.7710 (tt0) cc_final: 0.7012 (pp30) REVERT: N 243 VAL cc_start: 0.8171 (t) cc_final: 0.7303 (m) REVERT: N 244 LEU cc_start: 0.8117 (tt) cc_final: 0.7718 (tt) REVERT: N 256 ARG cc_start: 0.8349 (ttm110) cc_final: 0.7648 (ttm110) REVERT: N 267 LYS cc_start: 0.8684 (ptmt) cc_final: 0.7594 (mmtt) REVERT: O 48 MET cc_start: -0.2089 (ppp) cc_final: -0.3000 (ppp) REVERT: O 104 MET cc_start: 0.7995 (pmm) cc_final: 0.7733 (pmm) REVERT: O 110 PHE cc_start: 0.8045 (m-80) cc_final: 0.7644 (m-80) REVERT: O 132 MET cc_start: 0.8181 (tmm) cc_final: 0.7842 (tmm) REVERT: O 201 PHE cc_start: 0.8763 (t80) cc_final: 0.7754 (t80) REVERT: O 205 LYS cc_start: 0.9097 (mmtm) cc_final: 0.8849 (mmtp) REVERT: O 208 GLN cc_start: 0.8564 (tm130) cc_final: 0.8272 (tm-30) REVERT: O 209 ARG cc_start: 0.8645 (ptm-80) cc_final: 0.8271 (ptm-80) REVERT: O 211 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8203 (tp40) REVERT: P 101 VAL cc_start: 0.9142 (p) cc_final: 0.8836 (p) REVERT: P 104 MET cc_start: 0.9141 (mmp) cc_final: 0.8727 (mmp) REVERT: P 132 MET cc_start: 0.5916 (tmm) cc_final: 0.5552 (tmm) REVERT: P 170 MET cc_start: 0.7335 (mtt) cc_final: 0.6910 (mpp) REVERT: P 222 ARG cc_start: 0.5813 (mtp85) cc_final: 0.5471 (mmm-85) REVERT: P 230 LYS cc_start: 0.7227 (mmmt) cc_final: 0.6937 (mmtm) REVERT: P 254 LYS cc_start: 0.8620 (mtpp) cc_final: 0.7989 (tppt) outliers start: 12 outliers final: 1 residues processed: 1163 average time/residue: 0.2142 time to fit residues: 391.0442 Evaluate side-chains 1070 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1067 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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: 0.6980 chunk 80 optimal weight: 0.0980 chunk 237 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 376 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 313 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 ASN B 102 GLN B 158 GLN B 211 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 GLN G 208 GLN ** 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 139 HIS J 62 HIS J 102 GLN J 157 HIS J 158 GLN 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 GLN ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 102 GLN O 207 GLN O 208 GLN ** 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 = 0.4601 r_free = 0.4601 target = 0.204109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157954 restraints weight = 73223.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.163621 restraints weight = 47165.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167639 restraints weight = 33533.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.170538 restraints weight = 25526.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.172668 restraints weight = 20562.372| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34119 Z= 0.156 Angle : 0.678 12.829 46515 Z= 0.363 Chirality : 0.048 0.271 5006 Planarity : 0.005 0.091 5714 Dihedral : 14.662 169.095 5007 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % 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: 1.15 (0.12), residues: 1867 sheet: -0.66 (0.17), residues: 939 loop : -1.40 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 189 TYR 0.020 0.002 TYR N 134 PHE 0.028 0.002 PHE K 174 TRP 0.037 0.002 TRP P 78 HIS 0.016 0.002 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (34119) covalent geometry : angle 0.67752 / 0.36 (46515) hydrogen bonds : bond 0.04306 / 2.90 ( 1746) hydrogen bonds : angle 5.40091 / 3.87 ( 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 1148 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1143 time to evaluate : 1.200 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: A 15 TRP cc_start: 0.6339 (m-10) cc_final: 0.5373 (m-90) REVERT: A 60 ILE cc_start: 0.8748 (mm) cc_final: 0.8441 (mm) REVERT: A 62 HIS cc_start: 0.7933 (t70) cc_final: 0.7577 (t70) REVERT: A 79 VAL cc_start: 0.7737 (t) cc_final: 0.7242 (p) REVERT: A 92 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8490 (mtpp) REVERT: A 100 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7540 (mtm180) REVERT: A 107 TYR cc_start: 0.8492 (t80) cc_final: 0.7879 (t80) REVERT: A 113 LYS cc_start: 0.7840 (mmmm) cc_final: 0.7551 (mmmm) REVERT: A 118 ASP cc_start: 0.7593 (p0) cc_final: 0.7226 (p0) REVERT: A 132 MET cc_start: 0.8030 (mmm) cc_final: 0.7757 (mmm) REVERT: A 143 ILE cc_start: 0.7949 (pt) cc_final: 0.7408 (pt) REVERT: A 146 ASN cc_start: 0.8013 (m110) cc_final: 0.7379 (m-40) REVERT: A 155 ARG cc_start: 0.8535 (tpt90) cc_final: 0.7723 (mmm160) REVERT: A 158 GLN cc_start: 0.8906 (tt0) cc_final: 0.8592 (tt0) REVERT: A 161 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8276 (tppt) REVERT: A 164 LEU cc_start: 0.8241 (mt) cc_final: 0.7901 (mt) REVERT: A 201 PHE cc_start: 0.8032 (t80) cc_final: 0.7735 (t80) REVERT: A 203 PHE cc_start: 0.8336 (t80) cc_final: 0.7956 (t80) REVERT: A 208 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 226 TYR cc_start: 0.6215 (p90) cc_final: 0.5619 (p90) REVERT: A 254 LYS cc_start: 0.8236 (pptt) cc_final: 0.7876 (pptt) REVERT: A 258 THR cc_start: 0.8732 (p) cc_final: 0.8508 (p) REVERT: A 260 ARG cc_start: 0.7443 (ptm160) cc_final: 0.7136 (ptm160) REVERT: B 15 TRP cc_start: 0.7938 (m100) cc_final: 0.7499 (m100) REVERT: B 40 CYS cc_start: 0.7219 (t) cc_final: 0.6782 (p) REVERT: B 63 TRP cc_start: 0.7918 (m100) cc_final: 0.6276 (m100) REVERT: B 64 GLN cc_start: 0.6888 (tp40) cc_final: 0.6236 (mm-40) REVERT: B 65 VAL cc_start: 0.8635 (t) cc_final: 0.8286 (t) REVERT: B 75 ILE cc_start: 0.7776 (pt) cc_final: 0.7482 (mp) REVERT: B 92 LYS cc_start: 0.8777 (tppt) cc_final: 0.8221 (tptp) REVERT: B 104 MET cc_start: 0.8601 (mmp) cc_final: 0.8242 (mmp) REVERT: B 105 LYS cc_start: 0.9090 (mtpp) cc_final: 0.8797 (mtpp) REVERT: B 116 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6481 (tm-30) REVERT: B 129 GLN cc_start: 0.8498 (pt0) cc_final: 0.8107 (pt0) REVERT: B 131 LEU cc_start: 0.8960 (tt) cc_final: 0.8663 (tt) REVERT: B 137 ILE cc_start: 0.8499 (tt) cc_final: 0.8234 (tt) REVERT: B 139 HIS cc_start: 0.8128 (t70) cc_final: 0.7908 (t70) REVERT: B 162 ASN cc_start: 0.8863 (m110) cc_final: 0.8655 (m110) REVERT: B 165 GLU cc_start: 0.7998 (tp30) cc_final: 0.7577 (tp30) REVERT: B 178 LEU cc_start: 0.9035 (mm) cc_final: 0.8650 (mm) REVERT: B 198 MET cc_start: 0.8146 (tpt) cc_final: 0.7735 (tpp) REVERT: B 204 ASN cc_start: 0.7606 (p0) cc_final: 0.7319 (p0) REVERT: C 7 LEU cc_start: 0.8760 (tt) cc_final: 0.8523 (tt) REVERT: C 35 ASP cc_start: 0.8628 (m-30) cc_final: 0.8415 (m-30) REVERT: C 110 PHE cc_start: 0.7582 (m-80) cc_final: 0.7211 (m-80) REVERT: C 132 MET cc_start: 0.8236 (ppp) cc_final: 0.7806 (ppp) REVERT: C 209 ARG cc_start: 0.8544 (ptt90) cc_final: 0.7976 (ptt90) REVERT: D 203 PHE cc_start: 0.7936 (t80) cc_final: 0.7723 (t80) REVERT: D 218 GLN cc_start: 0.8435 (mm110) cc_final: 0.7931 (mm110) REVERT: D 223 PHE cc_start: 0.6515 (p90) cc_final: 0.6087 (p90) REVERT: D 226 TYR cc_start: 0.6955 (p90) cc_final: 0.6215 (p90) REVERT: D 244 LEU cc_start: 0.8184 (mt) cc_final: 0.7625 (pp) REVERT: D 254 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7390 (tptt) REVERT: D 268 ASP cc_start: 0.7176 (t70) cc_final: 0.6964 (t70) REVERT: E 10 GLU cc_start: 0.8176 (tp30) cc_final: 0.7771 (tp30) REVERT: E 12 HIS cc_start: 0.7995 (t70) cc_final: 0.7503 (t70) REVERT: E 13 ASN cc_start: 0.8791 (m110) cc_final: 0.8563 (m110) REVERT: E 15 TRP cc_start: 0.8739 (m-10) cc_final: 0.8496 (m-10) REVERT: E 22 LEU cc_start: 0.8138 (pp) cc_final: 0.7891 (pp) REVERT: E 26 PHE cc_start: 0.7848 (m-80) cc_final: 0.7641 (m-80) REVERT: E 87 TYR cc_start: 0.7148 (t80) cc_final: 0.5800 (t80) REVERT: E 89 GLU cc_start: 0.7779 (pm20) cc_final: 0.5351 (mp0) REVERT: E 150 GLN cc_start: 0.7906 (mm110) cc_final: 0.7190 (mm-40) REVERT: E 159 THR cc_start: 0.8578 (m) cc_final: 0.8004 (p) REVERT: E 178 LEU cc_start: 0.8952 (mt) cc_final: 0.8508 (mt) REVERT: E 199 ASP cc_start: 0.8391 (m-30) cc_final: 0.7553 (m-30) REVERT: E 207 GLN cc_start: 0.8493 (mm110) cc_final: 0.8175 (mm-40) REVERT: E 236 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8572 (mm-30) REVERT: F 23 HIS cc_start: 0.7786 (t70) cc_final: 0.7526 (t70) REVERT: F 86 ILE cc_start: 0.6800 (pt) cc_final: 0.6063 (mm) REVERT: F 162 ASN cc_start: 0.8747 (m-40) cc_final: 0.8526 (m110) REVERT: F 199 ASP cc_start: 0.8500 (m-30) cc_final: 0.8249 (m-30) REVERT: F 202 ILE cc_start: 0.8353 (mt) cc_final: 0.8123 (mt) REVERT: F 203 PHE cc_start: 0.7836 (t80) cc_final: 0.6924 (t80) REVERT: F 205 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7612 (mtmt) REVERT: F 206 GLU cc_start: 0.8202 (pp20) cc_final: 0.7973 (pp20) REVERT: F 230 LYS cc_start: 0.8300 (mmmt) cc_final: 0.7762 (mmmm) REVERT: F 233 HIS cc_start: 0.7638 (m90) cc_final: 0.7265 (m90) REVERT: F 236 GLU cc_start: 0.8007 (pm20) cc_final: 0.7605 (mp0) REVERT: F 242 GLN cc_start: 0.7526 (tt0) cc_final: 0.6639 (pp30) REVERT: F 243 VAL cc_start: 0.8212 (t) cc_final: 0.7011 (m) REVERT: F 244 LEU cc_start: 0.7981 (tt) cc_final: 0.7517 (tt) REVERT: F 256 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8042 (ttm110) REVERT: F 260 ARG cc_start: 0.6959 (mtm110) cc_final: 0.6748 (ttp-110) REVERT: F 267 LYS cc_start: 0.8666 (ptpt) cc_final: 0.8215 (pttt) REVERT: G 48 MET cc_start: -0.0286 (ppp) cc_final: -0.1152 (ppp) REVERT: G 62 HIS cc_start: 0.7368 (t70) cc_final: 0.7054 (t70) REVERT: G 85 LEU cc_start: 0.7196 (tp) cc_final: 0.6805 (tp) REVERT: G 110 PHE cc_start: 0.7605 (m-80) cc_final: 0.7152 (m-80) REVERT: G 131 LEU cc_start: 0.9218 (mt) cc_final: 0.8998 (mt) REVERT: G 157 HIS cc_start: 0.8937 (m90) cc_final: 0.8568 (m90) REVERT: G 164 LEU cc_start: 0.8526 (mt) cc_final: 0.8012 (mt) REVERT: G 197 PRO cc_start: 0.8494 (Cg_exo) cc_final: 0.8128 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8932 (m-30) cc_final: 0.8694 (m-30) REVERT: G 201 PHE cc_start: 0.8899 (t80) cc_final: 0.8249 (t80) REVERT: G 205 LYS cc_start: 0.9232 (mmtm) cc_final: 0.8999 (mptt) REVERT: G 208 GLN cc_start: 0.8498 (tm130) cc_final: 0.8161 (tm-30) REVERT: H 61 ASP cc_start: 0.7314 (m-30) cc_final: 0.7096 (m-30) REVERT: H 62 HIS cc_start: 0.7585 (t-90) cc_final: 0.7036 (t-170) REVERT: H 78 TRP cc_start: 0.6586 (m-10) cc_final: 0.6109 (m-10) REVERT: H 87 TYR cc_start: 0.8283 (t80) cc_final: 0.7783 (t80) REVERT: H 101 VAL cc_start: 0.8845 (p) cc_final: 0.8609 (p) REVERT: H 104 MET cc_start: 0.9141 (mmp) cc_final: 0.8539 (mmp) REVERT: H 109 MET cc_start: 0.8082 (tpt) cc_final: 0.7860 (tpt) REVERT: H 110 PHE cc_start: 0.8042 (m-10) cc_final: 0.7566 (m-10) REVERT: H 164 LEU cc_start: 0.9165 (mm) cc_final: 0.8879 (pp) REVERT: H 222 ARG cc_start: 0.5945 (mmm-85) cc_final: 0.5731 (mmm160) REVERT: H 223 PHE cc_start: 0.6993 (m-80) cc_final: 0.6540 (m-80) REVERT: H 267 LYS cc_start: 0.7132 (ptmm) cc_final: 0.6535 (tmtt) REVERT: H 271 PHE cc_start: 0.6665 (p90) cc_final: 0.6296 (p90) REVERT: H 272 ILE cc_start: 0.7781 (mm) cc_final: 0.7316 (mt) REVERT: I 66 ASP cc_start: 0.7277 (t0) cc_final: 0.6998 (t70) REVERT: I 79 VAL cc_start: 0.7764 (t) cc_final: 0.7315 (p) REVERT: I 92 LYS cc_start: 0.8933 (mtmm) cc_final: 0.8486 (mtpp) REVERT: I 97 GLN cc_start: 0.7699 (pm20) cc_final: 0.7294 (pm20) REVERT: I 98 GLU cc_start: 0.8275 (mp0) cc_final: 0.7961 (mp0) REVERT: I 100 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7873 (mtm180) REVERT: I 105 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8218 (mtmm) REVERT: I 118 ASP cc_start: 0.7816 (p0) cc_final: 0.7445 (p0) REVERT: I 132 MET cc_start: 0.8138 (mmm) cc_final: 0.7848 (mmm) REVERT: I 146 ASN cc_start: 0.7891 (m110) cc_final: 0.7255 (m110) REVERT: I 158 GLN cc_start: 0.9081 (tt0) cc_final: 0.8131 (pt0) REVERT: I 164 LEU cc_start: 0.8473 (mt) cc_final: 0.8181 (mt) REVERT: I 203 PHE cc_start: 0.8366 (t80) cc_final: 0.7869 (t80) REVERT: I 206 GLU cc_start: 0.8102 (tp30) cc_final: 0.7878 (tp30) REVERT: I 208 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7809 (tm-30) REVERT: I 211 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7830 (tp-100) REVERT: I 260 ARG cc_start: 0.7084 (ptm160) cc_final: 0.6840 (ptm160) REVERT: I 264 ILE cc_start: 0.7901 (mm) cc_final: 0.7691 (mm) REVERT: J 40 CYS cc_start: 0.7084 (t) cc_final: 0.6686 (p) REVERT: J 63 TRP cc_start: 0.7786 (m100) cc_final: 0.6458 (m100) REVERT: J 64 GLN cc_start: 0.7006 (tp40) cc_final: 0.6306 (tp40) REVERT: J 65 VAL cc_start: 0.8804 (t) cc_final: 0.8586 (t) REVERT: J 86 ILE cc_start: 0.8729 (pt) cc_final: 0.7913 (mm) REVERT: J 89 GLU cc_start: 0.7805 (tt0) cc_final: 0.7427 (tt0) REVERT: J 92 LYS cc_start: 0.8756 (tptp) cc_final: 0.8424 (tptp) REVERT: J 100 ARG cc_start: 0.8465 (mtt180) cc_final: 0.8046 (mtm-85) REVERT: J 101 VAL cc_start: 0.9079 (t) cc_final: 0.8796 (t) REVERT: J 104 MET cc_start: 0.8269 (tpp) cc_final: 0.7623 (tpp) REVERT: J 131 LEU cc_start: 0.8616 (tt) cc_final: 0.8277 (tt) REVERT: J 138 GLU cc_start: 0.7771 (tp30) cc_final: 0.7466 (tp30) REVERT: J 139 HIS cc_start: 0.8506 (t70) cc_final: 0.8212 (t70) REVERT: J 160 LEU cc_start: 0.8608 (tt) cc_final: 0.8346 (pp) REVERT: J 162 ASN cc_start: 0.8977 (m110) cc_final: 0.8755 (m110) REVERT: J 186 ASN cc_start: 0.7728 (m-40) cc_final: 0.7331 (m-40) REVERT: J 198 MET cc_start: 0.8054 (tpt) cc_final: 0.7847 (tpp) REVERT: J 204 ASN cc_start: 0.8199 (m110) cc_final: 0.7536 (m110) REVERT: J 205 LYS cc_start: 0.8304 (tptp) cc_final: 0.7815 (tptp) REVERT: J 208 GLN cc_start: 0.7992 (pt0) cc_final: 0.7765 (pt0) REVERT: K 7 LEU cc_start: 0.8703 (tt) cc_final: 0.8499 (tt) REVERT: K 14 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8351 (mmtm) REVERT: K 15 TRP cc_start: 0.8106 (m100) cc_final: 0.7632 (m100) REVERT: K 30 ARG cc_start: 0.9022 (ttt180) cc_final: 0.8672 (ttt180) REVERT: K 34 GLU cc_start: 0.8793 (pt0) cc_final: 0.8294 (pp20) REVERT: K 35 ASP cc_start: 0.8740 (m-30) cc_final: 0.8419 (m-30) REVERT: K 40 CYS cc_start: 0.8345 (m) cc_final: 0.7716 (p) REVERT: K 132 MET cc_start: 0.7419 (ppp) cc_final: 0.7190 (ppp) REVERT: K 245 TRP cc_start: 0.7986 (m100) cc_final: 0.7774 (m100) REVERT: L 63 TRP cc_start: 0.6126 (m100) cc_final: 0.5650 (m100) REVERT: L 223 PHE cc_start: 0.6264 (p90) cc_final: 0.5916 (p90) REVERT: L 226 TYR cc_start: 0.7180 (p90) cc_final: 0.6150 (p90) REVERT: L 269 VAL cc_start: 0.7756 (m) cc_final: 0.7533 (m) REVERT: M 7 LEU cc_start: 0.8199 (tt) cc_final: 0.7998 (tt) REVERT: M 13 ASN cc_start: 0.8800 (m110) cc_final: 0.8557 (m110) REVERT: M 18 ASP cc_start: 0.7448 (t70) cc_final: 0.7107 (t70) REVERT: M 22 LEU cc_start: 0.8033 (pp) cc_final: 0.7810 (pp) REVERT: M 76 LEU cc_start: 0.7451 (tp) cc_final: 0.7239 (tp) REVERT: M 78 TRP cc_start: 0.6133 (m100) cc_final: 0.5646 (m100) REVERT: M 87 TYR cc_start: 0.7414 (t80) cc_final: 0.6845 (t80) REVERT: M 109 MET cc_start: 0.8364 (tmm) cc_final: 0.8162 (tmm) REVERT: M 154 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8776 (mm-30) REVERT: M 158 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7493 (tm-30) REVERT: M 159 THR cc_start: 0.8669 (m) cc_final: 0.7927 (p) REVERT: M 162 ASN cc_start: 0.8140 (m-40) cc_final: 0.7907 (m110) REVERT: M 199 ASP cc_start: 0.8587 (m-30) cc_final: 0.7673 (m-30) REVERT: M 209 ARG cc_start: 0.8954 (tmt170) cc_final: 0.8602 (ttp80) REVERT: N 11 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: N 23 HIS cc_start: 0.7675 (t70) cc_final: 0.7381 (t70) REVERT: N 65 VAL cc_start: 0.7577 (t) cc_final: 0.7048 (p) REVERT: N 104 MET cc_start: 0.8309 (ptm) cc_final: 0.7899 (ptm) REVERT: N 110 PHE cc_start: 0.8072 (m-80) cc_final: 0.7359 (m-80) REVERT: N 154 GLU cc_start: 0.8340 (tp30) cc_final: 0.7788 (mm-30) REVERT: N 202 ILE cc_start: 0.8355 (mt) cc_final: 0.8123 (mt) REVERT: N 203 PHE cc_start: 0.7952 (t80) cc_final: 0.7034 (t80) REVERT: N 205 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8260 (mtmt) REVERT: N 206 GLU cc_start: 0.8063 (pp20) cc_final: 0.7742 (pp20) REVERT: N 213 GLN cc_start: 0.8785 (mt0) cc_final: 0.8270 (mt0) REVERT: N 230 LYS cc_start: 0.8126 (mttt) cc_final: 0.7728 (ttpp) REVERT: N 233 HIS cc_start: 0.7728 (m90) cc_final: 0.7262 (m-70) REVERT: N 242 GLN cc_start: 0.7826 (tt0) cc_final: 0.7174 (pp30) REVERT: N 243 VAL cc_start: 0.8290 (t) cc_final: 0.7555 (m) REVERT: N 244 LEU cc_start: 0.8251 (tt) cc_final: 0.7939 (tt) REVERT: N 256 ARG cc_start: 0.8447 (ttm110) cc_final: 0.7765 (ttm110) REVERT: N 267 LYS cc_start: 0.8689 (ptmt) cc_final: 0.8449 (ptpt) REVERT: N 270 LYS cc_start: 0.7736 (mptt) cc_final: 0.6889 (mptt) REVERT: O 40 CYS cc_start: 0.5932 (t) cc_final: 0.5669 (t) REVERT: O 48 MET cc_start: -0.1286 (ppp) cc_final: -0.1755 (ppp) REVERT: O 104 MET cc_start: 0.8033 (pmm) cc_final: 0.7827 (pmm) REVERT: O 110 PHE cc_start: 0.8169 (m-80) cc_final: 0.7703 (m-80) REVERT: O 132 MET cc_start: 0.8151 (tmm) cc_final: 0.7705 (tmm) REVERT: O 193 LEU cc_start: 0.8772 (mm) cc_final: 0.8517 (mm) REVERT: O 201 PHE cc_start: 0.8815 (t80) cc_final: 0.7965 (t80) REVERT: O 202 ILE cc_start: 0.8671 (mt) cc_final: 0.8463 (mt) REVERT: O 205 LYS cc_start: 0.9152 (mmtm) cc_final: 0.8870 (mmtp) REVERT: O 208 GLN cc_start: 0.8740 (tm130) cc_final: 0.8479 (tm-30) REVERT: O 209 ARG cc_start: 0.8791 (ptm-80) cc_final: 0.8408 (ptm-80) REVERT: O 211 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8277 (tp40) REVERT: P 87 TYR cc_start: 0.8708 (t80) cc_final: 0.8242 (t80) REVERT: P 101 VAL cc_start: 0.9081 (p) cc_final: 0.8865 (p) REVERT: P 104 MET cc_start: 0.9216 (mmp) cc_final: 0.8805 (mmp) REVERT: P 106 TRP cc_start: 0.8464 (t60) cc_final: 0.8072 (t60) REVERT: P 132 MET cc_start: 0.6384 (tmm) cc_final: 0.5814 (tmm) REVERT: P 170 MET cc_start: 0.7354 (mtt) cc_final: 0.6957 (mpp) REVERT: P 222 ARG cc_start: 0.6073 (mtp85) cc_final: 0.5810 (mmm-85) REVERT: P 230 LYS cc_start: 0.7276 (mmmt) cc_final: 0.6990 (mmtm) REVERT: P 254 LYS cc_start: 0.8669 (mtpp) cc_final: 0.7880 (tppt) outliers start: 5 outliers final: 1 residues processed: 1143 average time/residue: 0.2137 time to fit residues: 383.7589 Evaluate side-chains 1063 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1061 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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: 0.0970 chunk 86 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 302 optimal weight: 0.0070 chunk 146 optimal weight: 0.9990 chunk 181 optimal weight: 0.0270 chunk 338 optimal weight: 3.9990 chunk 207 optimal weight: 0.0020 chunk 154 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 0.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN B 158 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 266 ASN E 129 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 69 HIS H 102 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** 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** K 242 GLN L 158 GLN M 69 HIS ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 62 HIS O 102 GLN ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 GLN O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.207506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.160707 restraints weight = 70778.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.166670 restraints weight = 45506.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.170950 restraints weight = 32270.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.174053 restraints weight = 24504.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.176231 restraints weight = 19640.074| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34119 Z= 0.142 Angle : 0.672 12.661 46515 Z= 0.359 Chirality : 0.048 0.333 5006 Planarity : 0.005 0.076 5714 Dihedral : 14.704 168.428 5007 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % 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: -0.10 (0.13), residues: 3851 helix: 1.09 (0.12), residues: 1862 sheet: -0.62 (0.17), residues: 916 loop : -1.46 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 189 TYR 0.024 0.001 TYR N 134 PHE 0.028 0.002 PHE L 203 TRP 0.033 0.002 TRP O 63 HIS 0.017 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (34119) covalent geometry : angle 0.67171 / 0.36 (46515) hydrogen bonds : bond 0.04038 / 2.74 ( 1746) hydrogen bonds : angle 5.28238 / 3.80 ( 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 1137 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1134 time to evaluate : 1.115 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: 0.8607 (mm) cc_final: 0.8338 (mm) REVERT: A 62 HIS cc_start: 0.7984 (t70) cc_final: 0.7531 (t70) REVERT: A 64 GLN cc_start: 0.6488 (pm20) cc_final: 0.6130 (pm20) REVERT: A 79 VAL cc_start: 0.7796 (t) cc_final: 0.7270 (p) REVERT: A 92 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8563 (mtpp) REVERT: A 100 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7244 (mtm-85) REVERT: A 107 TYR cc_start: 0.8405 (t80) cc_final: 0.7832 (t80) REVERT: A 113 LYS cc_start: 0.7874 (mmmm) cc_final: 0.7550 (mmmm) REVERT: A 118 ASP cc_start: 0.7311 (p0) cc_final: 0.7037 (p0) REVERT: A 129 GLN cc_start: 0.8025 (tt0) cc_final: 0.7621 (tt0) REVERT: A 132 MET cc_start: 0.8002 (mmm) cc_final: 0.7724 (mmm) REVERT: A 146 ASN cc_start: 0.8004 (m110) cc_final: 0.7330 (m-40) REVERT: A 155 ARG cc_start: 0.8541 (tpt90) cc_final: 0.7721 (mmm160) REVERT: A 158 GLN cc_start: 0.8913 (tt0) cc_final: 0.8574 (tt0) REVERT: A 164 LEU cc_start: 0.8187 (mt) cc_final: 0.7854 (mt) REVERT: A 182 LEU cc_start: 0.7917 (mt) cc_final: 0.7503 (tt) REVERT: A 183 ILE cc_start: 0.8607 (tt) cc_final: 0.8401 (pt) REVERT: A 201 PHE cc_start: 0.8000 (t80) cc_final: 0.7691 (t80) REVERT: A 203 PHE cc_start: 0.8285 (t80) cc_final: 0.7876 (t80) REVERT: A 208 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 223 PHE cc_start: 0.6652 (m-80) cc_final: 0.6441 (m-10) REVERT: A 226 TYR cc_start: 0.5985 (p90) cc_final: 0.4002 (p90) REVERT: A 242 GLN cc_start: 0.6290 (tp-100) cc_final: 0.6059 (tp-100) REVERT: A 254 LYS cc_start: 0.8264 (pptt) cc_final: 0.7764 (pptt) REVERT: A 260 ARG cc_start: 0.7362 (ptm160) cc_final: 0.7095 (ptm160) REVERT: B 15 TRP cc_start: 0.7890 (m100) cc_final: 0.7385 (m100) REVERT: B 40 CYS cc_start: 0.7251 (t) cc_final: 0.6816 (p) REVERT: B 63 TRP cc_start: 0.7973 (m100) cc_final: 0.6191 (m100) REVERT: B 64 GLN cc_start: 0.7037 (tp40) cc_final: 0.6186 (mm-40) REVERT: B 65 VAL cc_start: 0.8599 (t) cc_final: 0.8203 (t) REVERT: B 70 TYR cc_start: 0.7695 (t80) cc_final: 0.7328 (t80) REVERT: B 75 ILE cc_start: 0.7828 (pt) cc_final: 0.7521 (mp) REVERT: B 86 ILE cc_start: 0.8591 (pt) cc_final: 0.8074 (mm) REVERT: B 92 LYS cc_start: 0.8696 (tppt) cc_final: 0.8391 (tppp) REVERT: B 101 VAL cc_start: 0.8974 (t) cc_final: 0.8684 (t) REVERT: B 102 GLN cc_start: 0.8417 (mp10) cc_final: 0.8158 (mm-40) REVERT: B 104 MET cc_start: 0.8585 (mmp) cc_final: 0.8205 (mmp) REVERT: B 116 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6719 (tm-30) REVERT: B 131 LEU cc_start: 0.8997 (tt) cc_final: 0.8778 (tt) REVERT: B 139 HIS cc_start: 0.8054 (t70) cc_final: 0.7811 (t70) REVERT: B 165 GLU cc_start: 0.7982 (tp30) cc_final: 0.7589 (tp30) REVERT: B 170 MET cc_start: 0.8478 (tpt) cc_final: 0.8233 (tpt) REVERT: B 178 LEU cc_start: 0.9043 (mm) cc_final: 0.8680 (mm) REVERT: B 184 THR cc_start: 0.8875 (p) cc_final: 0.8586 (p) REVERT: B 198 MET cc_start: 0.8154 (tpt) cc_final: 0.7736 (tpp) REVERT: B 204 ASN cc_start: 0.7657 (p0) cc_final: 0.7349 (p0) REVERT: B 208 GLN cc_start: 0.8112 (pt0) cc_final: 0.7901 (pt0) REVERT: C 18 ASP cc_start: 0.8622 (t70) cc_final: 0.8414 (t70) REVERT: C 28 ILE cc_start: 0.8055 (tp) cc_final: 0.7796 (tp) REVERT: C 35 ASP cc_start: 0.8589 (m-30) cc_final: 0.8374 (m-30) REVERT: C 110 PHE cc_start: 0.7613 (m-80) cc_final: 0.7359 (m-80) REVERT: C 132 MET cc_start: 0.8249 (ppp) cc_final: 0.7840 (ppp) REVERT: C 161 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8784 (tmmt) REVERT: C 199 ASP cc_start: 0.8821 (m-30) cc_final: 0.8574 (m-30) REVERT: C 209 ARG cc_start: 0.8540 (ptt90) cc_final: 0.7983 (ptt90) REVERT: D 203 PHE cc_start: 0.7926 (t80) cc_final: 0.7702 (t80) REVERT: D 223 PHE cc_start: 0.6281 (p90) cc_final: 0.5867 (p90) REVERT: D 226 TYR cc_start: 0.6855 (p90) cc_final: 0.6075 (p90) REVERT: D 244 LEU cc_start: 0.8171 (mt) cc_final: 0.7602 (pp) REVERT: D 254 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7534 (tptt) REVERT: D 268 ASP cc_start: 0.7146 (t70) cc_final: 0.6929 (t70) REVERT: E 10 GLU cc_start: 0.8102 (tp30) cc_final: 0.7682 (tp30) REVERT: E 13 ASN cc_start: 0.8741 (m110) cc_final: 0.8455 (m110) REVERT: E 18 ASP cc_start: 0.7550 (t70) cc_final: 0.7305 (t70) REVERT: E 87 TYR cc_start: 0.7140 (t80) cc_final: 0.6875 (t80) REVERT: E 100 ARG cc_start: 0.8778 (ptp90) cc_final: 0.8398 (ptp-170) REVERT: E 150 GLN cc_start: 0.8015 (mm110) cc_final: 0.7098 (mm-40) REVERT: E 159 THR cc_start: 0.8560 (m) cc_final: 0.7967 (p) REVERT: E 178 LEU cc_start: 0.8883 (mt) cc_final: 0.8652 (mt) REVERT: E 199 ASP cc_start: 0.8416 (m-30) cc_final: 0.7629 (m-30) REVERT: E 201 PHE cc_start: 0.8363 (t80) cc_final: 0.7930 (t80) REVERT: E 204 ASN cc_start: 0.8556 (t0) cc_final: 0.8280 (t0) REVERT: E 205 LYS cc_start: 0.8964 (mttt) cc_final: 0.8402 (mmtp) REVERT: E 206 GLU cc_start: 0.8671 (pt0) cc_final: 0.7726 (pp20) REVERT: E 242 GLN cc_start: 0.6433 (pp30) cc_final: 0.6017 (pp30) REVERT: E 270 LYS cc_start: 0.8259 (mttm) cc_final: 0.8041 (mttm) REVERT: F 23 HIS cc_start: 0.7750 (t70) cc_final: 0.7402 (t70) REVERT: F 82 ASN cc_start: 0.8197 (m110) cc_final: 0.7908 (m110) REVERT: F 104 MET cc_start: 0.7857 (ptm) cc_final: 0.7370 (ppp) REVERT: F 154 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7545 (mm-30) REVERT: F 199 ASP cc_start: 0.8533 (m-30) cc_final: 0.8266 (m-30) REVERT: F 203 PHE cc_start: 0.7763 (t80) cc_final: 0.7314 (t80) REVERT: F 205 LYS cc_start: 0.8512 (mtmm) cc_final: 0.7969 (mtmm) REVERT: F 208 GLN cc_start: 0.8498 (tt0) cc_final: 0.8067 (tm-30) REVERT: F 230 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7760 (mmmm) REVERT: F 233 HIS cc_start: 0.7594 (m90) cc_final: 0.7236 (m90) REVERT: F 236 GLU cc_start: 0.7978 (pm20) cc_final: 0.7694 (pp20) REVERT: F 242 GLN cc_start: 0.7479 (tt0) cc_final: 0.6507 (pp30) REVERT: F 243 VAL cc_start: 0.8079 (t) cc_final: 0.7126 (m) REVERT: F 244 LEU cc_start: 0.7940 (tt) cc_final: 0.7532 (tt) REVERT: F 256 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8031 (ttm110) REVERT: F 267 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8091 (pttt) REVERT: G 48 MET cc_start: -0.0257 (ppp) cc_final: -0.1150 (ppp) REVERT: G 62 HIS cc_start: 0.7318 (t70) cc_final: 0.6926 (t70) REVERT: G 85 LEU cc_start: 0.7118 (tp) cc_final: 0.6651 (tp) REVERT: G 104 MET cc_start: 0.7833 (pmm) cc_final: 0.7612 (pmm) REVERT: G 110 PHE cc_start: 0.7630 (m-80) cc_final: 0.7189 (m-80) REVERT: G 130 LEU cc_start: 0.8885 (pp) cc_final: 0.8675 (pp) REVERT: G 131 LEU cc_start: 0.9252 (mt) cc_final: 0.9011 (mt) REVERT: G 155 ARG cc_start: 0.9125 (ptp-110) cc_final: 0.8847 (ptp-110) REVERT: G 158 GLN cc_start: 0.9150 (tp-100) cc_final: 0.8657 (tp-100) REVERT: G 164 LEU cc_start: 0.8604 (mt) cc_final: 0.8296 (pp) REVERT: G 165 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8054 (mm-30) REVERT: G 171 PHE cc_start: 0.7681 (m-10) cc_final: 0.7429 (m-80) REVERT: G 197 PRO cc_start: 0.8478 (Cg_exo) cc_final: 0.8124 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8937 (m-30) cc_final: 0.8636 (m-30) REVERT: G 201 PHE cc_start: 0.8820 (t80) cc_final: 0.8301 (t80) REVERT: G 205 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8936 (mmtm) REVERT: G 208 GLN cc_start: 0.8419 (tm130) cc_final: 0.8066 (tm-30) REVERT: H 61 ASP cc_start: 0.7304 (m-30) cc_final: 0.7095 (m-30) REVERT: H 62 HIS cc_start: 0.7499 (t-90) cc_final: 0.6951 (t-170) REVERT: H 78 TRP cc_start: 0.6713 (m-10) cc_final: 0.6142 (m-10) REVERT: H 87 TYR cc_start: 0.8349 (t80) cc_final: 0.7830 (t80) REVERT: H 101 VAL cc_start: 0.8829 (p) cc_final: 0.8619 (p) REVERT: H 104 MET cc_start: 0.9087 (mmp) cc_final: 0.8478 (mmp) REVERT: H 109 MET cc_start: 0.8089 (tpt) cc_final: 0.7850 (tpt) REVERT: H 110 PHE cc_start: 0.8007 (m-10) cc_final: 0.7526 (m-10) REVERT: H 223 PHE cc_start: 0.6943 (m-80) cc_final: 0.6557 (m-80) REVERT: H 271 PHE cc_start: 0.6832 (p90) cc_final: 0.6504 (p90) REVERT: H 272 ILE cc_start: 0.7775 (mm) cc_final: 0.7276 (mt) REVERT: I 60 ILE cc_start: 0.8617 (mp) cc_final: 0.8367 (mp) REVERT: I 79 VAL cc_start: 0.7713 (t) cc_final: 0.7253 (p) REVERT: I 97 GLN cc_start: 0.7627 (pm20) cc_final: 0.6976 (pm20) REVERT: I 98 GLU cc_start: 0.8238 (mp0) cc_final: 0.7937 (mp0) REVERT: I 100 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7547 (mtm-85) REVERT: I 105 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8161 (mtmm) REVERT: I 118 ASP cc_start: 0.7719 (p0) cc_final: 0.7404 (p0) REVERT: I 143 ILE cc_start: 0.8079 (tp) cc_final: 0.7321 (tp) REVERT: I 146 ASN cc_start: 0.7930 (m110) cc_final: 0.7204 (m110) REVERT: I 155 ARG cc_start: 0.8353 (tpt90) cc_final: 0.7748 (mmm160) REVERT: I 158 GLN cc_start: 0.9058 (tt0) cc_final: 0.8687 (tt0) REVERT: I 184 THR cc_start: 0.8257 (m) cc_final: 0.7920 (p) REVERT: I 198 MET cc_start: 0.8454 (ttm) cc_final: 0.8236 (ttm) REVERT: I 201 PHE cc_start: 0.8185 (t80) cc_final: 0.7970 (t80) REVERT: I 203 PHE cc_start: 0.8225 (t80) cc_final: 0.7805 (t80) REVERT: I 208 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7810 (tm-30) REVERT: I 211 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7796 (tp-100) REVERT: I 251 ILE cc_start: 0.7130 (pt) cc_final: 0.6917 (pt) REVERT: I 264 ILE cc_start: 0.7907 (mm) cc_final: 0.7693 (mm) REVERT: J 40 CYS cc_start: 0.7088 (t) cc_final: 0.6727 (p) REVERT: J 62 HIS cc_start: 0.7343 (t-90) cc_final: 0.7087 (t-90) REVERT: J 63 TRP cc_start: 0.7846 (m100) cc_final: 0.6128 (m100) REVERT: J 64 GLN cc_start: 0.7102 (tp40) cc_final: 0.6237 (mm110) REVERT: J 65 VAL cc_start: 0.8760 (t) cc_final: 0.8391 (t) REVERT: J 73 LYS cc_start: 0.8201 (mttt) cc_final: 0.7753 (mtmt) REVERT: J 86 ILE cc_start: 0.8775 (pt) cc_final: 0.8057 (mm) REVERT: J 89 GLU cc_start: 0.7714 (tt0) cc_final: 0.7432 (tt0) REVERT: J 92 LYS cc_start: 0.8806 (tptp) cc_final: 0.8439 (tptp) REVERT: J 101 VAL cc_start: 0.9114 (t) cc_final: 0.8812 (t) REVERT: J 104 MET cc_start: 0.8236 (tpp) cc_final: 0.7453 (tpp) REVERT: J 116 GLN cc_start: 0.7203 (tm-30) cc_final: 0.6906 (tm-30) REVERT: J 131 LEU cc_start: 0.8688 (tt) cc_final: 0.8317 (tt) REVERT: J 138 GLU cc_start: 0.7755 (tp30) cc_final: 0.7427 (tp30) REVERT: J 139 HIS cc_start: 0.8457 (t70) cc_final: 0.8145 (t70) REVERT: J 178 LEU cc_start: 0.8989 (mm) cc_final: 0.8739 (mm) REVERT: J 186 ASN cc_start: 0.7693 (m-40) cc_final: 0.6932 (m-40) REVERT: J 198 MET cc_start: 0.8045 (tpt) cc_final: 0.7831 (tpp) REVERT: J 204 ASN cc_start: 0.8268 (m110) cc_final: 0.7097 (p0) REVERT: J 205 LYS cc_start: 0.8234 (tptp) cc_final: 0.7635 (tptp) REVERT: J 208 GLN cc_start: 0.7986 (pt0) cc_final: 0.7709 (pt0) REVERT: K 14 LYS cc_start: 0.8567 (mmtm) cc_final: 0.8309 (mmtm) REVERT: K 40 CYS cc_start: 0.8260 (m) cc_final: 0.7661 (p) REVERT: K 132 MET cc_start: 0.7441 (ppp) cc_final: 0.7198 (ppp) REVERT: K 245 TRP cc_start: 0.7757 (m100) cc_final: 0.7546 (m100) REVERT: L 209 ARG cc_start: 0.8730 (mmp-170) cc_final: 0.8481 (mmm160) REVERT: L 226 TYR cc_start: 0.6628 (p90) cc_final: 0.5853 (p90) REVERT: L 254 LYS cc_start: 0.8087 (tmtt) cc_final: 0.7369 (tptt) REVERT: L 256 ARG cc_start: 0.7715 (tmm160) cc_final: 0.7494 (ttp80) REVERT: M 10 GLU cc_start: 0.8157 (tp30) cc_final: 0.7908 (tp30) REVERT: M 13 ASN cc_start: 0.8771 (m110) cc_final: 0.8528 (m110) REVERT: M 18 ASP cc_start: 0.7505 (t70) cc_final: 0.7118 (t70) REVERT: M 154 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8801 (mm-30) REVERT: M 155 ARG cc_start: 0.8569 (ttt180) cc_final: 0.8242 (mtt90) REVERT: M 158 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7486 (tm-30) REVERT: M 159 THR cc_start: 0.8805 (m) cc_final: 0.8257 (p) REVERT: M 162 ASN cc_start: 0.8073 (m-40) cc_final: 0.7856 (m110) REVERT: M 178 LEU cc_start: 0.8816 (mt) cc_final: 0.8584 (mt) REVERT: M 199 ASP cc_start: 0.8558 (m-30) cc_final: 0.7738 (m-30) REVERT: M 202 ILE cc_start: 0.8821 (mm) cc_final: 0.8328 (mm) REVERT: M 205 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8481 (mtmm) REVERT: M 206 GLU cc_start: 0.8563 (pt0) cc_final: 0.8060 (pt0) REVERT: N 11 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6840 (pm20) REVERT: N 23 HIS cc_start: 0.7647 (t70) cc_final: 0.7375 (t70) REVERT: N 65 VAL cc_start: 0.7457 (t) cc_final: 0.7165 (p) REVERT: N 104 MET cc_start: 0.8047 (ptm) cc_final: 0.7726 (ptm) REVERT: N 105 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9120 (mttt) REVERT: N 110 PHE cc_start: 0.8055 (m-80) cc_final: 0.7808 (m-80) REVERT: N 154 GLU cc_start: 0.8363 (tp30) cc_final: 0.7917 (mm-30) REVERT: N 203 PHE cc_start: 0.7832 (t80) cc_final: 0.7407 (t80) REVERT: N 208 GLN cc_start: 0.8339 (tt0) cc_final: 0.7998 (tm-30) REVERT: N 233 HIS cc_start: 0.7669 (m90) cc_final: 0.7237 (m-70) REVERT: N 236 GLU cc_start: 0.7823 (mp0) cc_final: 0.7481 (mp0) REVERT: N 237 TRP cc_start: 0.7788 (m-10) cc_final: 0.7497 (m-90) REVERT: N 242 GLN cc_start: 0.7773 (tt0) cc_final: 0.7107 (pp30) REVERT: N 243 VAL cc_start: 0.8284 (t) cc_final: 0.7556 (m) REVERT: N 244 LEU cc_start: 0.8220 (tt) cc_final: 0.7960 (tt) REVERT: N 256 ARG cc_start: 0.8387 (ttm110) cc_final: 0.7704 (ttm110) REVERT: N 258 THR cc_start: 0.8592 (p) cc_final: 0.8280 (p) REVERT: O 40 CYS cc_start: 0.5607 (t) cc_final: 0.5383 (t) REVERT: O 48 MET cc_start: -0.1374 (ppp) cc_final: -0.1843 (ppp) REVERT: O 62 HIS cc_start: 0.6798 (p-80) cc_final: 0.6363 (p-80) REVERT: O 104 MET cc_start: 0.8131 (pmm) cc_final: 0.7885 (pmm) REVERT: O 110 PHE cc_start: 0.8244 (m-80) cc_final: 0.7831 (m-10) REVERT: O 115 LEU cc_start: 0.8839 (tp) cc_final: 0.8588 (tp) REVERT: O 132 MET cc_start: 0.8132 (tmm) cc_final: 0.7627 (tmm) REVERT: O 199 ASP cc_start: 0.8847 (m-30) cc_final: 0.8546 (m-30) REVERT: O 201 PHE cc_start: 0.8754 (t80) cc_final: 0.7860 (t80) REVERT: O 205 LYS cc_start: 0.9148 (mmtm) cc_final: 0.8853 (mmtp) REVERT: O 208 GLN cc_start: 0.8684 (tm130) cc_final: 0.8407 (tm-30) REVERT: O 209 ARG cc_start: 0.8751 (ptm-80) cc_final: 0.8394 (ptm-80) REVERT: O 211 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8245 (tp40) REVERT: P 87 TYR cc_start: 0.8727 (t80) cc_final: 0.8267 (t80) REVERT: P 101 VAL cc_start: 0.9159 (p) cc_final: 0.8918 (p) REVERT: P 104 MET cc_start: 0.9198 (mmp) cc_final: 0.8757 (mmp) REVERT: P 106 TRP cc_start: 0.8437 (t60) cc_final: 0.8111 (t60) REVERT: P 132 MET cc_start: 0.6433 (tmm) cc_final: 0.5853 (tmm) REVERT: P 137 ILE cc_start: 0.8036 (mm) cc_final: 0.7800 (mm) REVERT: P 170 MET cc_start: 0.7367 (mtt) cc_final: 0.6947 (mpp) REVERT: P 198 MET cc_start: 0.8514 (ppp) cc_final: 0.8312 (ppp) REVERT: P 222 ARG cc_start: 0.5951 (mtp85) cc_final: 0.5747 (mmm-85) REVERT: P 230 LYS cc_start: 0.7377 (mmmt) cc_final: 0.7141 (mmtm) REVERT: P 254 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8144 (tppt) outliers start: 3 outliers final: 0 residues processed: 1135 average time/residue: 0.2161 time to fit residues: 384.3689 Evaluate side-chains 1043 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1042 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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: 6.9990 chunk 135 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 311 optimal weight: 0.0000 chunk 67 optimal weight: 0.0870 chunk 127 optimal weight: 20.0000 chunk 357 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 211 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 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN G 211 GLN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 GLN ** 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** J 102 GLN J 148 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** K 242 GLN L 158 GLN M 69 HIS ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 102 GLN O 208 GLN P 207 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.205206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.158033 restraints weight = 71202.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.163889 restraints weight = 45803.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.168120 restraints weight = 32600.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.171166 restraints weight = 24796.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.173373 restraints weight = 19899.391| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34119 Z= 0.149 Angle : 0.682 13.213 46515 Z= 0.366 Chirality : 0.049 0.269 5006 Planarity : 0.005 0.063 5714 Dihedral : 14.772 168.809 5007 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % 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: -0.12 (0.13), residues: 3851 helix: 1.06 (0.12), residues: 1860 sheet: -0.66 (0.17), residues: 900 loop : -1.43 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 189 TYR 0.018 0.001 TYR M 70 PHE 0.033 0.002 PHE C 174 TRP 0.064 0.002 TRP D 63 HIS 0.032 0.002 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (34119) covalent geometry : angle 0.68160 / 0.37 (46515) hydrogen bonds : bond 0.04037 / 2.76 ( 1746) hydrogen bonds : angle 5.32366 / 3.84 ( 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 1130 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1125 time to evaluate : 0.886 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 15 TRP cc_start: 0.6597 (m-10) cc_final: 0.5873 (m100) REVERT: A 60 ILE cc_start: 0.8723 (mm) cc_final: 0.8409 (mm) REVERT: A 62 HIS cc_start: 0.7863 (t70) cc_final: 0.7458 (t70) REVERT: A 64 GLN cc_start: 0.6404 (pm20) cc_final: 0.5999 (pm20) REVERT: A 79 VAL cc_start: 0.7805 (t) cc_final: 0.7285 (p) REVERT: A 90 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7595 (tmm-80) REVERT: A 92 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8426 (mtpp) REVERT: A 100 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7578 (mtm180) REVERT: A 105 LYS cc_start: 0.9175 (mtpp) cc_final: 0.8917 (mtpp) REVERT: A 107 TYR cc_start: 0.8453 (t80) cc_final: 0.7850 (t80) REVERT: A 113 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7580 (mmmm) REVERT: A 131 LEU cc_start: 0.8397 (pp) cc_final: 0.8152 (pp) REVERT: A 132 MET cc_start: 0.8032 (mmm) cc_final: 0.7647 (mmm) REVERT: A 146 ASN cc_start: 0.7983 (m110) cc_final: 0.6992 (m-40) REVERT: A 155 ARG cc_start: 0.8653 (tpt90) cc_final: 0.7774 (mmm160) REVERT: A 158 GLN cc_start: 0.8909 (tt0) cc_final: 0.8545 (tt0) REVERT: A 201 PHE cc_start: 0.8119 (t80) cc_final: 0.7847 (t80) REVERT: A 203 PHE cc_start: 0.8291 (t80) cc_final: 0.7907 (t80) REVERT: A 208 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 223 PHE cc_start: 0.6706 (m-80) cc_final: 0.6282 (m-10) REVERT: A 226 TYR cc_start: 0.6077 (p90) cc_final: 0.5677 (p90) REVERT: A 258 THR cc_start: 0.8756 (p) cc_final: 0.8485 (p) REVERT: A 260 ARG cc_start: 0.7382 (ptm160) cc_final: 0.7130 (ptm160) REVERT: B 15 TRP cc_start: 0.7888 (m100) cc_final: 0.7358 (m100) REVERT: B 40 CYS cc_start: 0.7410 (t) cc_final: 0.6897 (p) REVERT: B 63 TRP cc_start: 0.7939 (m100) cc_final: 0.6328 (m100) REVERT: B 64 GLN cc_start: 0.7090 (tp40) cc_final: 0.6088 (mm-40) REVERT: B 65 VAL cc_start: 0.8643 (t) cc_final: 0.8159 (t) REVERT: B 70 TYR cc_start: 0.7846 (t80) cc_final: 0.7341 (t80) REVERT: B 75 ILE cc_start: 0.7857 (pt) cc_final: 0.7603 (mp) REVERT: B 86 ILE cc_start: 0.8670 (pt) cc_final: 0.8215 (mm) REVERT: B 89 GLU cc_start: 0.7835 (tt0) cc_final: 0.7595 (tt0) REVERT: B 92 LYS cc_start: 0.8712 (tppt) cc_final: 0.8241 (tptp) REVERT: B 101 VAL cc_start: 0.8985 (t) cc_final: 0.8682 (t) REVERT: B 102 GLN cc_start: 0.8402 (mp10) cc_final: 0.8149 (mm-40) REVERT: B 104 MET cc_start: 0.8607 (mmp) cc_final: 0.8321 (mmp) REVERT: B 116 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6750 (tm-30) REVERT: B 137 ILE cc_start: 0.8448 (tt) cc_final: 0.8161 (tt) REVERT: B 138 GLU cc_start: 0.7920 (tp30) cc_final: 0.7648 (tp30) REVERT: B 139 HIS cc_start: 0.8429 (t70) cc_final: 0.7855 (t70) REVERT: B 165 GLU cc_start: 0.7904 (tp30) cc_final: 0.7570 (tp30) REVERT: B 178 LEU cc_start: 0.9078 (mm) cc_final: 0.8650 (mm) REVERT: B 186 ASN cc_start: 0.8284 (m-40) cc_final: 0.7528 (m-40) REVERT: B 198 MET cc_start: 0.8144 (tpt) cc_final: 0.7741 (tpp) REVERT: B 204 ASN cc_start: 0.7648 (p0) cc_final: 0.7381 (p0) REVERT: C 7 LEU cc_start: 0.8724 (tt) cc_final: 0.8501 (tt) REVERT: C 28 ILE cc_start: 0.8072 (tp) cc_final: 0.7662 (tp) REVERT: C 110 PHE cc_start: 0.7752 (m-80) cc_final: 0.7486 (m-80) REVERT: C 132 MET cc_start: 0.8293 (ppp) cc_final: 0.7867 (ppp) REVERT: C 157 HIS cc_start: 0.7729 (m90) cc_final: 0.7474 (m-70) REVERT: C 190 LYS cc_start: 0.6439 (mttm) cc_final: 0.6222 (mmmt) REVERT: C 209 ARG cc_start: 0.8528 (ptt90) cc_final: 0.8092 (ptt90) REVERT: C 244 LEU cc_start: 0.8328 (mm) cc_final: 0.7500 (mm) REVERT: C 245 TRP cc_start: 0.8183 (m-90) cc_final: 0.7850 (m-90) REVERT: D 223 PHE cc_start: 0.6410 (p90) cc_final: 0.5856 (p90) REVERT: D 226 TYR cc_start: 0.6601 (p90) cc_final: 0.5972 (p90) REVERT: D 254 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7681 (tptm) REVERT: D 263 VAL cc_start: 0.8149 (m) cc_final: 0.7925 (t) REVERT: D 267 LYS cc_start: 0.8158 (ptpt) cc_final: 0.7687 (tptt) REVERT: D 268 ASP cc_start: 0.7153 (t70) cc_final: 0.6714 (t70) REVERT: D 270 LYS cc_start: 0.6297 (mttm) cc_final: 0.6084 (mttt) REVERT: E 10 GLU cc_start: 0.8008 (tp30) cc_final: 0.7557 (tp30) REVERT: E 15 TRP cc_start: 0.8620 (m-10) cc_final: 0.8367 (m-10) REVERT: E 18 ASP cc_start: 0.7542 (t70) cc_final: 0.7299 (t70) REVERT: E 87 TYR cc_start: 0.7203 (t80) cc_final: 0.5984 (t80) REVERT: E 89 GLU cc_start: 0.7766 (pm20) cc_final: 0.6176 (mp0) REVERT: E 97 GLN cc_start: 0.7813 (pm20) cc_final: 0.7482 (pm20) REVERT: E 100 ARG cc_start: 0.8801 (ptp90) cc_final: 0.8424 (ptt-90) REVERT: E 101 VAL cc_start: 0.8823 (t) cc_final: 0.8576 (t) REVERT: E 150 GLN cc_start: 0.7896 (mm110) cc_final: 0.7248 (mm-40) REVERT: E 159 THR cc_start: 0.8540 (m) cc_final: 0.7926 (p) REVERT: E 178 LEU cc_start: 0.8915 (mt) cc_final: 0.8680 (mt) REVERT: E 199 ASP cc_start: 0.8395 (m-30) cc_final: 0.7584 (m-30) REVERT: F 23 HIS cc_start: 0.7836 (t70) cc_final: 0.7518 (t70) REVERT: F 104 MET cc_start: 0.7945 (ptm) cc_final: 0.7414 (ppp) REVERT: F 158 GLN cc_start: 0.9174 (mt0) cc_final: 0.8926 (mt0) REVERT: F 199 ASP cc_start: 0.8489 (m-30) cc_final: 0.8145 (m-30) REVERT: F 202 ILE cc_start: 0.8299 (mt) cc_final: 0.8065 (mt) REVERT: F 203 PHE cc_start: 0.7808 (t80) cc_final: 0.6940 (t80) REVERT: F 206 GLU cc_start: 0.8239 (pp20) cc_final: 0.7649 (pp20) REVERT: F 208 GLN cc_start: 0.8496 (tt0) cc_final: 0.7865 (tm-30) REVERT: F 212 GLN cc_start: 0.8560 (pp30) cc_final: 0.8250 (pp30) REVERT: F 230 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7872 (mmmm) REVERT: F 233 HIS cc_start: 0.7581 (m90) cc_final: 0.7255 (m90) REVERT: F 236 GLU cc_start: 0.7993 (pm20) cc_final: 0.7604 (mp0) REVERT: F 242 GLN cc_start: 0.7199 (tt0) cc_final: 0.6830 (tm-30) REVERT: F 243 VAL cc_start: 0.8307 (t) cc_final: 0.6700 (m) REVERT: F 244 LEU cc_start: 0.7951 (tt) cc_final: 0.7679 (tt) REVERT: F 256 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7925 (ttm110) REVERT: F 267 LYS cc_start: 0.8662 (ptmt) cc_final: 0.8143 (pttt) REVERT: G 48 MET cc_start: -0.0465 (ppp) cc_final: -0.1329 (ppp) REVERT: G 85 LEU cc_start: 0.7061 (tp) cc_final: 0.6583 (tp) REVERT: G 104 MET cc_start: 0.7840 (pmm) cc_final: 0.7637 (pmm) REVERT: G 110 PHE cc_start: 0.7828 (m-80) cc_final: 0.7063 (m-80) REVERT: G 130 LEU cc_start: 0.8888 (pp) cc_final: 0.8688 (pp) REVERT: G 131 LEU cc_start: 0.9263 (mt) cc_final: 0.9016 (mt) REVERT: G 155 ARG cc_start: 0.9153 (ptp-110) cc_final: 0.8917 (ptp-110) REVERT: G 164 LEU cc_start: 0.8591 (mt) cc_final: 0.8327 (pp) REVERT: G 165 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8042 (mm-30) REVERT: G 171 PHE cc_start: 0.7599 (m-10) cc_final: 0.7386 (m-80) REVERT: G 197 PRO cc_start: 0.8613 (Cg_exo) cc_final: 0.8314 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8946 (m-30) cc_final: 0.8586 (m-30) REVERT: G 201 PHE cc_start: 0.8790 (t80) cc_final: 0.8246 (t80) REVERT: G 205 LYS cc_start: 0.9246 (mmtm) cc_final: 0.8990 (mmtm) REVERT: G 208 GLN cc_start: 0.8448 (tm130) cc_final: 0.8231 (tm-30) REVERT: H 62 HIS cc_start: 0.7675 (t-90) cc_final: 0.7085 (t-170) REVERT: H 78 TRP cc_start: 0.6890 (m-10) cc_final: 0.6552 (m-10) REVERT: H 87 TYR cc_start: 0.8450 (t80) cc_final: 0.7972 (t80) REVERT: H 101 VAL cc_start: 0.8861 (p) cc_final: 0.8631 (p) REVERT: H 104 MET cc_start: 0.9081 (mmp) cc_final: 0.8486 (mmp) REVERT: H 106 TRP cc_start: 0.8396 (t60) cc_final: 0.7899 (t60) REVERT: H 109 MET cc_start: 0.7978 (tpt) cc_final: 0.7755 (tpt) REVERT: H 110 PHE cc_start: 0.8140 (m-10) cc_final: 0.7820 (m-10) REVERT: H 207 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7756 (mm-40) REVERT: I 79 VAL cc_start: 0.7711 (t) cc_final: 0.7290 (p) REVERT: I 97 GLN cc_start: 0.7868 (pm20) cc_final: 0.7619 (pm20) REVERT: I 98 GLU cc_start: 0.8135 (mp0) cc_final: 0.7866 (mp0) REVERT: I 100 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7609 (mtm-85) REVERT: I 105 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8758 (mtpp) REVERT: I 118 ASP cc_start: 0.7764 (p0) cc_final: 0.7345 (p0) REVERT: I 132 MET cc_start: 0.8211 (mmm) cc_final: 0.7828 (mmm) REVERT: I 143 ILE cc_start: 0.8209 (tp) cc_final: 0.7522 (tp) REVERT: I 146 ASN cc_start: 0.7983 (m110) cc_final: 0.7299 (m110) REVERT: I 155 ARG cc_start: 0.8335 (tpt90) cc_final: 0.7681 (mmm160) REVERT: I 158 GLN cc_start: 0.9066 (tt0) cc_final: 0.8708 (tt0) REVERT: I 160 LEU cc_start: 0.8657 (tt) cc_final: 0.8430 (tt) REVERT: I 164 LEU cc_start: 0.8406 (mt) cc_final: 0.8122 (mt) REVERT: I 178 LEU cc_start: 0.8000 (tp) cc_final: 0.7569 (tp) REVERT: I 184 THR cc_start: 0.8279 (m) cc_final: 0.7970 (p) REVERT: I 198 MET cc_start: 0.8399 (ttm) cc_final: 0.8154 (ttm) REVERT: I 203 PHE cc_start: 0.8264 (t80) cc_final: 0.7844 (t80) REVERT: I 208 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7880 (tm-30) REVERT: I 209 ARG cc_start: 0.7316 (tpp80) cc_final: 0.6901 (tpp80) REVERT: I 260 ARG cc_start: 0.7321 (ptm160) cc_final: 0.7027 (ptm160) REVERT: I 261 TYR cc_start: 0.7387 (m-10) cc_final: 0.6352 (m-10) REVERT: I 264 ILE cc_start: 0.7899 (mm) cc_final: 0.7633 (mm) REVERT: J 40 CYS cc_start: 0.7077 (t) cc_final: 0.6730 (p) REVERT: J 62 HIS cc_start: 0.7420 (t-90) cc_final: 0.7077 (t-90) REVERT: J 63 TRP cc_start: 0.7920 (m100) cc_final: 0.6085 (m100) REVERT: J 64 GLN cc_start: 0.7114 (tp40) cc_final: 0.6309 (mm110) REVERT: J 65 VAL cc_start: 0.8725 (t) cc_final: 0.8450 (t) REVERT: J 86 ILE cc_start: 0.8863 (pt) cc_final: 0.8060 (mm) REVERT: J 89 GLU cc_start: 0.7666 (tt0) cc_final: 0.7365 (tt0) REVERT: J 90 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8116 (tpp80) REVERT: J 92 LYS cc_start: 0.8795 (tptp) cc_final: 0.8436 (tptp) REVERT: J 100 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8268 (ptp90) REVERT: J 104 MET cc_start: 0.8197 (tpp) cc_final: 0.7390 (tpp) REVERT: J 116 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6976 (tm-30) REVERT: J 131 LEU cc_start: 0.8716 (tt) cc_final: 0.8396 (tt) REVERT: J 137 ILE cc_start: 0.8395 (tt) cc_final: 0.7987 (tt) REVERT: J 138 GLU cc_start: 0.7782 (tp30) cc_final: 0.7472 (tp30) REVERT: J 139 HIS cc_start: 0.8465 (t70) cc_final: 0.8080 (t70) REVERT: J 178 LEU cc_start: 0.9049 (mm) cc_final: 0.8654 (mm) REVERT: J 186 ASN cc_start: 0.7875 (m-40) cc_final: 0.7215 (m-40) REVERT: J 198 MET cc_start: 0.8019 (tpt) cc_final: 0.7815 (tpp) REVERT: J 204 ASN cc_start: 0.8033 (m110) cc_final: 0.7536 (m110) REVERT: J 205 LYS cc_start: 0.8148 (tptp) cc_final: 0.7616 (tptp) REVERT: J 207 GLN cc_start: 0.8085 (mp10) cc_final: 0.7684 (mp10) REVERT: J 208 GLN cc_start: 0.7953 (pt0) cc_final: 0.7626 (pt0) REVERT: K 14 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8338 (mmtm) REVERT: K 15 TRP cc_start: 0.8182 (m100) cc_final: 0.7558 (m100) REVERT: K 34 GLU cc_start: 0.8762 (pt0) cc_final: 0.8233 (pp20) REVERT: K 35 ASP cc_start: 0.8700 (m-30) cc_final: 0.8393 (m-30) REVERT: K 40 CYS cc_start: 0.8278 (m) cc_final: 0.7673 (p) REVERT: K 110 PHE cc_start: 0.7714 (m-80) cc_final: 0.7450 (m-80) REVERT: K 132 MET cc_start: 0.7456 (ppp) cc_final: 0.7241 (ppp) REVERT: K 222 ARG cc_start: 0.7091 (ttt-90) cc_final: 0.6781 (tmt170) REVERT: K 245 TRP cc_start: 0.7901 (m100) cc_final: 0.7632 (m100) REVERT: L 209 ARG cc_start: 0.8644 (mmp-170) cc_final: 0.8391 (mmm160) REVERT: L 223 PHE cc_start: 0.5893 (p90) cc_final: 0.5650 (p90) REVERT: L 226 TYR cc_start: 0.7088 (p90) cc_final: 0.6120 (p90) REVERT: L 254 LYS cc_start: 0.8300 (tmtt) cc_final: 0.7771 (tptt) REVERT: L 263 VAL cc_start: 0.7835 (m) cc_final: 0.7632 (t) REVERT: L 269 VAL cc_start: 0.7713 (m) cc_final: 0.7503 (m) REVERT: M 10 GLU cc_start: 0.8022 (tp30) cc_final: 0.7685 (tp30) REVERT: M 18 ASP cc_start: 0.7587 (t70) cc_final: 0.7319 (t70) REVERT: M 63 TRP cc_start: 0.7046 (m100) cc_final: 0.6631 (m100) REVERT: M 87 TYR cc_start: 0.7550 (t80) cc_final: 0.5793 (t80) REVERT: M 89 GLU cc_start: 0.7213 (pp20) cc_final: 0.6617 (mp0) REVERT: M 155 ARG cc_start: 0.8560 (ttt180) cc_final: 0.8268 (mtt90) REVERT: M 158 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7351 (tm-30) REVERT: M 159 THR cc_start: 0.8818 (m) cc_final: 0.8199 (p) REVERT: M 162 ASN cc_start: 0.8108 (m-40) cc_final: 0.7850 (m110) REVERT: M 178 LEU cc_start: 0.8811 (mt) cc_final: 0.8434 (mt) REVERT: M 199 ASP cc_start: 0.8678 (m-30) cc_final: 0.7758 (m-30) REVERT: M 202 ILE cc_start: 0.8959 (mm) cc_final: 0.8534 (mm) REVERT: M 205 LYS cc_start: 0.9091 (mtmm) cc_final: 0.8384 (mtmm) REVERT: M 206 GLU cc_start: 0.8598 (pt0) cc_final: 0.8090 (pt0) REVERT: N 23 HIS cc_start: 0.7704 (t70) cc_final: 0.7444 (t70) REVERT: N 65 VAL cc_start: 0.7494 (t) cc_final: 0.7193 (p) REVERT: N 104 MET cc_start: 0.8060 (ptm) cc_final: 0.7648 (ptm) REVERT: N 110 PHE cc_start: 0.8027 (m-80) cc_final: 0.7796 (m-80) REVERT: N 157 HIS cc_start: 0.7653 (m90) cc_final: 0.7175 (m90) REVERT: N 158 GLN cc_start: 0.9013 (mp10) cc_final: 0.8810 (mp10) REVERT: N 203 PHE cc_start: 0.7845 (t80) cc_final: 0.7433 (t80) REVERT: N 208 GLN cc_start: 0.8353 (tt0) cc_final: 0.7996 (tm-30) REVERT: N 213 GLN cc_start: 0.8774 (mt0) cc_final: 0.8132 (mt0) REVERT: N 233 HIS cc_start: 0.7675 (m90) cc_final: 0.7326 (m-70) REVERT: N 242 GLN cc_start: 0.7780 (tt0) cc_final: 0.7150 (pp30) REVERT: N 243 VAL cc_start: 0.8267 (t) cc_final: 0.7493 (m) REVERT: N 244 LEU cc_start: 0.8190 (tt) cc_final: 0.7939 (tt) REVERT: N 256 ARG cc_start: 0.8350 (ttm110) cc_final: 0.7696 (ttm110) REVERT: N 270 LYS cc_start: 0.8320 (mptt) cc_final: 0.7319 (mptt) REVERT: O 40 CYS cc_start: 0.5687 (t) cc_final: 0.5412 (t) REVERT: O 48 MET cc_start: -0.1416 (ppp) cc_final: -0.1844 (ppp) REVERT: O 104 MET cc_start: 0.8136 (pmm) cc_final: 0.7928 (pmm) REVERT: O 110 PHE cc_start: 0.8070 (m-80) cc_final: 0.7783 (m-10) REVERT: O 115 LEU cc_start: 0.8795 (tp) cc_final: 0.8561 (tp) REVERT: O 132 MET cc_start: 0.8135 (tmm) cc_final: 0.7562 (tmm) REVERT: O 157 HIS cc_start: 0.8937 (p90) cc_final: 0.8721 (p90) REVERT: O 199 ASP cc_start: 0.8848 (m-30) cc_final: 0.8559 (m-30) REVERT: O 201 PHE cc_start: 0.8684 (t80) cc_final: 0.7880 (t80) REVERT: O 205 LYS cc_start: 0.9178 (mmtm) cc_final: 0.8855 (mmtp) REVERT: O 208 GLN cc_start: 0.8603 (tm130) cc_final: 0.8274 (tm-30) REVERT: O 209 ARG cc_start: 0.8792 (ptm-80) cc_final: 0.8436 (ptm-80) REVERT: O 211 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8212 (tp40) REVERT: P 87 TYR cc_start: 0.8672 (t80) cc_final: 0.8337 (t80) REVERT: P 101 VAL cc_start: 0.9163 (p) cc_final: 0.8910 (p) REVERT: P 104 MET cc_start: 0.9161 (mmp) cc_final: 0.8720 (mmp) REVERT: P 106 TRP cc_start: 0.8511 (t60) cc_final: 0.8171 (t60) REVERT: P 132 MET cc_start: 0.6379 (tmm) cc_final: 0.5804 (tmm) REVERT: P 137 ILE cc_start: 0.8113 (mm) cc_final: 0.7883 (mm) REVERT: P 170 MET cc_start: 0.7416 (mtt) cc_final: 0.6934 (mpp) REVERT: P 172 ASN cc_start: 0.8783 (m-40) cc_final: 0.8457 (p0) outliers start: 5 outliers final: 2 residues processed: 1128 average time/residue: 0.2123 time to fit residues: 375.4215 Evaluate side-chains 1036 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1034 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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: 20.0000 chunk 74 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 355 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 120 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 356 optimal weight: 7.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 HIS G 208 GLN ** H 129 GLN ** 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** J 102 GLN J 158 GLN J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4582 r_free = 0.4582 target = 0.203260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.156692 restraints weight = 70579.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.162465 restraints weight = 45048.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.166500 restraints weight = 31933.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.169439 restraints weight = 24381.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.171677 restraints weight = 19635.674| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 34119 Z= 0.152 Angle : 0.677 12.856 46515 Z= 0.364 Chirality : 0.048 0.257 5006 Planarity : 0.005 0.062 5714 Dihedral : 14.806 169.208 5007 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 0.06 % Allowed : 2.07 % Favored : 97.87 % 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: 1.02 (0.12), residues: 1870 sheet: -0.64 (0.17), residues: 868 loop : -1.49 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 189 TYR 0.022 0.001 TYR O 70 PHE 0.032 0.002 PHE F 271 TRP 0.071 0.002 TRP F 237 HIS 0.017 0.001 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (34119) covalent geometry : angle 0.67735 / 0.36 (46515) hydrogen bonds : bond 0.04026 / 2.74 ( 1746) hydrogen bonds : angle 5.33447 / 3.85 ( 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 1137 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1135 time to evaluate : 1.183 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: A 15 TRP cc_start: 0.6580 (m-10) cc_final: 0.5711 (m100) REVERT: A 48 MET cc_start: 0.4986 (mmm) cc_final: 0.3861 (mmm) REVERT: A 60 ILE cc_start: 0.8710 (mm) cc_final: 0.8275 (mm) REVERT: A 62 HIS cc_start: 0.7814 (t70) cc_final: 0.7559 (t70) REVERT: A 64 GLN cc_start: 0.6424 (pm20) cc_final: 0.6050 (pm20) REVERT: A 79 VAL cc_start: 0.7860 (t) cc_final: 0.7414 (p) REVERT: A 82 ASN cc_start: 0.8237 (t0) cc_final: 0.7889 (p0) REVERT: A 92 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8510 (mtpp) REVERT: A 97 GLN cc_start: 0.7555 (pm20) cc_final: 0.7065 (pm20) REVERT: A 100 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7486 (mtm-85) REVERT: A 105 LYS cc_start: 0.9175 (mtpp) cc_final: 0.8900 (mtpp) REVERT: A 107 TYR cc_start: 0.8506 (t80) cc_final: 0.7852 (t80) REVERT: A 113 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7636 (mmmm) REVERT: A 116 GLN cc_start: 0.7314 (tm-30) cc_final: 0.6994 (tm-30) REVERT: A 132 MET cc_start: 0.8055 (mmm) cc_final: 0.7753 (mmm) REVERT: A 146 ASN cc_start: 0.8045 (m110) cc_final: 0.7340 (m-40) REVERT: A 155 ARG cc_start: 0.8670 (tpt90) cc_final: 0.7788 (mmm160) REVERT: A 158 GLN cc_start: 0.8882 (tt0) cc_final: 0.8512 (tt0) REVERT: A 164 LEU cc_start: 0.8168 (mt) cc_final: 0.7890 (mt) REVERT: A 201 PHE cc_start: 0.8190 (t80) cc_final: 0.7899 (t80) REVERT: A 203 PHE cc_start: 0.8313 (t80) cc_final: 0.7910 (t80) REVERT: A 208 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 226 TYR cc_start: 0.6177 (p90) cc_final: 0.5804 (p90) REVERT: A 258 THR cc_start: 0.8775 (p) cc_final: 0.8521 (p) REVERT: A 260 ARG cc_start: 0.7424 (ptm160) cc_final: 0.7165 (ptm160) REVERT: A 272 ILE cc_start: 0.8290 (mm) cc_final: 0.8077 (mm) REVERT: B 15 TRP cc_start: 0.7887 (m100) cc_final: 0.7397 (m100) REVERT: B 40 CYS cc_start: 0.7455 (t) cc_final: 0.6909 (p) REVERT: B 63 TRP cc_start: 0.7913 (m100) cc_final: 0.6323 (m100) REVERT: B 64 GLN cc_start: 0.7060 (tp40) cc_final: 0.6182 (mm-40) REVERT: B 65 VAL cc_start: 0.8642 (t) cc_final: 0.8187 (t) REVERT: B 70 TYR cc_start: 0.7882 (t80) cc_final: 0.7553 (t80) REVERT: B 75 ILE cc_start: 0.7950 (pt) cc_final: 0.7674 (mp) REVERT: B 86 ILE cc_start: 0.8708 (pt) cc_final: 0.8088 (mm) REVERT: B 89 GLU cc_start: 0.7833 (tt0) cc_final: 0.7111 (tt0) REVERT: B 92 LYS cc_start: 0.8704 (tppt) cc_final: 0.8244 (tptp) REVERT: B 101 VAL cc_start: 0.8905 (t) cc_final: 0.8582 (t) REVERT: B 102 GLN cc_start: 0.8491 (mp10) cc_final: 0.8225 (mm-40) REVERT: B 104 MET cc_start: 0.8665 (mmp) cc_final: 0.8407 (mmp) REVERT: B 105 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8629 (mtpp) REVERT: B 116 GLN cc_start: 0.7369 (tm-30) cc_final: 0.6836 (tm-30) REVERT: B 131 LEU cc_start: 0.9048 (tt) cc_final: 0.8621 (tt) REVERT: B 132 MET cc_start: 0.8515 (mmp) cc_final: 0.7739 (mmp) REVERT: B 137 ILE cc_start: 0.8492 (tt) cc_final: 0.8256 (tt) REVERT: B 138 GLU cc_start: 0.7911 (tp30) cc_final: 0.7651 (tp30) REVERT: B 139 HIS cc_start: 0.8452 (t70) cc_final: 0.7916 (t70) REVERT: B 165 GLU cc_start: 0.7946 (tp30) cc_final: 0.7601 (tp30) REVERT: B 178 LEU cc_start: 0.9085 (mm) cc_final: 0.8685 (mm) REVERT: B 186 ASN cc_start: 0.8345 (m-40) cc_final: 0.7786 (m-40) REVERT: B 198 MET cc_start: 0.8077 (tpt) cc_final: 0.7655 (tpp) REVERT: C 11 GLU cc_start: 0.7887 (tp30) cc_final: 0.6726 (tp30) REVERT: C 28 ILE cc_start: 0.8236 (tp) cc_final: 0.7791 (tp) REVERT: C 105 LYS cc_start: 0.8363 (mmtp) cc_final: 0.8122 (mtmm) REVERT: C 110 PHE cc_start: 0.7860 (m-80) cc_final: 0.7525 (m-80) REVERT: C 157 HIS cc_start: 0.7801 (m90) cc_final: 0.7557 (m-70) REVERT: C 190 LYS cc_start: 0.6469 (mttm) cc_final: 0.6123 (mmmt) REVERT: C 209 ARG cc_start: 0.8572 (ptt90) cc_final: 0.8247 (ptt90) REVERT: C 222 ARG cc_start: 0.7497 (ttt-90) cc_final: 0.7192 (tmt170) REVERT: C 244 LEU cc_start: 0.8251 (mm) cc_final: 0.7525 (mm) REVERT: C 245 TRP cc_start: 0.8189 (m-90) cc_final: 0.7957 (m-90) REVERT: D 209 ARG cc_start: 0.8740 (mmp-170) cc_final: 0.8420 (mmp-170) REVERT: D 218 GLN cc_start: 0.8480 (mm110) cc_final: 0.7924 (mm110) REVERT: D 223 PHE cc_start: 0.6267 (p90) cc_final: 0.5640 (p90) REVERT: D 226 TYR cc_start: 0.6936 (p90) cc_final: 0.5888 (p90) REVERT: D 238 GLN cc_start: 0.7277 (pp30) cc_final: 0.6908 (pp30) REVERT: D 254 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7673 (tptm) REVERT: D 262 LEU cc_start: 0.7826 (mp) cc_final: 0.7605 (mp) REVERT: D 263 VAL cc_start: 0.8206 (m) cc_final: 0.8001 (t) REVERT: D 267 LYS cc_start: 0.8255 (ptpt) cc_final: 0.7800 (tptt) REVERT: D 268 ASP cc_start: 0.7125 (t70) cc_final: 0.6799 (t70) REVERT: E 10 GLU cc_start: 0.7958 (tp30) cc_final: 0.7438 (tp30) REVERT: E 16 HIS cc_start: 0.7953 (m-70) cc_final: 0.7611 (m170) REVERT: E 89 GLU cc_start: 0.7773 (pm20) cc_final: 0.6573 (mp0) REVERT: E 100 ARG cc_start: 0.8798 (ptp90) cc_final: 0.8386 (ptt-90) REVERT: E 101 VAL cc_start: 0.8820 (t) cc_final: 0.8580 (t) REVERT: E 150 GLN cc_start: 0.8071 (mm110) cc_final: 0.7539 (mm110) REVERT: E 158 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7577 (tm-30) REVERT: E 159 THR cc_start: 0.8555 (m) cc_final: 0.7914 (p) REVERT: E 178 LEU cc_start: 0.8931 (mt) cc_final: 0.8674 (mt) REVERT: E 199 ASP cc_start: 0.8392 (m-30) cc_final: 0.7561 (m-30) REVERT: E 201 PHE cc_start: 0.8410 (t80) cc_final: 0.8008 (t80) REVERT: E 204 ASN cc_start: 0.8591 (t0) cc_final: 0.8355 (t0) REVERT: E 205 LYS cc_start: 0.8856 (mttt) cc_final: 0.8649 (mmtp) REVERT: E 206 GLU cc_start: 0.8577 (pt0) cc_final: 0.8262 (pt0) REVERT: E 242 GLN cc_start: 0.5879 (pp30) cc_final: 0.5433 (pp30) REVERT: F 11 GLU cc_start: 0.7680 (mp0) cc_final: 0.7449 (mp0) REVERT: F 15 TRP cc_start: 0.7096 (m100) cc_final: 0.6291 (m100) REVERT: F 23 HIS cc_start: 0.7633 (t70) cc_final: 0.7359 (t70) REVERT: F 65 VAL cc_start: 0.7049 (t) cc_final: 0.6805 (p) REVERT: F 102 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8706 (mp10) REVERT: F 104 MET cc_start: 0.7998 (ptm) cc_final: 0.7380 (ppp) REVERT: F 105 LYS cc_start: 0.8971 (mtmm) cc_final: 0.8629 (mttt) REVERT: F 158 GLN cc_start: 0.9220 (mt0) cc_final: 0.8844 (mt0) REVERT: F 162 ASN cc_start: 0.8750 (m-40) cc_final: 0.8493 (m110) REVERT: F 199 ASP cc_start: 0.8467 (m-30) cc_final: 0.8140 (m-30) REVERT: F 203 PHE cc_start: 0.7756 (t80) cc_final: 0.6963 (t80) REVERT: F 205 LYS cc_start: 0.8516 (mtmm) cc_final: 0.7982 (ptpp) REVERT: F 212 GLN cc_start: 0.8564 (pp30) cc_final: 0.8284 (pp30) REVERT: F 230 LYS cc_start: 0.8379 (mmmt) cc_final: 0.7894 (mmmm) REVERT: F 233 HIS cc_start: 0.7619 (m90) cc_final: 0.7315 (m90) REVERT: F 236 GLU cc_start: 0.7786 (pm20) cc_final: 0.7546 (mp0) REVERT: F 242 GLN cc_start: 0.7242 (tt0) cc_final: 0.6926 (tm-30) REVERT: F 243 VAL cc_start: 0.8367 (t) cc_final: 0.6794 (m) REVERT: F 244 LEU cc_start: 0.8052 (tt) cc_final: 0.7774 (tt) REVERT: F 256 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7914 (ttm110) REVERT: F 267 LYS cc_start: 0.8688 (ptmt) cc_final: 0.8274 (pttt) REVERT: G 48 MET cc_start: -0.0477 (ppp) cc_final: -0.1350 (ppp) REVERT: G 85 LEU cc_start: 0.7272 (tp) cc_final: 0.6895 (tp) REVERT: G 104 MET cc_start: 0.7827 (pmm) cc_final: 0.7570 (pmm) REVERT: G 110 PHE cc_start: 0.7841 (m-80) cc_final: 0.7126 (m-80) REVERT: G 130 LEU cc_start: 0.8905 (pp) cc_final: 0.8702 (pp) REVERT: G 131 LEU cc_start: 0.9281 (mt) cc_final: 0.9029 (mt) REVERT: G 183 ILE cc_start: 0.7219 (mt) cc_final: 0.6870 (mt) REVERT: G 197 PRO cc_start: 0.8591 (Cg_exo) cc_final: 0.8322 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8946 (m-30) cc_final: 0.8540 (m-30) REVERT: G 201 PHE cc_start: 0.8781 (t80) cc_final: 0.8339 (t80) REVERT: G 205 LYS cc_start: 0.9250 (mmtm) cc_final: 0.8991 (mmtm) REVERT: G 208 GLN cc_start: 0.8486 (tm130) cc_final: 0.8280 (tm-30) REVERT: G 209 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8310 (ttp80) REVERT: G 210 ILE cc_start: 0.8509 (pt) cc_final: 0.7969 (pt) REVERT: H 78 TRP cc_start: 0.6921 (m-10) cc_final: 0.6573 (m-10) REVERT: H 87 TYR cc_start: 0.8467 (t80) cc_final: 0.7972 (t80) REVERT: H 95 THR cc_start: 0.5129 (t) cc_final: 0.4927 (p) REVERT: H 101 VAL cc_start: 0.8808 (p) cc_final: 0.8580 (p) REVERT: H 104 MET cc_start: 0.9072 (mmp) cc_final: 0.8469 (mmp) REVERT: H 106 TRP cc_start: 0.8402 (t60) cc_final: 0.7851 (t60) REVERT: H 109 MET cc_start: 0.8002 (tpt) cc_final: 0.7775 (tpt) REVERT: H 110 PHE cc_start: 0.8144 (m-10) cc_final: 0.7816 (m-10) REVERT: H 207 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7787 (mm-40) REVERT: H 223 PHE cc_start: 0.7182 (m-80) cc_final: 0.6762 (m-80) REVERT: H 267 LYS cc_start: 0.7599 (ptmm) cc_final: 0.7347 (ptmm) REVERT: I 66 ASP cc_start: 0.7468 (t70) cc_final: 0.7088 (t70) REVERT: I 79 VAL cc_start: 0.7988 (t) cc_final: 0.7515 (p) REVERT: I 97 GLN cc_start: 0.7887 (pm20) cc_final: 0.7638 (pm20) REVERT: I 98 GLU cc_start: 0.8172 (mp0) cc_final: 0.7790 (mp0) REVERT: I 100 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7639 (mtm-85) REVERT: I 118 ASP cc_start: 0.7701 (p0) cc_final: 0.7357 (p0) REVERT: I 132 MET cc_start: 0.8209 (mmm) cc_final: 0.7910 (mmm) REVERT: I 143 ILE cc_start: 0.8429 (tp) cc_final: 0.7773 (tp) REVERT: I 146 ASN cc_start: 0.8001 (m110) cc_final: 0.7322 (m110) REVERT: I 155 ARG cc_start: 0.8265 (tpt90) cc_final: 0.7574 (mmm160) REVERT: I 158 GLN cc_start: 0.9069 (tt0) cc_final: 0.8632 (tt0) REVERT: I 159 THR cc_start: 0.8620 (p) cc_final: 0.8306 (m) REVERT: I 164 LEU cc_start: 0.8472 (mt) cc_final: 0.8235 (mt) REVERT: I 198 MET cc_start: 0.8467 (ttm) cc_final: 0.8220 (tpp) REVERT: I 203 PHE cc_start: 0.8258 (t80) cc_final: 0.7835 (t80) REVERT: I 208 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7923 (tm-30) REVERT: I 209 ARG cc_start: 0.7348 (tpp80) cc_final: 0.6912 (tpp80) REVERT: I 258 THR cc_start: 0.8651 (p) cc_final: 0.8421 (p) REVERT: I 264 ILE cc_start: 0.7889 (mm) cc_final: 0.7594 (mm) REVERT: J 40 CYS cc_start: 0.7139 (t) cc_final: 0.6751 (p) REVERT: J 62 HIS cc_start: 0.7308 (t-90) cc_final: 0.6955 (t-90) REVERT: J 63 TRP cc_start: 0.7833 (m100) cc_final: 0.6022 (m100) REVERT: J 64 GLN cc_start: 0.7130 (tp40) cc_final: 0.6268 (mm110) REVERT: J 65 VAL cc_start: 0.8715 (t) cc_final: 0.8388 (t) REVERT: J 86 ILE cc_start: 0.8916 (pt) cc_final: 0.8083 (mm) REVERT: J 89 GLU cc_start: 0.7609 (tt0) cc_final: 0.7387 (tt0) REVERT: J 92 LYS cc_start: 0.8823 (tptp) cc_final: 0.8469 (tptp) REVERT: J 100 ARG cc_start: 0.8638 (ptp90) cc_final: 0.8259 (ptt-90) REVERT: J 104 MET cc_start: 0.8223 (tpp) cc_final: 0.7453 (tpp) REVERT: J 116 GLN cc_start: 0.7226 (tm-30) cc_final: 0.6998 (tm-30) REVERT: J 131 LEU cc_start: 0.8744 (tt) cc_final: 0.8405 (tt) REVERT: J 138 GLU cc_start: 0.7737 (tp30) cc_final: 0.7489 (tp30) REVERT: J 139 HIS cc_start: 0.8492 (t70) cc_final: 0.8124 (t70) REVERT: J 189 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6815 (ptp-170) REVERT: J 198 MET cc_start: 0.7998 (tpt) cc_final: 0.7770 (tpp) REVERT: J 204 ASN cc_start: 0.8276 (m110) cc_final: 0.7169 (p0) REVERT: J 205 LYS cc_start: 0.8255 (tptp) cc_final: 0.7612 (tptp) REVERT: J 208 GLN cc_start: 0.8028 (pt0) cc_final: 0.7626 (pt0) REVERT: K 15 TRP cc_start: 0.8265 (m100) cc_final: 0.7637 (m100) REVERT: K 25 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8227 (tm-30) REVERT: K 34 GLU cc_start: 0.8739 (pt0) cc_final: 0.8277 (pp20) REVERT: K 35 ASP cc_start: 0.8678 (m-30) cc_final: 0.8363 (m-30) REVERT: K 40 CYS cc_start: 0.8277 (m) cc_final: 0.7725 (p) REVERT: K 110 PHE cc_start: 0.7809 (m-80) cc_final: 0.7570 (m-80) REVERT: K 190 LYS cc_start: 0.6363 (mttm) cc_final: 0.5859 (mmmt) REVERT: K 208 GLN cc_start: 0.8538 (tt0) cc_final: 0.8232 (tt0) REVERT: K 222 ARG cc_start: 0.7208 (ttt-90) cc_final: 0.6947 (tmt170) REVERT: L 209 ARG cc_start: 0.8687 (mmp-170) cc_final: 0.8451 (mmp-170) REVERT: L 223 PHE cc_start: 0.5976 (p90) cc_final: 0.5592 (p90) REVERT: L 226 TYR cc_start: 0.6654 (p90) cc_final: 0.6003 (p90) REVERT: L 254 LYS cc_start: 0.8299 (tmtt) cc_final: 0.7692 (tppt) REVERT: L 263 VAL cc_start: 0.8001 (m) cc_final: 0.7766 (t) REVERT: L 269 VAL cc_start: 0.7727 (m) cc_final: 0.7474 (m) REVERT: M 7 LEU cc_start: 0.8086 (tt) cc_final: 0.7875 (tt) REVERT: M 10 GLU cc_start: 0.8049 (tp30) cc_final: 0.7677 (tp30) REVERT: M 18 ASP cc_start: 0.7631 (t70) cc_final: 0.7375 (t70) REVERT: M 63 TRP cc_start: 0.7199 (m100) cc_final: 0.6866 (m100) REVERT: M 76 LEU cc_start: 0.7274 (mm) cc_final: 0.6996 (mm) REVERT: M 78 TRP cc_start: 0.6736 (m-90) cc_final: 0.6323 (m100) REVERT: M 154 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8750 (mm-30) REVERT: M 155 ARG cc_start: 0.8558 (ttt180) cc_final: 0.8253 (mtt90) REVERT: M 158 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7334 (tm-30) REVERT: M 159 THR cc_start: 0.8813 (m) cc_final: 0.8196 (p) REVERT: M 162 ASN cc_start: 0.8108 (m-40) cc_final: 0.7841 (m110) REVERT: M 174 PHE cc_start: 0.7108 (t80) cc_final: 0.6852 (t80) REVERT: M 178 LEU cc_start: 0.8838 (mt) cc_final: 0.8246 (mt) REVERT: M 199 ASP cc_start: 0.8646 (m-30) cc_final: 0.7693 (m-30) REVERT: M 202 ILE cc_start: 0.9118 (mm) cc_final: 0.8808 (mm) REVERT: M 205 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8428 (mtmm) REVERT: M 206 GLU cc_start: 0.8590 (pt0) cc_final: 0.8063 (pt0) REVERT: N 23 HIS cc_start: 0.7678 (t70) cc_final: 0.7417 (t70) REVERT: N 65 VAL cc_start: 0.7563 (t) cc_final: 0.7248 (p) REVERT: N 104 MET cc_start: 0.8155 (ptm) cc_final: 0.7818 (ptm) REVERT: N 105 LYS cc_start: 0.9301 (mtmm) cc_final: 0.8960 (mttt) REVERT: N 110 PHE cc_start: 0.8081 (m-80) cc_final: 0.7877 (m-80) REVERT: N 154 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7199 (mm-30) REVERT: N 170 MET cc_start: 0.7025 (mpp) cc_final: 0.6798 (mpp) REVERT: N 203 PHE cc_start: 0.7756 (t80) cc_final: 0.7346 (t80) REVERT: N 208 GLN cc_start: 0.8390 (tt0) cc_final: 0.8018 (tm-30) REVERT: N 213 GLN cc_start: 0.8745 (mt0) cc_final: 0.8126 (mt0) REVERT: N 233 HIS cc_start: 0.7692 (m90) cc_final: 0.7363 (m-70) REVERT: N 236 GLU cc_start: 0.7809 (mp0) cc_final: 0.7465 (mp0) REVERT: N 242 GLN cc_start: 0.7818 (tt0) cc_final: 0.7191 (pp30) REVERT: N 243 VAL cc_start: 0.8495 (t) cc_final: 0.7504 (m) REVERT: N 244 LEU cc_start: 0.8239 (tt) cc_final: 0.7988 (tt) REVERT: N 256 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7672 (ttm110) REVERT: N 267 LYS cc_start: 0.8847 (ptmt) cc_final: 0.8472 (pttt) REVERT: O 40 CYS cc_start: 0.5685 (t) cc_final: 0.5468 (t) REVERT: O 48 MET cc_start: -0.1436 (ppp) cc_final: -0.1904 (ppp) REVERT: O 85 LEU cc_start: 0.7650 (tp) cc_final: 0.7244 (tp) REVERT: O 104 MET cc_start: 0.8081 (pmm) cc_final: 0.7823 (pmm) REVERT: O 110 PHE cc_start: 0.8173 (m-80) cc_final: 0.7413 (m-10) REVERT: O 132 MET cc_start: 0.8130 (tmm) cc_final: 0.7727 (tmm) REVERT: O 157 HIS cc_start: 0.9056 (p90) cc_final: 0.8755 (p90) REVERT: O 193 LEU cc_start: 0.8738 (mm) cc_final: 0.8528 (mm) REVERT: O 199 ASP cc_start: 0.8822 (m-30) cc_final: 0.8404 (m-30) REVERT: O 201 PHE cc_start: 0.8712 (t80) cc_final: 0.7912 (t80) REVERT: O 205 LYS cc_start: 0.9225 (mmtm) cc_final: 0.8916 (mmtp) REVERT: O 209 ARG cc_start: 0.8800 (ptm-80) cc_final: 0.8411 (ptm-80) REVERT: O 211 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8159 (tp40) REVERT: P 87 TYR cc_start: 0.8672 (t80) cc_final: 0.8383 (t80) REVERT: P 101 VAL cc_start: 0.9151 (p) cc_final: 0.8901 (p) REVERT: P 104 MET cc_start: 0.9157 (mmp) cc_final: 0.8644 (mmp) REVERT: P 106 TRP cc_start: 0.8459 (t60) cc_final: 0.8108 (t60) REVERT: P 132 MET cc_start: 0.6395 (tmm) cc_final: 0.5812 (tmm) REVERT: P 137 ILE cc_start: 0.8157 (mm) cc_final: 0.7873 (mm) REVERT: P 170 MET cc_start: 0.7446 (mtt) cc_final: 0.6955 (mpp) REVERT: P 172 ASN cc_start: 0.8795 (m-40) cc_final: 0.8457 (p0) REVERT: P 228 THR cc_start: 0.6126 (t) cc_final: 0.5877 (t) REVERT: P 254 LYS cc_start: 0.8626 (mtpp) cc_final: 0.7852 (tppt) outliers start: 2 outliers final: 1 residues processed: 1137 average time/residue: 0.2181 time to fit residues: 388.4547 Evaluate side-chains 1055 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1054 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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: 2.9990 chunk 362 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN C 17 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 204 ASN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 GLN ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN M 69 HIS ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN N 186 ASN O 102 GLN O 208 GLN P 148 GLN P 157 HIS P 242 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.198322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.151745 restraints weight = 71567.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.157413 restraints weight = 45388.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161382 restraints weight = 31986.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.164241 restraints weight = 24246.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.166349 restraints weight = 19453.314| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 34119 Z= 0.200 Angle : 0.739 14.869 46515 Z= 0.400 Chirality : 0.050 0.235 5006 Planarity : 0.005 0.107 5714 Dihedral : 14.910 170.468 5007 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -0.38 (0.13), residues: 3851 helix: 0.87 (0.12), residues: 1864 sheet: -0.76 (0.17), residues: 839 loop : -1.58 (0.16), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 222 TYR 0.019 0.001 TYR K 261 PHE 0.036 0.002 PHE E 203 TRP 0.051 0.003 TRP D 63 HIS 0.021 0.002 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (34119) covalent geometry : angle 0.73878 / 0.40 (46515) hydrogen bonds : bond 0.04356 / 2.98 ( 1746) hydrogen bonds : angle 5.54623 / 4.01 ( 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 1149 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1149 time to evaluate : 1.165 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: A 15 TRP cc_start: 0.6812 (m-10) cc_final: 0.6038 (m-10) REVERT: A 60 ILE cc_start: 0.8700 (mm) cc_final: 0.8254 (mm) REVERT: A 62 HIS cc_start: 0.7750 (t70) cc_final: 0.7452 (t70) REVERT: A 64 GLN cc_start: 0.6542 (pm20) cc_final: 0.6286 (pm20) REVERT: A 66 ASP cc_start: 0.7363 (t0) cc_final: 0.7148 (t70) REVERT: A 79 VAL cc_start: 0.8054 (t) cc_final: 0.7552 (p) REVERT: A 80 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6507 (tm-30) REVERT: A 81 THR cc_start: 0.8718 (p) cc_final: 0.8377 (t) REVERT: A 85 LEU cc_start: 0.8023 (tt) cc_final: 0.7707 (tt) REVERT: A 90 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7705 (tmm-80) REVERT: A 92 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8384 (mtpp) REVERT: A 97 GLN cc_start: 0.7896 (pm20) cc_final: 0.7466 (pm20) REVERT: A 100 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7473 (mtm-85) REVERT: A 107 TYR cc_start: 0.8455 (t80) cc_final: 0.8136 (t80) REVERT: A 113 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7708 (mmmm) REVERT: A 116 GLN cc_start: 0.7447 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 118 ASP cc_start: 0.7511 (p0) cc_final: 0.7217 (p0) REVERT: A 129 GLN cc_start: 0.7896 (tt0) cc_final: 0.7575 (tt0) REVERT: A 135 LEU cc_start: 0.8795 (mt) cc_final: 0.8452 (mt) REVERT: A 155 ARG cc_start: 0.8593 (tpt90) cc_final: 0.7658 (mmm160) REVERT: A 158 GLN cc_start: 0.8863 (tt0) cc_final: 0.8494 (tt0) REVERT: A 161 LYS cc_start: 0.8793 (tptt) cc_final: 0.8562 (tptt) REVERT: A 164 LEU cc_start: 0.8357 (mt) cc_final: 0.8133 (mt) REVERT: A 188 LYS cc_start: 0.6905 (mmmt) cc_final: 0.6293 (mmtm) REVERT: A 198 MET cc_start: 0.8400 (ttm) cc_final: 0.8160 (ttm) REVERT: A 203 PHE cc_start: 0.8505 (t80) cc_final: 0.8074 (t80) REVERT: A 226 TYR cc_start: 0.6490 (p90) cc_final: 0.6015 (p90) REVERT: A 258 THR cc_start: 0.8763 (p) cc_final: 0.8511 (p) REVERT: A 260 ARG cc_start: 0.7542 (ptm160) cc_final: 0.7276 (ptm160) REVERT: B 15 TRP cc_start: 0.7923 (m100) cc_final: 0.7428 (m100) REVERT: B 40 CYS cc_start: 0.7494 (t) cc_final: 0.6927 (p) REVERT: B 63 TRP cc_start: 0.7874 (m100) cc_final: 0.5960 (m100) REVERT: B 64 GLN cc_start: 0.7087 (tp40) cc_final: 0.6573 (mm110) REVERT: B 65 VAL cc_start: 0.8645 (t) cc_final: 0.8202 (t) REVERT: B 70 TYR cc_start: 0.8022 (t80) cc_final: 0.7642 (t80) REVERT: B 86 ILE cc_start: 0.8824 (pt) cc_final: 0.8100 (mm) REVERT: B 87 TYR cc_start: 0.8217 (t80) cc_final: 0.7950 (t80) REVERT: B 89 GLU cc_start: 0.7782 (tt0) cc_final: 0.7174 (tt0) REVERT: B 90 ARG cc_start: 0.8786 (tpt-90) cc_final: 0.8031 (tpp80) REVERT: B 92 LYS cc_start: 0.8785 (tppt) cc_final: 0.8177 (tptp) REVERT: B 100 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8297 (mtt180) REVERT: B 101 VAL cc_start: 0.8932 (t) cc_final: 0.8692 (t) REVERT: B 102 GLN cc_start: 0.8692 (mp10) cc_final: 0.8286 (mm-40) REVERT: B 104 MET cc_start: 0.8632 (mmp) cc_final: 0.8346 (mmp) REVERT: B 129 GLN cc_start: 0.8463 (pt0) cc_final: 0.8029 (pt0) REVERT: B 131 LEU cc_start: 0.9007 (tt) cc_final: 0.8532 (tt) REVERT: B 132 MET cc_start: 0.8617 (mmp) cc_final: 0.7902 (mmp) REVERT: B 138 GLU cc_start: 0.7889 (tp30) cc_final: 0.7590 (tp30) REVERT: B 139 HIS cc_start: 0.8511 (t70) cc_final: 0.7982 (t70) REVERT: B 165 GLU cc_start: 0.7987 (tp30) cc_final: 0.7689 (tp30) REVERT: B 178 LEU cc_start: 0.9203 (mm) cc_final: 0.8799 (mm) REVERT: B 186 ASN cc_start: 0.8306 (m-40) cc_final: 0.7819 (m-40) REVERT: B 198 MET cc_start: 0.8069 (tpt) cc_final: 0.7658 (tpp) REVERT: B 204 ASN cc_start: 0.8125 (p0) cc_final: 0.7680 (p0) REVERT: C 5 ILE cc_start: 0.9295 (mt) cc_final: 0.9058 (mt) REVERT: C 7 LEU cc_start: 0.8735 (tt) cc_final: 0.8274 (tt) REVERT: C 11 GLU cc_start: 0.7967 (tp30) cc_final: 0.7550 (tp30) REVERT: C 28 ILE cc_start: 0.7750 (tp) cc_final: 0.7447 (tp) REVERT: C 39 GLN cc_start: 0.8435 (tp40) cc_final: 0.7747 (tp40) REVERT: C 110 PHE cc_start: 0.7825 (m-80) cc_final: 0.7615 (m-80) REVERT: C 132 MET cc_start: 0.8284 (ppp) cc_final: 0.7847 (ppp) REVERT: C 157 HIS cc_start: 0.8019 (m90) cc_final: 0.7654 (m-70) REVERT: C 164 LEU cc_start: 0.8936 (mt) cc_final: 0.8422 (tp) REVERT: C 186 ASN cc_start: 0.8056 (m-40) cc_final: 0.7815 (m110) REVERT: C 198 MET cc_start: 0.8504 (tpt) cc_final: 0.8182 (tpt) REVERT: C 208 GLN cc_start: 0.8611 (tt0) cc_final: 0.8106 (mt0) REVERT: C 244 LEU cc_start: 0.8250 (mm) cc_final: 0.7702 (mm) REVERT: D 209 ARG cc_start: 0.8759 (mmp-170) cc_final: 0.8461 (mmp-170) REVERT: D 223 PHE cc_start: 0.6411 (p90) cc_final: 0.5942 (p90) REVERT: D 226 TYR cc_start: 0.7215 (p90) cc_final: 0.6204 (p90) REVERT: D 244 LEU cc_start: 0.8517 (mt) cc_final: 0.8264 (mt) REVERT: D 262 LEU cc_start: 0.7780 (mp) cc_final: 0.7554 (mp) REVERT: D 263 VAL cc_start: 0.8377 (m) cc_final: 0.8158 (t) REVERT: E 10 GLU cc_start: 0.7894 (tp30) cc_final: 0.7406 (tp30) REVERT: E 15 TRP cc_start: 0.8618 (m-10) cc_final: 0.8238 (m-10) REVERT: E 16 HIS cc_start: 0.7994 (m-70) cc_final: 0.7280 (m170) REVERT: E 100 ARG cc_start: 0.8814 (ptp90) cc_final: 0.8583 (ptp-170) REVERT: E 150 GLN cc_start: 0.8124 (mm110) cc_final: 0.7671 (mm110) REVERT: E 178 LEU cc_start: 0.8947 (mt) cc_final: 0.8677 (mt) REVERT: E 199 ASP cc_start: 0.8438 (m-30) cc_final: 0.7617 (m-30) REVERT: E 201 PHE cc_start: 0.8450 (t80) cc_final: 0.8094 (t80) REVERT: E 205 LYS cc_start: 0.8850 (mttt) cc_final: 0.8426 (mmtp) REVERT: E 224 CYS cc_start: 0.5712 (p) cc_final: 0.5258 (p) REVERT: F 23 HIS cc_start: 0.7566 (t70) cc_final: 0.7281 (t70) REVERT: F 65 VAL cc_start: 0.7564 (t) cc_final: 0.7332 (p) REVERT: F 104 MET cc_start: 0.8115 (ptm) cc_final: 0.7521 (ppp) REVERT: F 150 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7871 (mt0) REVERT: F 155 ARG cc_start: 0.8693 (tmt-80) cc_final: 0.8461 (tmt-80) REVERT: F 205 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8070 (mtmt) REVERT: F 207 GLN cc_start: 0.8531 (mp10) cc_final: 0.8148 (mp10) REVERT: F 208 GLN cc_start: 0.8333 (tt0) cc_final: 0.8089 (tm-30) REVERT: F 230 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8051 (mmmm) REVERT: F 237 TRP cc_start: 0.8376 (m100) cc_final: 0.8055 (m100) REVERT: F 242 GLN cc_start: 0.7343 (tt0) cc_final: 0.6703 (pp30) REVERT: F 243 VAL cc_start: 0.8435 (t) cc_final: 0.7633 (p) REVERT: F 244 LEU cc_start: 0.8191 (tt) cc_final: 0.7863 (tt) REVERT: F 256 ARG cc_start: 0.8368 (ttm110) cc_final: 0.7972 (ttm110) REVERT: G 48 MET cc_start: -0.0511 (ppp) cc_final: -0.1326 (ppp) REVERT: G 85 LEU cc_start: 0.7324 (tp) cc_final: 0.6885 (tp) REVERT: G 110 PHE cc_start: 0.7839 (m-80) cc_final: 0.7534 (m-80) REVERT: G 116 GLN cc_start: 0.8183 (mt0) cc_final: 0.7781 (tp40) REVERT: G 130 LEU cc_start: 0.8923 (pp) cc_final: 0.8710 (pp) REVERT: G 131 LEU cc_start: 0.9292 (mt) cc_final: 0.9051 (mt) REVERT: G 157 HIS cc_start: 0.8856 (p90) cc_final: 0.8644 (p90) REVERT: G 171 PHE cc_start: 0.7046 (m-80) cc_final: 0.6704 (m-80) REVERT: G 197 PRO cc_start: 0.8575 (Cg_exo) cc_final: 0.8287 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8933 (m-30) cc_final: 0.8466 (m-30) REVERT: G 201 PHE cc_start: 0.8801 (t80) cc_final: 0.8397 (t80) REVERT: G 205 LYS cc_start: 0.9257 (mmtm) cc_final: 0.9011 (mmtm) REVERT: G 209 ARG cc_start: 0.8949 (ttp80) cc_final: 0.8435 (ttp80) REVERT: G 210 ILE cc_start: 0.8652 (pt) cc_final: 0.8085 (pt) REVERT: H 78 TRP cc_start: 0.7070 (m-10) cc_final: 0.6670 (m-10) REVERT: H 87 TYR cc_start: 0.8490 (t80) cc_final: 0.7976 (t80) REVERT: H 101 VAL cc_start: 0.8818 (p) cc_final: 0.8596 (p) REVERT: H 104 MET cc_start: 0.9099 (mmp) cc_final: 0.8465 (mmp) REVERT: H 106 TRP cc_start: 0.8354 (t60) cc_final: 0.7808 (t60) REVERT: H 109 MET cc_start: 0.7995 (tpt) cc_final: 0.7281 (tpt) REVERT: H 110 PHE cc_start: 0.8306 (m-10) cc_final: 0.7895 (m-10) REVERT: H 207 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7792 (mm-40) REVERT: H 238 GLN cc_start: 0.6807 (mm110) cc_final: 0.6459 (mm-40) REVERT: H 267 LYS cc_start: 0.7611 (ptmm) cc_final: 0.7360 (ptmm) REVERT: I 60 ILE cc_start: 0.8904 (mp) cc_final: 0.8292 (mm) REVERT: I 66 ASP cc_start: 0.7564 (t70) cc_final: 0.7065 (t70) REVERT: I 79 VAL cc_start: 0.8059 (t) cc_final: 0.7360 (p) REVERT: I 81 THR cc_start: 0.8705 (p) cc_final: 0.8413 (t) REVERT: I 86 ILE cc_start: 0.8527 (pt) cc_final: 0.7929 (mp) REVERT: I 98 GLU cc_start: 0.8231 (mp0) cc_final: 0.7859 (mp0) REVERT: I 100 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7762 (mtm-85) REVERT: I 113 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7620 (mmmm) REVERT: I 118 ASP cc_start: 0.7717 (p0) cc_final: 0.7397 (p0) REVERT: I 143 ILE cc_start: 0.8650 (tp) cc_final: 0.8204 (tp) REVERT: I 146 ASN cc_start: 0.8005 (m110) cc_final: 0.7357 (m110) REVERT: I 152 LEU cc_start: 0.7442 (pt) cc_final: 0.6348 (mp) REVERT: I 153 VAL cc_start: 0.8915 (m) cc_final: 0.8659 (m) REVERT: I 155 ARG cc_start: 0.8327 (tpt90) cc_final: 0.7635 (mmm160) REVERT: I 158 GLN cc_start: 0.9019 (tt0) cc_final: 0.8598 (tt0) REVERT: I 159 THR cc_start: 0.8562 (p) cc_final: 0.8326 (m) REVERT: I 160 LEU cc_start: 0.8783 (tt) cc_final: 0.8514 (tt) REVERT: I 164 LEU cc_start: 0.8602 (mt) cc_final: 0.8291 (mt) REVERT: I 183 ILE cc_start: 0.9017 (mt) cc_final: 0.8555 (mm) REVERT: I 198 MET cc_start: 0.8573 (ttm) cc_final: 0.8296 (tpp) REVERT: I 203 PHE cc_start: 0.8345 (t80) cc_final: 0.7910 (t80) REVERT: I 208 GLN cc_start: 0.8282 (tm-30) cc_final: 0.8023 (tm-30) REVERT: I 209 ARG cc_start: 0.7462 (tpp80) cc_final: 0.7043 (tpp80) REVERT: I 258 THR cc_start: 0.8745 (p) cc_final: 0.8536 (p) REVERT: I 260 ARG cc_start: 0.7458 (ptm160) cc_final: 0.7122 (ptm160) REVERT: I 261 TYR cc_start: 0.7579 (m-10) cc_final: 0.6591 (m-10) REVERT: I 264 ILE cc_start: 0.7961 (mm) cc_final: 0.7695 (mm) REVERT: J 13 ASN cc_start: 0.7141 (m-40) cc_final: 0.6908 (m-40) REVERT: J 40 CYS cc_start: 0.7271 (t) cc_final: 0.6942 (t) REVERT: J 62 HIS cc_start: 0.7370 (t-90) cc_final: 0.6912 (t-90) REVERT: J 63 TRP cc_start: 0.7780 (m100) cc_final: 0.5982 (m100) REVERT: J 64 GLN cc_start: 0.7041 (tp40) cc_final: 0.6326 (mm110) REVERT: J 65 VAL cc_start: 0.8708 (t) cc_final: 0.8444 (t) REVERT: J 86 ILE cc_start: 0.9037 (pt) cc_final: 0.8072 (mm) REVERT: J 92 LYS cc_start: 0.8864 (tptp) cc_final: 0.8484 (tptp) REVERT: J 98 GLU cc_start: 0.8182 (pm20) cc_final: 0.7932 (pm20) REVERT: J 100 ARG cc_start: 0.8627 (ptp90) cc_final: 0.8230 (ptp90) REVERT: J 102 GLN cc_start: 0.8552 (mp10) cc_final: 0.7995 (mp10) REVERT: J 104 MET cc_start: 0.8264 (tpp) cc_final: 0.7628 (tpp) REVERT: J 116 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7091 (tm-30) REVERT: J 131 LEU cc_start: 0.8677 (tt) cc_final: 0.8350 (tt) REVERT: J 139 HIS cc_start: 0.8526 (t70) cc_final: 0.8065 (t70) REVERT: J 178 LEU cc_start: 0.9153 (mm) cc_final: 0.8849 (mm) REVERT: J 182 LEU cc_start: 0.8475 (mt) cc_final: 0.8267 (mt) REVERT: J 198 MET cc_start: 0.8065 (tpt) cc_final: 0.7812 (tpp) REVERT: J 204 ASN cc_start: 0.8367 (m110) cc_final: 0.7313 (p0) REVERT: J 208 GLN cc_start: 0.8071 (pt0) cc_final: 0.7774 (pt0) REVERT: K 15 TRP cc_start: 0.8285 (m100) cc_final: 0.7595 (m100) REVERT: K 34 GLU cc_start: 0.8695 (pt0) cc_final: 0.8275 (pp20) REVERT: K 35 ASP cc_start: 0.8724 (m-30) cc_final: 0.8352 (m-30) REVERT: K 110 PHE cc_start: 0.7845 (m-80) cc_final: 0.7629 (m-80) REVERT: K 208 GLN cc_start: 0.8736 (tt0) cc_final: 0.7861 (mt0) REVERT: K 212 GLN cc_start: 0.7652 (mp10) cc_final: 0.7319 (mp10) REVERT: K 222 ARG cc_start: 0.7259 (ttt-90) cc_final: 0.7046 (tmt170) REVERT: L 209 ARG cc_start: 0.8660 (mmp-170) cc_final: 0.8354 (mmp-170) REVERT: L 226 TYR cc_start: 0.7204 (p90) cc_final: 0.6103 (p90) REVERT: L 248 ASP cc_start: 0.8191 (p0) cc_final: 0.7874 (p0) REVERT: L 254 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7689 (tppt) REVERT: L 263 VAL cc_start: 0.8188 (m) cc_final: 0.7937 (t) REVERT: L 269 VAL cc_start: 0.7740 (m) cc_final: 0.7488 (m) REVERT: M 7 LEU cc_start: 0.8284 (tt) cc_final: 0.7814 (tt) REVERT: M 14 LYS cc_start: 0.8279 (mttp) cc_final: 0.8070 (mtpt) REVERT: M 16 HIS cc_start: 0.7768 (m-70) cc_final: 0.7264 (m170) REVERT: M 63 TRP cc_start: 0.7336 (m100) cc_final: 0.7099 (m100) REVERT: M 78 TRP cc_start: 0.6868 (m-90) cc_final: 0.6392 (m-90) REVERT: M 109 MET cc_start: 0.8750 (tmm) cc_final: 0.8036 (ttt) REVERT: M 130 LEU cc_start: 0.8192 (mt) cc_final: 0.7158 (mt) REVERT: M 133 LYS cc_start: 0.9097 (ptpp) cc_final: 0.8716 (pttp) REVERT: M 158 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7801 (tm-30) REVERT: M 159 THR cc_start: 0.8845 (m) cc_final: 0.8288 (p) REVERT: M 174 PHE cc_start: 0.7268 (t80) cc_final: 0.6966 (t80) REVERT: M 178 LEU cc_start: 0.8852 (mt) cc_final: 0.8225 (mt) REVERT: M 199 ASP cc_start: 0.8612 (m-30) cc_final: 0.7722 (m-30) REVERT: M 202 ILE cc_start: 0.9107 (mm) cc_final: 0.8792 (mm) REVERT: M 205 LYS cc_start: 0.9091 (mtmm) cc_final: 0.8417 (mtmm) REVERT: M 206 GLU cc_start: 0.8594 (pt0) cc_final: 0.8064 (pt0) REVERT: M 207 GLN cc_start: 0.8496 (mm110) cc_final: 0.8276 (mm110) REVERT: M 209 ARG cc_start: 0.8776 (tmt170) cc_final: 0.8401 (ttp80) REVERT: N 23 HIS cc_start: 0.7709 (t70) cc_final: 0.7465 (t70) REVERT: N 65 VAL cc_start: 0.7441 (t) cc_final: 0.7103 (p) REVERT: N 102 GLN cc_start: 0.8881 (mp10) cc_final: 0.8311 (mp10) REVERT: N 104 MET cc_start: 0.8181 (ptm) cc_final: 0.7857 (ptm) REVERT: N 105 LYS cc_start: 0.9346 (mtmm) cc_final: 0.9005 (mttt) REVERT: N 110 PHE cc_start: 0.8110 (m-80) cc_final: 0.7852 (m-80) REVERT: N 127 SER cc_start: 0.8583 (t) cc_final: 0.8341 (t) REVERT: N 157 HIS cc_start: 0.7757 (m90) cc_final: 0.7444 (m90) REVERT: N 158 GLN cc_start: 0.9044 (mp10) cc_final: 0.8759 (mp10) REVERT: N 183 ILE cc_start: 0.7049 (mt) cc_final: 0.6837 (mt) REVERT: N 203 PHE cc_start: 0.8051 (t80) cc_final: 0.7728 (t80) REVERT: N 205 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8273 (mtmm) REVERT: N 213 GLN cc_start: 0.8777 (mt0) cc_final: 0.8116 (mt0) REVERT: N 233 HIS cc_start: 0.7741 (m90) cc_final: 0.7385 (m-70) REVERT: N 236 GLU cc_start: 0.7919 (mp0) cc_final: 0.7548 (mp0) REVERT: N 242 GLN cc_start: 0.7850 (tt0) cc_final: 0.7267 (pp30) REVERT: N 243 VAL cc_start: 0.8561 (t) cc_final: 0.7607 (m) REVERT: N 244 LEU cc_start: 0.8323 (tt) cc_final: 0.8063 (tt) REVERT: N 256 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7726 (ttm110) REVERT: O 40 CYS cc_start: 0.5848 (t) cc_final: 0.5637 (t) REVERT: O 48 MET cc_start: -0.1480 (ppp) cc_final: -0.1947 (ppp) REVERT: O 85 LEU cc_start: 0.7670 (tp) cc_final: 0.7375 (tp) REVERT: O 110 PHE cc_start: 0.8070 (m-80) cc_final: 0.7593 (m-10) REVERT: O 132 MET cc_start: 0.8090 (tmm) cc_final: 0.7619 (tmm) REVERT: O 152 LEU cc_start: 0.8710 (tp) cc_final: 0.8298 (tp) REVERT: O 158 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8856 (tp-100) REVERT: O 193 LEU cc_start: 0.8737 (mm) cc_final: 0.8470 (mm) REVERT: O 199 ASP cc_start: 0.8837 (m-30) cc_final: 0.8477 (m-30) REVERT: O 201 PHE cc_start: 0.8803 (t80) cc_final: 0.7978 (t80) REVERT: O 205 LYS cc_start: 0.9250 (mmtm) cc_final: 0.9019 (mmtp) REVERT: O 209 ARG cc_start: 0.8833 (ptm-80) cc_final: 0.8469 (ptm-80) REVERT: P 87 TYR cc_start: 0.8708 (t80) cc_final: 0.8419 (t80) REVERT: P 104 MET cc_start: 0.9135 (mmp) cc_final: 0.8623 (mmp) REVERT: P 106 TRP cc_start: 0.8530 (t60) cc_final: 0.8123 (t60) REVERT: P 115 LEU cc_start: 0.4660 (tp) cc_final: 0.4418 (tp) REVERT: P 132 MET cc_start: 0.6624 (tmm) cc_final: 0.6152 (tmm) REVERT: P 137 ILE cc_start: 0.8384 (mm) cc_final: 0.8154 (mm) REVERT: P 170 MET cc_start: 0.7808 (mtt) cc_final: 0.7278 (mpp) REVERT: P 205 LYS cc_start: 0.7954 (pttm) cc_final: 0.7668 (ptpp) REVERT: P 207 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7885 (mm-40) REVERT: P 222 ARG cc_start: 0.6331 (mmm-85) cc_final: 0.5604 (mmm160) REVERT: P 272 ILE cc_start: 0.7664 (mp) cc_final: 0.7388 (mp) outliers start: 0 outliers final: 0 residues processed: 1149 average time/residue: 0.2164 time to fit residues: 389.7385 Evaluate side-chains 1066 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1066 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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: 0.7980 chunk 261 optimal weight: 2.9990 chunk 360 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 385 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 158 GLN E 204 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 GLN ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS N 62 HIS O 62 HIS O 102 GLN O 208 GLN P 157 HIS P 242 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.198339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151853 restraints weight = 72463.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.157528 restraints weight = 45570.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161564 restraints weight = 31985.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.164425 restraints weight = 24180.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.166503 restraints weight = 19420.200| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34119 Z= 0.165 Angle : 0.735 17.252 46515 Z= 0.393 Chirality : 0.050 0.254 5006 Planarity : 0.005 0.075 5714 Dihedral : 14.904 170.382 5007 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.40 (0.13), residues: 3851 helix: 0.77 (0.12), residues: 1877 sheet: -0.69 (0.17), residues: 855 loop : -1.53 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 189 TYR 0.025 0.001 TYR K 107 PHE 0.049 0.002 PHE N 201 TRP 0.045 0.002 TRP F 78 HIS 0.018 0.001 HIS G 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (34119) covalent geometry : angle 0.73489 / 0.39 (46515) hydrogen bonds : bond 0.04224 / 2.89 ( 1746) hydrogen bonds : angle 5.47512 / 3.97 ( 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 1149 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1149 time to evaluate : 1.207 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: A 60 ILE cc_start: 0.8689 (mm) cc_final: 0.8276 (mm) REVERT: A 66 ASP cc_start: 0.7410 (t0) cc_final: 0.7205 (t70) REVERT: A 79 VAL cc_start: 0.8094 (t) cc_final: 0.7590 (p) REVERT: A 81 THR cc_start: 0.8724 (p) cc_final: 0.8480 (t) REVERT: A 92 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8384 (mtpp) REVERT: A 100 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7457 (mtm-85) REVERT: A 107 TYR cc_start: 0.8400 (t80) cc_final: 0.8080 (t80) REVERT: A 113 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7692 (mmmm) REVERT: A 116 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6998 (tm-30) REVERT: A 118 ASP cc_start: 0.7499 (p0) cc_final: 0.7270 (p0) REVERT: A 129 GLN cc_start: 0.7880 (tt0) cc_final: 0.7582 (tt0) REVERT: A 132 MET cc_start: 0.8220 (mmm) cc_final: 0.7927 (mmm) REVERT: A 135 LEU cc_start: 0.8798 (mt) cc_final: 0.8456 (mt) REVERT: A 155 ARG cc_start: 0.8613 (tpt90) cc_final: 0.7623 (mmm160) REVERT: A 158 GLN cc_start: 0.8836 (tt0) cc_final: 0.8468 (tt0) REVERT: A 164 LEU cc_start: 0.8352 (mt) cc_final: 0.8107 (mt) REVERT: A 184 THR cc_start: 0.8508 (m) cc_final: 0.8272 (p) REVERT: A 188 LYS cc_start: 0.6981 (mmmt) cc_final: 0.6330 (mmtm) REVERT: A 203 PHE cc_start: 0.8366 (t80) cc_final: 0.7972 (t80) REVERT: A 226 TYR cc_start: 0.6457 (p90) cc_final: 0.6082 (p90) REVERT: A 260 ARG cc_start: 0.7424 (ptm160) cc_final: 0.7203 (ptm160) REVERT: B 15 TRP cc_start: 0.7787 (m100) cc_final: 0.7304 (m100) REVERT: B 40 CYS cc_start: 0.7471 (t) cc_final: 0.6858 (p) REVERT: B 63 TRP cc_start: 0.7750 (m100) cc_final: 0.6057 (m100) REVERT: B 64 GLN cc_start: 0.7106 (tp40) cc_final: 0.6621 (mm110) REVERT: B 65 VAL cc_start: 0.8661 (t) cc_final: 0.8279 (t) REVERT: B 70 TYR cc_start: 0.8278 (t80) cc_final: 0.7827 (t80) REVERT: B 86 ILE cc_start: 0.8877 (pt) cc_final: 0.8099 (mm) REVERT: B 87 TYR cc_start: 0.8082 (t80) cc_final: 0.7758 (t80) REVERT: B 89 GLU cc_start: 0.7614 (tt0) cc_final: 0.7099 (tt0) REVERT: B 90 ARG cc_start: 0.8723 (tpt-90) cc_final: 0.8149 (tpp80) REVERT: B 92 LYS cc_start: 0.8797 (tppt) cc_final: 0.8209 (tptp) REVERT: B 102 GLN cc_start: 0.8436 (mp10) cc_final: 0.8190 (mp10) REVERT: B 104 MET cc_start: 0.8591 (mmp) cc_final: 0.8181 (mmp) REVERT: B 105 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8621 (mtpp) REVERT: B 129 GLN cc_start: 0.8456 (pt0) cc_final: 0.8045 (pt0) REVERT: B 131 LEU cc_start: 0.9015 (tt) cc_final: 0.8590 (tt) REVERT: B 132 MET cc_start: 0.8608 (mmp) cc_final: 0.7838 (mmp) REVERT: B 137 ILE cc_start: 0.8526 (tt) cc_final: 0.8283 (tt) REVERT: B 138 GLU cc_start: 0.7873 (tp30) cc_final: 0.7578 (tp30) REVERT: B 139 HIS cc_start: 0.8522 (t70) cc_final: 0.7974 (t70) REVERT: B 164 LEU cc_start: 0.8952 (tp) cc_final: 0.8736 (tp) REVERT: B 165 GLU cc_start: 0.7967 (tp30) cc_final: 0.7646 (tp30) REVERT: B 178 LEU cc_start: 0.9183 (mm) cc_final: 0.8812 (mm) REVERT: B 188 LYS cc_start: 0.7036 (mmtp) cc_final: 0.6657 (mmtp) REVERT: B 189 ARG cc_start: 0.7556 (ptp90) cc_final: 0.7274 (ptp90) REVERT: B 198 MET cc_start: 0.8074 (tpt) cc_final: 0.7619 (tpp) REVERT: B 204 ASN cc_start: 0.8056 (p0) cc_final: 0.7626 (p0) REVERT: B 208 GLN cc_start: 0.8491 (mt0) cc_final: 0.7983 (mt0) REVERT: C 5 ILE cc_start: 0.9236 (mt) cc_final: 0.8994 (mt) REVERT: C 7 LEU cc_start: 0.8641 (tt) cc_final: 0.8286 (tt) REVERT: C 11 GLU cc_start: 0.8455 (tp30) cc_final: 0.7442 (tp30) REVERT: C 39 GLN cc_start: 0.8477 (tp40) cc_final: 0.7805 (tp40) REVERT: C 110 PHE cc_start: 0.7907 (m-80) cc_final: 0.7616 (m-80) REVERT: C 132 MET cc_start: 0.8364 (ppp) cc_final: 0.7918 (ppp) REVERT: C 157 HIS cc_start: 0.8038 (m90) cc_final: 0.7665 (m-70) REVERT: C 190 LYS cc_start: 0.6818 (mttm) cc_final: 0.6478 (mmmt) REVERT: C 198 MET cc_start: 0.8578 (tpt) cc_final: 0.8049 (tpt) REVERT: C 199 ASP cc_start: 0.8883 (m-30) cc_final: 0.8629 (m-30) REVERT: C 202 ILE cc_start: 0.8267 (mt) cc_final: 0.8037 (mt) REVERT: C 244 LEU cc_start: 0.8193 (mm) cc_final: 0.7826 (mm) REVERT: D 209 ARG cc_start: 0.8738 (mmp-170) cc_final: 0.8467 (mmp-170) REVERT: D 218 GLN cc_start: 0.8480 (mm110) cc_final: 0.7905 (mm110) REVERT: D 226 TYR cc_start: 0.7256 (p90) cc_final: 0.6287 (p90) REVERT: D 254 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7993 (ttmt) REVERT: D 262 LEU cc_start: 0.7984 (mp) cc_final: 0.7725 (mp) REVERT: D 263 VAL cc_start: 0.8436 (m) cc_final: 0.8191 (t) REVERT: E 10 GLU cc_start: 0.7910 (tp30) cc_final: 0.7427 (tp30) REVERT: E 12 HIS cc_start: 0.8269 (t70) cc_final: 0.7142 (t70) REVERT: E 15 TRP cc_start: 0.8625 (m-10) cc_final: 0.8233 (m-10) REVERT: E 16 HIS cc_start: 0.7940 (m-70) cc_final: 0.6972 (m170) REVERT: E 100 ARG cc_start: 0.8763 (ptp90) cc_final: 0.8562 (ptp-170) REVERT: E 150 GLN cc_start: 0.8103 (mm110) cc_final: 0.7441 (mm110) REVERT: E 158 GLN cc_start: 0.8397 (mp10) cc_final: 0.8182 (mp10) REVERT: E 178 LEU cc_start: 0.8940 (mt) cc_final: 0.8671 (mt) REVERT: E 201 PHE cc_start: 0.8509 (t80) cc_final: 0.7761 (t80) REVERT: E 205 LYS cc_start: 0.8815 (mttt) cc_final: 0.8405 (mmtp) REVERT: E 212 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8383 (tm-30) REVERT: E 224 CYS cc_start: 0.5731 (p) cc_final: 0.5175 (p) REVERT: F 23 HIS cc_start: 0.7678 (t70) cc_final: 0.7282 (t70) REVERT: F 65 VAL cc_start: 0.7121 (t) cc_final: 0.6724 (p) REVERT: F 104 MET cc_start: 0.8032 (ptm) cc_final: 0.7498 (ppp) REVERT: F 105 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8858 (mttt) REVERT: F 158 GLN cc_start: 0.9244 (mt0) cc_final: 0.8916 (mt0) REVERT: F 202 ILE cc_start: 0.8500 (mt) cc_final: 0.8016 (mt) REVERT: F 205 LYS cc_start: 0.8603 (mtmm) cc_final: 0.7908 (mtmt) REVERT: F 207 GLN cc_start: 0.8433 (mp10) cc_final: 0.8025 (mp10) REVERT: F 208 GLN cc_start: 0.8340 (tt0) cc_final: 0.8113 (tt0) REVERT: F 212 GLN cc_start: 0.8528 (pp30) cc_final: 0.8258 (pp30) REVERT: F 230 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8039 (mmmm) REVERT: F 233 HIS cc_start: 0.7739 (m-70) cc_final: 0.7507 (m-70) REVERT: F 237 TRP cc_start: 0.8254 (m100) cc_final: 0.7868 (m100) REVERT: F 242 GLN cc_start: 0.7336 (tt0) cc_final: 0.6707 (pp30) REVERT: F 243 VAL cc_start: 0.8443 (t) cc_final: 0.7651 (p) REVERT: F 244 LEU cc_start: 0.8220 (tt) cc_final: 0.7880 (tt) REVERT: F 256 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7935 (ttm110) REVERT: G 48 MET cc_start: -0.0495 (ppp) cc_final: -0.1363 (ppp) REVERT: G 70 TYR cc_start: 0.6702 (t80) cc_final: 0.4145 (t80) REVERT: G 85 LEU cc_start: 0.7329 (tp) cc_final: 0.7010 (tp) REVERT: G 110 PHE cc_start: 0.7814 (m-80) cc_final: 0.6789 (m-10) REVERT: G 116 GLN cc_start: 0.8196 (mt0) cc_final: 0.7821 (tp40) REVERT: G 130 LEU cc_start: 0.8897 (pp) cc_final: 0.8691 (pp) REVERT: G 131 LEU cc_start: 0.9305 (mt) cc_final: 0.9066 (mt) REVERT: G 152 LEU cc_start: 0.8418 (tp) cc_final: 0.8079 (tp) REVERT: G 157 HIS cc_start: 0.8847 (p90) cc_final: 0.8577 (p90) REVERT: G 164 LEU cc_start: 0.8550 (mt) cc_final: 0.8123 (mt) REVERT: G 168 ILE cc_start: 0.7854 (mt) cc_final: 0.7553 (mt) REVERT: G 170 MET cc_start: 0.7436 (mmp) cc_final: 0.7197 (mmp) REVERT: G 171 PHE cc_start: 0.6972 (m-80) cc_final: 0.6455 (m-80) REVERT: G 197 PRO cc_start: 0.8497 (Cg_exo) cc_final: 0.8239 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8905 (m-30) cc_final: 0.8464 (m-30) REVERT: G 201 PHE cc_start: 0.8754 (t80) cc_final: 0.8314 (t80) REVERT: G 205 LYS cc_start: 0.9264 (mmtm) cc_final: 0.8987 (mmtm) REVERT: G 209 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8608 (ttp80) REVERT: G 210 ILE cc_start: 0.8694 (pt) cc_final: 0.8402 (pt) REVERT: H 62 HIS cc_start: 0.7241 (p-80) cc_final: 0.7006 (p-80) REVERT: H 78 TRP cc_start: 0.7136 (m-10) cc_final: 0.6731 (m-10) REVERT: H 87 TYR cc_start: 0.8498 (t80) cc_final: 0.8008 (t80) REVERT: H 104 MET cc_start: 0.9096 (mmp) cc_final: 0.8446 (mmp) REVERT: H 106 TRP cc_start: 0.8397 (t60) cc_final: 0.7612 (t60) REVERT: H 207 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7605 (mm-40) REVERT: H 223 PHE cc_start: 0.7479 (m-80) cc_final: 0.7034 (m-80) REVERT: H 238 GLN cc_start: 0.6918 (mm110) cc_final: 0.6627 (mm-40) REVERT: H 267 LYS cc_start: 0.7657 (ptmm) cc_final: 0.7402 (ptmm) REVERT: I 60 ILE cc_start: 0.8902 (mp) cc_final: 0.8308 (mm) REVERT: I 66 ASP cc_start: 0.7577 (t70) cc_final: 0.7026 (t70) REVERT: I 79 VAL cc_start: 0.8131 (t) cc_final: 0.7541 (p) REVERT: I 80 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6306 (tm-30) REVERT: I 81 THR cc_start: 0.8731 (p) cc_final: 0.8429 (t) REVERT: I 86 ILE cc_start: 0.8558 (pt) cc_final: 0.7942 (mp) REVERT: I 98 GLU cc_start: 0.8182 (mp0) cc_final: 0.7807 (mp0) REVERT: I 100 ARG cc_start: 0.8314 (mtt90) cc_final: 0.7901 (mtm180) REVERT: I 113 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7620 (mmmm) REVERT: I 116 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6707 (tm-30) REVERT: I 143 ILE cc_start: 0.8773 (tp) cc_final: 0.8242 (tp) REVERT: I 146 ASN cc_start: 0.8089 (m110) cc_final: 0.7358 (m110) REVERT: I 152 LEU cc_start: 0.7381 (pt) cc_final: 0.6393 (mp) REVERT: I 153 VAL cc_start: 0.8936 (m) cc_final: 0.8728 (p) REVERT: I 155 ARG cc_start: 0.8315 (tpt90) cc_final: 0.7548 (mmm160) REVERT: I 158 GLN cc_start: 0.9004 (tt0) cc_final: 0.8578 (tt0) REVERT: I 159 THR cc_start: 0.8581 (p) cc_final: 0.8321 (m) REVERT: I 160 LEU cc_start: 0.8709 (tt) cc_final: 0.8443 (tt) REVERT: I 164 LEU cc_start: 0.8586 (mt) cc_final: 0.8338 (mt) REVERT: I 183 ILE cc_start: 0.8982 (mt) cc_final: 0.8552 (mm) REVERT: I 190 LYS cc_start: 0.7698 (mptt) cc_final: 0.7332 (mptt) REVERT: I 198 MET cc_start: 0.8592 (ttm) cc_final: 0.8227 (tpp) REVERT: I 203 PHE cc_start: 0.8348 (t80) cc_final: 0.7969 (t80) REVERT: I 208 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7975 (tm-30) REVERT: I 209 ARG cc_start: 0.7272 (tpp80) cc_final: 0.6930 (tpp80) REVERT: I 258 THR cc_start: 0.8742 (p) cc_final: 0.8519 (p) REVERT: I 264 ILE cc_start: 0.7974 (mm) cc_final: 0.7708 (mm) REVERT: J 7 LEU cc_start: 0.7790 (mt) cc_final: 0.7448 (mt) REVERT: J 13 ASN cc_start: 0.7123 (m-40) cc_final: 0.6716 (m-40) REVERT: J 40 CYS cc_start: 0.7265 (t) cc_final: 0.6917 (t) REVERT: J 62 HIS cc_start: 0.7362 (t-90) cc_final: 0.6952 (t-90) REVERT: J 63 TRP cc_start: 0.7646 (m100) cc_final: 0.6023 (m100) REVERT: J 82 ASN cc_start: 0.8087 (p0) cc_final: 0.7851 (p0) REVERT: J 86 ILE cc_start: 0.9011 (pt) cc_final: 0.8138 (mm) REVERT: J 92 LYS cc_start: 0.8909 (tptp) cc_final: 0.8524 (tptp) REVERT: J 100 ARG cc_start: 0.8629 (ptp90) cc_final: 0.8164 (ptp90) REVERT: J 104 MET cc_start: 0.8349 (tpp) cc_final: 0.7548 (tpp) REVERT: J 106 TRP cc_start: 0.8402 (t60) cc_final: 0.8181 (t60) REVERT: J 116 GLN cc_start: 0.7474 (tm-30) cc_final: 0.6976 (tm-30) REVERT: J 131 LEU cc_start: 0.8618 (tt) cc_final: 0.8296 (tt) REVERT: J 139 HIS cc_start: 0.8540 (t70) cc_final: 0.8030 (t70) REVERT: J 158 GLN cc_start: 0.8455 (mp-120) cc_final: 0.7885 (tp40) REVERT: J 162 ASN cc_start: 0.8852 (m110) cc_final: 0.8045 (m-40) REVERT: J 165 GLU cc_start: 0.8098 (tp30) cc_final: 0.7843 (tp30) REVERT: J 178 LEU cc_start: 0.9260 (mm) cc_final: 0.8942 (mm) REVERT: J 183 ILE cc_start: 0.8774 (mt) cc_final: 0.8523 (mt) REVERT: J 184 THR cc_start: 0.9028 (p) cc_final: 0.8561 (p) REVERT: J 189 ARG cc_start: 0.7058 (mtm-85) cc_final: 0.6473 (ptp-170) REVERT: J 198 MET cc_start: 0.8085 (tpt) cc_final: 0.7836 (tpp) REVERT: J 204 ASN cc_start: 0.8263 (m110) cc_final: 0.7286 (p0) REVERT: J 207 GLN cc_start: 0.7967 (mp10) cc_final: 0.7731 (mp10) REVERT: J 208 GLN cc_start: 0.8056 (pt0) cc_final: 0.7724 (pt0) REVERT: K 15 TRP cc_start: 0.8298 (m100) cc_final: 0.7643 (m100) REVERT: K 34 GLU cc_start: 0.8681 (pt0) cc_final: 0.8239 (pp20) REVERT: K 35 ASP cc_start: 0.8657 (m-30) cc_final: 0.8298 (m-30) REVERT: K 208 GLN cc_start: 0.8679 (tt0) cc_final: 0.7924 (mt0) REVERT: L 209 ARG cc_start: 0.8702 (mmp-170) cc_final: 0.8377 (mmp-170) REVERT: L 223 PHE cc_start: 0.5778 (p90) cc_final: 0.5380 (p90) REVERT: L 226 TYR cc_start: 0.7191 (p90) cc_final: 0.6009 (p90) REVERT: L 248 ASP cc_start: 0.8041 (p0) cc_final: 0.7827 (p0) REVERT: L 254 LYS cc_start: 0.8307 (tmtt) cc_final: 0.7709 (tppt) REVERT: L 269 VAL cc_start: 0.7725 (m) cc_final: 0.7463 (m) REVERT: M 7 LEU cc_start: 0.8343 (tt) cc_final: 0.7633 (tt) REVERT: M 11 GLU cc_start: 0.8345 (mp0) cc_final: 0.7994 (mp0) REVERT: M 14 LYS cc_start: 0.8275 (mttp) cc_final: 0.7534 (mtpt) REVERT: M 16 HIS cc_start: 0.7758 (m-70) cc_final: 0.7319 (m170) REVERT: M 18 ASP cc_start: 0.7627 (t70) cc_final: 0.7324 (t70) REVERT: M 36 ILE cc_start: 0.8594 (mt) cc_final: 0.8343 (mt) REVERT: M 78 TRP cc_start: 0.6805 (m-90) cc_final: 0.6476 (m-90) REVERT: M 109 MET cc_start: 0.8758 (tmm) cc_final: 0.8076 (ttt) REVERT: M 154 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8731 (mm-30) REVERT: M 155 ARG cc_start: 0.8586 (ttt180) cc_final: 0.8335 (mtt90) REVERT: M 158 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7846 (tm-30) REVERT: M 159 THR cc_start: 0.8822 (m) cc_final: 0.8290 (p) REVERT: M 174 PHE cc_start: 0.7348 (t80) cc_final: 0.6988 (t80) REVERT: M 178 LEU cc_start: 0.8861 (mt) cc_final: 0.8248 (mt) REVERT: M 202 ILE cc_start: 0.8789 (mm) cc_final: 0.8247 (mm) REVERT: M 205 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8414 (mtmm) REVERT: M 206 GLU cc_start: 0.8552 (pt0) cc_final: 0.8098 (pt0) REVERT: M 207 GLN cc_start: 0.8615 (mm110) cc_final: 0.8368 (mm110) REVERT: M 209 ARG cc_start: 0.8742 (tmt170) cc_final: 0.8361 (ttp80) REVERT: N 23 HIS cc_start: 0.7737 (t70) cc_final: 0.7475 (t70) REVERT: N 65 VAL cc_start: 0.7445 (t) cc_final: 0.7168 (p) REVERT: N 104 MET cc_start: 0.8092 (ptm) cc_final: 0.7459 (ppp) REVERT: N 105 LYS cc_start: 0.9353 (mtmm) cc_final: 0.9021 (mttt) REVERT: N 201 PHE cc_start: 0.7630 (t80) cc_final: 0.7367 (t80) REVERT: N 203 PHE cc_start: 0.8032 (t80) cc_final: 0.7739 (t80) REVERT: N 210 ILE cc_start: 0.8328 (pt) cc_final: 0.8040 (pt) REVERT: N 213 GLN cc_start: 0.8794 (mt0) cc_final: 0.8202 (mt0) REVERT: N 233 HIS cc_start: 0.7702 (m90) cc_final: 0.7384 (m-70) REVERT: N 236 GLU cc_start: 0.7780 (mp0) cc_final: 0.7420 (mp0) REVERT: N 242 GLN cc_start: 0.7664 (tt0) cc_final: 0.7115 (pp30) REVERT: N 243 VAL cc_start: 0.8541 (t) cc_final: 0.7956 (p) REVERT: N 244 LEU cc_start: 0.8285 (tt) cc_final: 0.8058 (tt) REVERT: N 256 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7743 (ttm110) REVERT: N 266 ASN cc_start: 0.8149 (p0) cc_final: 0.7849 (m-40) REVERT: O 40 CYS cc_start: 0.5881 (t) cc_final: 0.5678 (t) REVERT: O 48 MET cc_start: -0.1473 (ppp) cc_final: -0.1922 (ppp) REVERT: O 85 LEU cc_start: 0.7750 (tp) cc_final: 0.7369 (tp) REVERT: O 110 PHE cc_start: 0.8143 (m-80) cc_final: 0.7740 (m-10) REVERT: O 132 MET cc_start: 0.8121 (tmm) cc_final: 0.7627 (tmm) REVERT: O 152 LEU cc_start: 0.8650 (tp) cc_final: 0.8364 (tp) REVERT: O 193 LEU cc_start: 0.8751 (mm) cc_final: 0.8504 (mm) REVERT: O 199 ASP cc_start: 0.8817 (m-30) cc_final: 0.8414 (m-30) REVERT: O 208 GLN cc_start: 0.8686 (tm130) cc_final: 0.8460 (tm-30) REVERT: O 209 ARG cc_start: 0.8799 (ptm-80) cc_final: 0.8440 (ptm-80) REVERT: P 87 TYR cc_start: 0.8699 (t80) cc_final: 0.8408 (t80) REVERT: P 104 MET cc_start: 0.9121 (mmp) cc_final: 0.8584 (mmp) REVERT: P 106 TRP cc_start: 0.8484 (t60) cc_final: 0.8050 (t60) REVERT: P 132 MET cc_start: 0.6644 (tmm) cc_final: 0.6128 (tmm) REVERT: P 137 ILE cc_start: 0.8365 (mm) cc_final: 0.8146 (mm) REVERT: P 170 MET cc_start: 0.7791 (mtt) cc_final: 0.7226 (mpp) REVERT: P 172 ASN cc_start: 0.8774 (m-40) cc_final: 0.8448 (p0) REVERT: P 207 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7935 (mm-40) REVERT: P 222 ARG cc_start: 0.6490 (mmm-85) cc_final: 0.5805 (mmm160) REVERT: P 223 PHE cc_start: 0.6717 (m-80) cc_final: 0.6299 (m-80) REVERT: P 233 HIS cc_start: 0.6621 (m-70) cc_final: 0.6385 (m-70) REVERT: P 238 GLN cc_start: 0.6523 (mm110) cc_final: 0.6284 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1149 average time/residue: 0.2128 time to fit residues: 383.4251 Evaluate side-chains 1076 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1076 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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: 0.9990 chunk 36 optimal weight: 0.6980 chunk 297 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 251 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 302 optimal weight: 0.3980 chunk 245 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 242 GLN C 102 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 204 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** 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** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 ASN M 69 HIS N 158 GLN O 208 GLN O 211 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.199225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152081 restraints weight = 70520.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.157927 restraints weight = 44228.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.161957 restraints weight = 30975.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.164906 restraints weight = 23467.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.167030 restraints weight = 18763.864| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34119 Z= 0.156 Angle : 0.741 15.395 46515 Z= 0.396 Chirality : 0.050 0.259 5006 Planarity : 0.005 0.131 5714 Dihedral : 14.917 170.403 5007 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -0.38 (0.13), residues: 3851 helix: 0.79 (0.12), residues: 1863 sheet: -0.68 (0.18), residues: 819 loop : -1.50 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 260 TYR 0.024 0.001 TYR K 107 PHE 0.050 0.002 PHE N 201 TRP 0.046 0.002 TRP B 106 HIS 0.019 0.001 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (34119) covalent geometry : angle 0.74101 / 0.40 (46515) hydrogen bonds : bond 0.04207 / 2.89 ( 1746) hydrogen bonds : angle 5.48040 / 3.97 ( 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 1144 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1144 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8142 (mm) REVERT: A 64 GLN cc_start: 0.6387 (pm20) cc_final: 0.6109 (pm20) REVERT: A 66 ASP cc_start: 0.7446 (t0) cc_final: 0.7242 (t70) REVERT: A 81 THR cc_start: 0.8647 (p) cc_final: 0.8344 (t) REVERT: A 92 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8429 (mtpp) REVERT: A 100 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7450 (mtm-85) REVERT: A 104 MET cc_start: 0.8466 (ttm) cc_final: 0.7871 (ttm) REVERT: A 107 TYR cc_start: 0.8328 (t80) cc_final: 0.7778 (t80) REVERT: A 113 LYS cc_start: 0.7985 (mmmm) cc_final: 0.7661 (mmmm) REVERT: A 116 GLN cc_start: 0.7374 (tm-30) cc_final: 0.6966 (tm-30) REVERT: A 118 ASP cc_start: 0.7474 (p0) cc_final: 0.7254 (p0) REVERT: A 129 GLN cc_start: 0.7956 (tt0) cc_final: 0.7615 (tt0) REVERT: A 132 MET cc_start: 0.8288 (mmm) cc_final: 0.8013 (mmm) REVERT: A 155 ARG cc_start: 0.8630 (tpt90) cc_final: 0.7633 (mmm160) REVERT: A 158 GLN cc_start: 0.8847 (tt0) cc_final: 0.8451 (tt0) REVERT: A 164 LEU cc_start: 0.8377 (mt) cc_final: 0.8110 (mt) REVERT: A 184 THR cc_start: 0.8496 (m) cc_final: 0.8214 (p) REVERT: A 188 LYS cc_start: 0.6873 (mmmt) cc_final: 0.6312 (mmtm) REVERT: A 203 PHE cc_start: 0.8369 (t80) cc_final: 0.7931 (t80) REVERT: A 226 TYR cc_start: 0.6546 (p90) cc_final: 0.6146 (p90) REVERT: A 254 LYS cc_start: 0.8385 (tmmt) cc_final: 0.7963 (tmmt) REVERT: A 260 ARG cc_start: 0.7379 (ptm160) cc_final: 0.7174 (ptm160) REVERT: B 15 TRP cc_start: 0.7765 (m100) cc_final: 0.7264 (m100) REVERT: B 40 CYS cc_start: 0.7461 (t) cc_final: 0.6855 (p) REVERT: B 63 TRP cc_start: 0.7821 (m100) cc_final: 0.6199 (m100) REVERT: B 64 GLN cc_start: 0.7108 (tp40) cc_final: 0.6326 (mm-40) REVERT: B 70 TYR cc_start: 0.8252 (t80) cc_final: 0.7748 (t80) REVERT: B 86 ILE cc_start: 0.8874 (pt) cc_final: 0.7966 (mm) REVERT: B 87 TYR cc_start: 0.7873 (t80) cc_final: 0.7628 (t80) REVERT: B 89 GLU cc_start: 0.7748 (tt0) cc_final: 0.7150 (tt0) REVERT: B 90 ARG cc_start: 0.8748 (tpt-90) cc_final: 0.8128 (tpp80) REVERT: B 92 LYS cc_start: 0.8846 (tppt) cc_final: 0.8209 (tptp) REVERT: B 102 GLN cc_start: 0.8257 (mp10) cc_final: 0.8036 (mp10) REVERT: B 104 MET cc_start: 0.8519 (mmp) cc_final: 0.8068 (mmp) REVERT: B 105 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8626 (mtpp) REVERT: B 129 GLN cc_start: 0.8438 (pt0) cc_final: 0.8045 (pt0) REVERT: B 131 LEU cc_start: 0.8945 (tt) cc_final: 0.8418 (tt) REVERT: B 132 MET cc_start: 0.8611 (mmp) cc_final: 0.7876 (mmp) REVERT: B 138 GLU cc_start: 0.7858 (tp30) cc_final: 0.7555 (tp30) REVERT: B 139 HIS cc_start: 0.8501 (t70) cc_final: 0.7956 (t70) REVERT: B 154 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8160 (mm-30) REVERT: B 158 GLN cc_start: 0.8318 (mp-120) cc_final: 0.7921 (mp10) REVERT: B 165 GLU cc_start: 0.7992 (tp30) cc_final: 0.7664 (tp30) REVERT: B 174 PHE cc_start: 0.7495 (t80) cc_final: 0.7275 (t80) REVERT: B 178 LEU cc_start: 0.9238 (mm) cc_final: 0.8845 (mm) REVERT: B 188 LYS cc_start: 0.6968 (mmtp) cc_final: 0.6497 (mmtp) REVERT: B 189 ARG cc_start: 0.7494 (ptp90) cc_final: 0.6851 (ptp90) REVERT: B 198 MET cc_start: 0.8040 (tpt) cc_final: 0.7604 (tpp) REVERT: B 204 ASN cc_start: 0.8135 (p0) cc_final: 0.7830 (p0) REVERT: B 208 GLN cc_start: 0.8584 (mt0) cc_final: 0.8307 (mt0) REVERT: C 7 LEU cc_start: 0.8640 (tt) cc_final: 0.8305 (tt) REVERT: C 11 GLU cc_start: 0.8459 (tp30) cc_final: 0.7457 (tp30) REVERT: C 39 GLN cc_start: 0.8466 (tp40) cc_final: 0.7807 (tp40) REVERT: C 110 PHE cc_start: 0.7838 (m-80) cc_final: 0.7612 (m-80) REVERT: C 132 MET cc_start: 0.8410 (ppp) cc_final: 0.8002 (ppp) REVERT: C 157 HIS cc_start: 0.8061 (m90) cc_final: 0.7644 (m-70) REVERT: C 190 LYS cc_start: 0.6807 (mttm) cc_final: 0.6481 (mmmt) REVERT: C 244 LEU cc_start: 0.8123 (mm) cc_final: 0.7724 (mm) REVERT: D 209 ARG cc_start: 0.8717 (mmp-170) cc_final: 0.8439 (mmp-170) REVERT: D 223 PHE cc_start: 0.5942 (p90) cc_final: 0.5535 (p90) REVERT: D 224 CYS cc_start: 0.7097 (p) cc_final: 0.6852 (p) REVERT: D 226 TYR cc_start: 0.7227 (p90) cc_final: 0.6178 (p90) REVERT: D 254 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7944 (ttmt) REVERT: D 262 LEU cc_start: 0.7937 (mp) cc_final: 0.7734 (mm) REVERT: D 263 VAL cc_start: 0.8496 (m) cc_final: 0.8256 (t) REVERT: E 10 GLU cc_start: 0.7956 (tp30) cc_final: 0.7462 (tp30) REVERT: E 12 HIS cc_start: 0.8300 (t70) cc_final: 0.7125 (t70) REVERT: E 15 TRP cc_start: 0.8609 (m-10) cc_final: 0.8202 (m-10) REVERT: E 16 HIS cc_start: 0.7946 (m-70) cc_final: 0.6962 (m170) REVERT: E 89 GLU cc_start: 0.7609 (pm20) cc_final: 0.6882 (mp0) REVERT: E 97 GLN cc_start: 0.8060 (pm20) cc_final: 0.7795 (pm20) REVERT: E 100 ARG cc_start: 0.8755 (ptp90) cc_final: 0.8186 (ptp-170) REVERT: E 133 LYS cc_start: 0.9097 (ptpp) cc_final: 0.8778 (pttm) REVERT: E 150 GLN cc_start: 0.8138 (mm110) cc_final: 0.7439 (mm110) REVERT: E 158 GLN cc_start: 0.8414 (mp10) cc_final: 0.8163 (mp10) REVERT: E 178 LEU cc_start: 0.8943 (mt) cc_final: 0.8663 (mt) REVERT: E 201 PHE cc_start: 0.8572 (t80) cc_final: 0.8095 (t80) REVERT: E 205 LYS cc_start: 0.8810 (mttt) cc_final: 0.8479 (mmtp) REVERT: E 212 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8489 (tm-30) REVERT: E 224 CYS cc_start: 0.5960 (p) cc_final: 0.5294 (p) REVERT: F 23 HIS cc_start: 0.7575 (t70) cc_final: 0.7260 (t70) REVERT: F 65 VAL cc_start: 0.6984 (t) cc_final: 0.6574 (p) REVERT: F 86 ILE cc_start: 0.8124 (pt) cc_final: 0.7495 (tp) REVERT: F 104 MET cc_start: 0.8062 (ptm) cc_final: 0.7503 (ppp) REVERT: F 105 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8833 (mttt) REVERT: F 164 LEU cc_start: 0.8411 (mt) cc_final: 0.8199 (mt) REVERT: F 230 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8042 (mmmm) REVERT: F 233 HIS cc_start: 0.7754 (m-70) cc_final: 0.7521 (m-70) REVERT: F 236 GLU cc_start: 0.7857 (pm20) cc_final: 0.7436 (pm20) REVERT: F 237 TRP cc_start: 0.8259 (m100) cc_final: 0.7995 (m100) REVERT: F 242 GLN cc_start: 0.7389 (tt0) cc_final: 0.6740 (pp30) REVERT: F 243 VAL cc_start: 0.8442 (t) cc_final: 0.7328 (m) REVERT: F 244 LEU cc_start: 0.8230 (tt) cc_final: 0.7829 (tt) REVERT: F 256 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7941 (ttm110) REVERT: F 260 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6910 (ptp-110) REVERT: G 22 LEU cc_start: 0.7895 (mm) cc_final: 0.7629 (mm) REVERT: G 48 MET cc_start: -0.0531 (ppp) cc_final: -0.1338 (ppp) REVERT: G 85 LEU cc_start: 0.7359 (tp) cc_final: 0.7029 (tp) REVERT: G 110 PHE cc_start: 0.7679 (m-80) cc_final: 0.7060 (m-10) REVERT: G 130 LEU cc_start: 0.8876 (pp) cc_final: 0.8639 (pp) REVERT: G 131 LEU cc_start: 0.9314 (mt) cc_final: 0.9076 (mt) REVERT: G 154 GLU cc_start: 0.8771 (pp20) cc_final: 0.8227 (pp20) REVERT: G 155 ARG cc_start: 0.9042 (mtp-110) cc_final: 0.8661 (ptp-110) REVERT: G 157 HIS cc_start: 0.8884 (p90) cc_final: 0.8566 (p90) REVERT: G 158 GLN cc_start: 0.9223 (tp40) cc_final: 0.8989 (tp40) REVERT: G 170 MET cc_start: 0.7552 (mmp) cc_final: 0.7270 (mmp) REVERT: G 171 PHE cc_start: 0.6975 (m-80) cc_final: 0.6531 (m-80) REVERT: G 209 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8637 (ttp80) REVERT: G 210 ILE cc_start: 0.8744 (pt) cc_final: 0.8313 (pt) REVERT: H 62 HIS cc_start: 0.7064 (p-80) cc_final: 0.6150 (p-80) REVERT: H 78 TRP cc_start: 0.7089 (m-10) cc_final: 0.5697 (m-10) REVERT: H 87 TYR cc_start: 0.8497 (t80) cc_final: 0.7959 (t80) REVERT: H 104 MET cc_start: 0.9096 (mmp) cc_final: 0.8430 (mmp) REVERT: H 106 TRP cc_start: 0.8410 (t60) cc_final: 0.7193 (t60) REVERT: H 109 MET cc_start: 0.7348 (tpt) cc_final: 0.6777 (tpt) REVERT: H 110 PHE cc_start: 0.7697 (m-10) cc_final: 0.6619 (m-10) REVERT: H 202 ILE cc_start: 0.9162 (mt) cc_final: 0.8730 (mm) REVERT: H 205 LYS cc_start: 0.8289 (mtmm) cc_final: 0.7887 (mtmt) REVERT: H 207 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7623 (mm-40) REVERT: H 223 PHE cc_start: 0.7516 (m-80) cc_final: 0.6997 (m-80) REVERT: H 267 LYS cc_start: 0.7749 (ptmm) cc_final: 0.7470 (ttpp) REVERT: I 60 ILE cc_start: 0.8885 (mp) cc_final: 0.8310 (mm) REVERT: I 66 ASP cc_start: 0.7525 (t70) cc_final: 0.6962 (t70) REVERT: I 79 VAL cc_start: 0.8132 (t) cc_final: 0.7468 (p) REVERT: I 80 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6344 (tm-30) REVERT: I 81 THR cc_start: 0.8768 (p) cc_final: 0.8458 (t) REVERT: I 86 ILE cc_start: 0.8549 (pt) cc_final: 0.7926 (mp) REVERT: I 98 GLU cc_start: 0.8163 (mp0) cc_final: 0.7771 (mp0) REVERT: I 100 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7900 (mtm180) REVERT: I 113 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7608 (mmmm) REVERT: I 116 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6537 (tm-30) REVERT: I 118 ASP cc_start: 0.7511 (p0) cc_final: 0.7294 (p0) REVERT: I 152 LEU cc_start: 0.7364 (pt) cc_final: 0.6388 (mp) REVERT: I 155 ARG cc_start: 0.8312 (tpt90) cc_final: 0.7553 (mmm160) REVERT: I 158 GLN cc_start: 0.9004 (tt0) cc_final: 0.8571 (tt0) REVERT: I 160 LEU cc_start: 0.8697 (tt) cc_final: 0.8437 (tt) REVERT: I 183 ILE cc_start: 0.8968 (mt) cc_final: 0.8522 (mm) REVERT: I 190 LYS cc_start: 0.7795 (mptt) cc_final: 0.7459 (mptt) REVERT: I 198 MET cc_start: 0.8632 (ttm) cc_final: 0.8279 (tpp) REVERT: I 203 PHE cc_start: 0.8358 (t80) cc_final: 0.7953 (t80) REVERT: I 209 ARG cc_start: 0.7357 (tpp80) cc_final: 0.7150 (tpp80) REVERT: I 258 THR cc_start: 0.8748 (p) cc_final: 0.8518 (p) REVERT: J 40 CYS cc_start: 0.7237 (t) cc_final: 0.6892 (t) REVERT: J 62 HIS cc_start: 0.7439 (t-90) cc_final: 0.6973 (t-90) REVERT: J 63 TRP cc_start: 0.7669 (m100) cc_final: 0.6070 (m100) REVERT: J 64 GLN cc_start: 0.7011 (tp40) cc_final: 0.5477 (mm-40) REVERT: J 70 TYR cc_start: 0.8382 (t80) cc_final: 0.6565 (t80) REVERT: J 71 GLU cc_start: 0.7858 (pp20) cc_final: 0.6522 (pp20) REVERT: J 82 ASN cc_start: 0.8002 (p0) cc_final: 0.7801 (p0) REVERT: J 86 ILE cc_start: 0.8979 (pt) cc_final: 0.8073 (mm) REVERT: J 92 LYS cc_start: 0.8917 (tptp) cc_final: 0.8547 (tptp) REVERT: J 100 ARG cc_start: 0.8609 (ptp90) cc_final: 0.8081 (ptp90) REVERT: J 104 MET cc_start: 0.8330 (tpp) cc_final: 0.7577 (tpp) REVERT: J 106 TRP cc_start: 0.8453 (t60) cc_final: 0.8217 (t60) REVERT: J 116 GLN cc_start: 0.7509 (tm-30) cc_final: 0.6578 (tm-30) REVERT: J 131 LEU cc_start: 0.8630 (tt) cc_final: 0.8321 (tt) REVERT: J 139 HIS cc_start: 0.8334 (t70) cc_final: 0.8011 (t70) REVERT: J 162 ASN cc_start: 0.8885 (m110) cc_final: 0.8678 (m-40) REVERT: J 165 GLU cc_start: 0.8313 (tp30) cc_final: 0.7871 (tp30) REVERT: J 174 PHE cc_start: 0.7523 (t80) cc_final: 0.7298 (t80) REVERT: J 178 LEU cc_start: 0.9260 (mm) cc_final: 0.8894 (mm) REVERT: J 186 ASN cc_start: 0.7860 (m-40) cc_final: 0.7418 (m-40) REVERT: J 189 ARG cc_start: 0.7114 (mtm-85) cc_final: 0.6666 (ptp-170) REVERT: J 198 MET cc_start: 0.8106 (tpt) cc_final: 0.7823 (tpp) REVERT: J 204 ASN cc_start: 0.8369 (m110) cc_final: 0.7280 (p0) REVERT: J 208 GLN cc_start: 0.8063 (pt0) cc_final: 0.7771 (pt0) REVERT: K 15 TRP cc_start: 0.8257 (m100) cc_final: 0.7586 (m100) REVERT: K 34 GLU cc_start: 0.8690 (pt0) cc_final: 0.8252 (pp20) REVERT: K 35 ASP cc_start: 0.8640 (m-30) cc_final: 0.8275 (m-30) REVERT: K 110 PHE cc_start: 0.7972 (m-80) cc_final: 0.7742 (m-80) REVERT: K 190 LYS cc_start: 0.6560 (mttm) cc_final: 0.6217 (mmmt) REVERT: L 226 TYR cc_start: 0.6563 (p90) cc_final: 0.5939 (p90) REVERT: L 254 LYS cc_start: 0.8336 (tmtt) cc_final: 0.7710 (tppt) REVERT: L 262 LEU cc_start: 0.8138 (mm) cc_final: 0.7823 (mm) REVERT: L 269 VAL cc_start: 0.7750 (m) cc_final: 0.7469 (m) REVERT: M 7 LEU cc_start: 0.8386 (tt) cc_final: 0.7622 (tt) REVERT: M 11 GLU cc_start: 0.8373 (mp0) cc_final: 0.7821 (mp0) REVERT: M 16 HIS cc_start: 0.7765 (m-70) cc_final: 0.7322 (m170) REVERT: M 18 ASP cc_start: 0.7642 (t70) cc_final: 0.7326 (t70) REVERT: M 22 LEU cc_start: 0.8025 (pp) cc_final: 0.7813 (pp) REVERT: M 36 ILE cc_start: 0.8535 (mt) cc_final: 0.8271 (mt) REVERT: M 109 MET cc_start: 0.8757 (tmm) cc_final: 0.8078 (ttt) REVERT: M 154 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8729 (mm-30) REVERT: M 155 ARG cc_start: 0.8630 (ttt180) cc_final: 0.8357 (mtt90) REVERT: M 158 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7840 (tm-30) REVERT: M 159 THR cc_start: 0.8808 (m) cc_final: 0.8265 (p) REVERT: M 174 PHE cc_start: 0.7409 (t80) cc_final: 0.7012 (t80) REVERT: M 178 LEU cc_start: 0.8867 (mt) cc_final: 0.8255 (mt) REVERT: M 202 ILE cc_start: 0.8743 (mm) cc_final: 0.8300 (mm) REVERT: M 205 LYS cc_start: 0.9028 (mtmm) cc_final: 0.7956 (mtmm) REVERT: M 206 GLU cc_start: 0.8576 (pt0) cc_final: 0.7913 (pt0) REVERT: M 207 GLN cc_start: 0.8518 (mm110) cc_final: 0.8289 (mm110) REVERT: M 209 ARG cc_start: 0.8756 (tmt170) cc_final: 0.8384 (ttp80) REVERT: N 23 HIS cc_start: 0.7739 (t70) cc_final: 0.7449 (t70) REVERT: N 65 VAL cc_start: 0.7483 (t) cc_final: 0.7237 (p) REVERT: N 104 MET cc_start: 0.8176 (ptm) cc_final: 0.7580 (ppp) REVERT: N 105 LYS cc_start: 0.9330 (mtmm) cc_final: 0.8918 (mttt) REVERT: N 157 HIS cc_start: 0.7672 (m90) cc_final: 0.7401 (m90) REVERT: N 183 ILE cc_start: 0.7149 (mt) cc_final: 0.6944 (mt) REVERT: N 202 ILE cc_start: 0.8391 (mt) cc_final: 0.7873 (mt) REVERT: N 203 PHE cc_start: 0.7894 (t80) cc_final: 0.7164 (t80) REVERT: N 206 GLU cc_start: 0.8136 (pp20) cc_final: 0.6614 (pp20) REVERT: N 213 GLN cc_start: 0.8789 (mt0) cc_final: 0.8440 (mt0) REVERT: N 233 HIS cc_start: 0.7735 (m90) cc_final: 0.7366 (m-70) REVERT: N 236 GLU cc_start: 0.7793 (mp0) cc_final: 0.7412 (mp0) REVERT: N 242 GLN cc_start: 0.7699 (tt0) cc_final: 0.7098 (pp30) REVERT: N 243 VAL cc_start: 0.8541 (t) cc_final: 0.8001 (p) REVERT: N 244 LEU cc_start: 0.8315 (tt) cc_final: 0.8089 (tt) REVERT: N 256 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7735 (ttm110) REVERT: N 266 ASN cc_start: 0.8136 (p0) cc_final: 0.7920 (m-40) REVERT: N 270 LYS cc_start: 0.8136 (mptt) cc_final: 0.7633 (mmtp) REVERT: O 48 MET cc_start: -0.1485 (ppp) cc_final: -0.1900 (ppp) REVERT: O 132 MET cc_start: 0.8081 (tmm) cc_final: 0.7567 (tmm) REVERT: O 152 LEU cc_start: 0.8709 (tp) cc_final: 0.8310 (tp) REVERT: O 158 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8731 (tp-100) REVERT: O 193 LEU cc_start: 0.8734 (mm) cc_final: 0.8469 (mm) REVERT: O 208 GLN cc_start: 0.8727 (tm130) cc_final: 0.8470 (tm-30) REVERT: O 209 ARG cc_start: 0.8813 (ptm-80) cc_final: 0.8512 (ptm-80) REVERT: O 211 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8180 (tp40) REVERT: P 87 TYR cc_start: 0.8706 (t80) cc_final: 0.8405 (t80) REVERT: P 104 MET cc_start: 0.9097 (mmp) cc_final: 0.8545 (mmp) REVERT: P 106 TRP cc_start: 0.8471 (t60) cc_final: 0.8043 (t60) REVERT: P 132 MET cc_start: 0.6643 (tmm) cc_final: 0.6126 (tmm) REVERT: P 137 ILE cc_start: 0.8375 (mm) cc_final: 0.8162 (mm) REVERT: P 170 MET cc_start: 0.7617 (mtt) cc_final: 0.7142 (mpp) REVERT: P 172 ASN cc_start: 0.8830 (m-40) cc_final: 0.8516 (p0) REVERT: P 207 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7863 (mm-40) REVERT: P 222 ARG cc_start: 0.6493 (mmm-85) cc_final: 0.5792 (mmm160) REVERT: P 223 PHE cc_start: 0.6783 (m-80) cc_final: 0.5436 (m-80) REVERT: P 233 HIS cc_start: 0.6585 (m-70) cc_final: 0.6365 (m-70) REVERT: P 236 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7449 (pp20) REVERT: P 270 LYS cc_start: 0.6625 (mmtm) cc_final: 0.6374 (mmtm) REVERT: P 272 ILE cc_start: 0.7951 (mp) cc_final: 0.7746 (mp) outliers start: 0 outliers final: 0 residues processed: 1144 average time/residue: 0.1962 time to fit residues: 353.4844 Evaluate side-chains 1067 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1067 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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: 3.9990 chunk 300 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 380 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 273 optimal weight: 0.6980 chunk 356 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 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 ** 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** E 204 ASN F 17 GLN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN J 242 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 GLN ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN L 162 ASN M 69 HIS ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 HIS O 208 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 = 0.4519 r_free = 0.4519 target = 0.197958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.151135 restraints weight = 70143.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.156974 restraints weight = 43560.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161038 restraints weight = 30380.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.163934 restraints weight = 22866.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.165903 restraints weight = 18256.835| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.5000 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= 0.164 Angle : 0.761 14.729 46515 Z= 0.407 Chirality : 0.051 0.630 5006 Planarity : 0.005 0.093 5714 Dihedral : 14.944 170.901 5007 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % 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: -0.45 (0.13), residues: 3851 helix: 0.71 (0.12), residues: 1863 sheet: -0.60 (0.18), residues: 819 loop : -1.59 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG N 209 TYR 0.021 0.001 TYR O 70 PHE 0.038 0.002 PHE N 203 TRP 0.053 0.002 TRP M 63 HIS 0.018 0.001 HIS G 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (34119) covalent geometry : angle 0.76132 / 0.41 (46515) hydrogen bonds : bond 0.04258 / 2.92 ( 1746) hydrogen bonds : angle 5.54787 / 4.00 ( 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 1151 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1150 time to evaluate : 0.874 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: A 60 ILE cc_start: 0.8508 (mm) cc_final: 0.8206 (mm) REVERT: A 64 GLN cc_start: 0.6437 (pm20) cc_final: 0.6143 (pm20) REVERT: A 70 TYR cc_start: 0.7802 (t80) cc_final: 0.7590 (t80) REVERT: A 81 THR cc_start: 0.8665 (p) cc_final: 0.8322 (t) REVERT: A 92 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8496 (mtpp) REVERT: A 100 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7601 (mtm-85) REVERT: A 104 MET cc_start: 0.8478 (ttm) cc_final: 0.7866 (ttm) REVERT: A 107 TYR cc_start: 0.8341 (t80) cc_final: 0.8027 (t80) REVERT: A 113 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7712 (mmmm) REVERT: A 129 GLN cc_start: 0.8156 (tt0) cc_final: 0.7797 (tt0) REVERT: A 135 LEU cc_start: 0.8897 (mt) cc_final: 0.8502 (mt) REVERT: A 155 ARG cc_start: 0.8627 (tpt90) cc_final: 0.7630 (mmm160) REVERT: A 158 GLN cc_start: 0.8827 (tt0) cc_final: 0.8414 (tt0) REVERT: A 161 LYS cc_start: 0.8597 (tptt) cc_final: 0.8389 (tptt) REVERT: A 164 LEU cc_start: 0.8437 (mt) cc_final: 0.8199 (mt) REVERT: A 184 THR cc_start: 0.8542 (m) cc_final: 0.8233 (p) REVERT: A 188 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6103 (mmtm) REVERT: A 190 LYS cc_start: 0.7788 (ptpp) cc_final: 0.6489 (mtpt) REVERT: A 203 PHE cc_start: 0.8337 (t80) cc_final: 0.7911 (t80) REVERT: A 211 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7778 (tp-100) REVERT: A 226 TYR cc_start: 0.6452 (p90) cc_final: 0.6155 (p90) REVERT: A 254 LYS cc_start: 0.8362 (tmmt) cc_final: 0.7903 (tmmt) REVERT: B 15 TRP cc_start: 0.7767 (m100) cc_final: 0.7250 (m100) REVERT: B 40 CYS cc_start: 0.7526 (t) cc_final: 0.6888 (p) REVERT: B 63 TRP cc_start: 0.7819 (m100) cc_final: 0.6230 (m100) REVERT: B 64 GLN cc_start: 0.7064 (tp40) cc_final: 0.6311 (mm-40) REVERT: B 70 TYR cc_start: 0.8446 (t80) cc_final: 0.7752 (t80) REVERT: B 86 ILE cc_start: 0.8883 (pt) cc_final: 0.7919 (mm) REVERT: B 87 TYR cc_start: 0.7916 (t80) cc_final: 0.7661 (t80) REVERT: B 89 GLU cc_start: 0.7753 (tt0) cc_final: 0.7184 (tt0) REVERT: B 90 ARG cc_start: 0.8760 (tpt-90) cc_final: 0.8195 (tpp80) REVERT: B 92 LYS cc_start: 0.8859 (tppt) cc_final: 0.8218 (tptp) REVERT: B 98 GLU cc_start: 0.8197 (pm20) cc_final: 0.7959 (pm20) REVERT: B 102 GLN cc_start: 0.8285 (mp10) cc_final: 0.8053 (mp10) REVERT: B 104 MET cc_start: 0.8562 (mmp) cc_final: 0.8057 (mmp) REVERT: B 105 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8643 (mtpp) REVERT: B 129 GLN cc_start: 0.8440 (pt0) cc_final: 0.8041 (pt0) REVERT: B 131 LEU cc_start: 0.8944 (tt) cc_final: 0.8494 (tt) REVERT: B 132 MET cc_start: 0.8641 (mmp) cc_final: 0.7854 (mmp) REVERT: B 138 GLU cc_start: 0.7861 (tp30) cc_final: 0.7604 (tp30) REVERT: B 139 HIS cc_start: 0.8506 (t70) cc_final: 0.7989 (t70) REVERT: B 158 GLN cc_start: 0.8182 (mp-120) cc_final: 0.7753 (mp-120) REVERT: B 165 GLU cc_start: 0.8034 (tp30) cc_final: 0.7697 (tp30) REVERT: B 174 PHE cc_start: 0.7649 (t80) cc_final: 0.7440 (t80) REVERT: B 178 LEU cc_start: 0.9212 (mm) cc_final: 0.8809 (mm) REVERT: B 183 ILE cc_start: 0.8661 (mt) cc_final: 0.8304 (mt) REVERT: B 188 LYS cc_start: 0.6994 (mmtp) cc_final: 0.6404 (mmtp) REVERT: B 189 ARG cc_start: 0.7653 (ptp90) cc_final: 0.7401 (ptp90) REVERT: B 198 MET cc_start: 0.8047 (tpt) cc_final: 0.7612 (tpp) REVERT: B 204 ASN cc_start: 0.8147 (p0) cc_final: 0.7855 (p0) REVERT: B 208 GLN cc_start: 0.8554 (mt0) cc_final: 0.8306 (mt0) REVERT: C 7 LEU cc_start: 0.8644 (tt) cc_final: 0.8259 (tt) REVERT: C 11 GLU cc_start: 0.8570 (tp30) cc_final: 0.7651 (tp30) REVERT: C 39 GLN cc_start: 0.8559 (tp40) cc_final: 0.7919 (tp40) REVERT: C 110 PHE cc_start: 0.7862 (m-80) cc_final: 0.7612 (m-80) REVERT: C 132 MET cc_start: 0.8428 (ppp) cc_final: 0.8006 (ppp) REVERT: C 157 HIS cc_start: 0.8076 (m90) cc_final: 0.7661 (m-70) REVERT: C 190 LYS cc_start: 0.6745 (mttm) cc_final: 0.6494 (mmmt) REVERT: C 245 TRP cc_start: 0.8304 (m-90) cc_final: 0.8025 (m-90) REVERT: D 209 ARG cc_start: 0.8714 (mmp-170) cc_final: 0.8416 (mmp-170) REVERT: D 223 PHE cc_start: 0.5969 (p90) cc_final: 0.5567 (p90) REVERT: D 226 TYR cc_start: 0.7232 (p90) cc_final: 0.6165 (p90) REVERT: D 254 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7853 (ttmt) REVERT: D 266 ASN cc_start: 0.8396 (m110) cc_final: 0.8163 (m110) REVERT: E 10 GLU cc_start: 0.7972 (tp30) cc_final: 0.7469 (tp30) REVERT: E 12 HIS cc_start: 0.8341 (t70) cc_final: 0.7129 (t70) REVERT: E 15 TRP cc_start: 0.8615 (m-10) cc_final: 0.8318 (m-10) REVERT: E 16 HIS cc_start: 0.8025 (m-70) cc_final: 0.7049 (m170) REVERT: E 89 GLU cc_start: 0.7759 (pm20) cc_final: 0.7110 (mp0) REVERT: E 97 GLN cc_start: 0.8027 (pm20) cc_final: 0.7752 (pm20) REVERT: E 100 ARG cc_start: 0.8710 (ptp90) cc_final: 0.8172 (ptp-170) REVERT: E 150 GLN cc_start: 0.8139 (mm110) cc_final: 0.7544 (mm110) REVERT: E 178 LEU cc_start: 0.8850 (mt) cc_final: 0.8531 (mt) REVERT: E 212 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8487 (tm-30) REVERT: F 11 GLU cc_start: 0.7538 (mp0) cc_final: 0.7275 (mp0) REVERT: F 23 HIS cc_start: 0.7588 (t70) cc_final: 0.7262 (t70) REVERT: F 65 VAL cc_start: 0.7065 (t) cc_final: 0.6619 (p) REVERT: F 86 ILE cc_start: 0.8178 (pt) cc_final: 0.7430 (tp) REVERT: F 89 GLU cc_start: 0.6206 (tp30) cc_final: 0.5825 (tp30) REVERT: F 102 GLN cc_start: 0.8959 (mp-120) cc_final: 0.8456 (mp-120) REVERT: F 104 MET cc_start: 0.8096 (ptm) cc_final: 0.7493 (ppp) REVERT: F 105 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8817 (mttt) REVERT: F 150 GLN cc_start: 0.8006 (pt0) cc_final: 0.7790 (pt0) REVERT: F 164 LEU cc_start: 0.8430 (mt) cc_final: 0.8222 (mt) REVERT: F 230 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8040 (mmmm) REVERT: F 233 HIS cc_start: 0.7766 (m-70) cc_final: 0.7525 (m-70) REVERT: F 237 TRP cc_start: 0.8212 (m100) cc_final: 0.7951 (m100) REVERT: F 242 GLN cc_start: 0.7452 (tt0) cc_final: 0.6773 (pp30) REVERT: F 243 VAL cc_start: 0.8497 (t) cc_final: 0.7408 (m) REVERT: F 244 LEU cc_start: 0.8278 (tt) cc_final: 0.7825 (tt) REVERT: F 256 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7950 (ttm110) REVERT: G 48 MET cc_start: -0.0516 (ppp) cc_final: -0.1325 (ppp) REVERT: G 110 PHE cc_start: 0.7652 (m-80) cc_final: 0.6879 (m-10) REVERT: G 131 LEU cc_start: 0.9337 (mt) cc_final: 0.9068 (mt) REVERT: G 154 GLU cc_start: 0.8752 (pp20) cc_final: 0.8167 (pp20) REVERT: G 155 ARG cc_start: 0.9057 (mtp-110) cc_final: 0.8725 (ptp-110) REVERT: G 157 HIS cc_start: 0.8899 (p90) cc_final: 0.8568 (p90) REVERT: G 158 GLN cc_start: 0.9189 (tp40) cc_final: 0.8987 (tp-100) REVERT: G 168 ILE cc_start: 0.7584 (tp) cc_final: 0.7200 (pt) REVERT: G 171 PHE cc_start: 0.7058 (m-80) cc_final: 0.6477 (m-80) REVERT: G 175 GLU cc_start: 0.8541 (mp0) cc_final: 0.8174 (mm-30) REVERT: G 199 ASP cc_start: 0.8733 (m-30) cc_final: 0.8475 (m-30) REVERT: G 202 ILE cc_start: 0.8852 (mt) cc_final: 0.8640 (mt) REVERT: G 209 ARG cc_start: 0.9085 (ttp80) cc_final: 0.8590 (ttp80) REVERT: G 210 ILE cc_start: 0.8770 (pt) cc_final: 0.8347 (pt) REVERT: H 62 HIS cc_start: 0.7109 (p-80) cc_final: 0.6624 (p-80) REVERT: H 78 TRP cc_start: 0.7115 (m-10) cc_final: 0.5748 (m-10) REVERT: H 87 TYR cc_start: 0.8507 (t80) cc_final: 0.7969 (t80) REVERT: H 104 MET cc_start: 0.9083 (mmp) cc_final: 0.8407 (mmp) REVERT: H 106 TRP cc_start: 0.8401 (t60) cc_final: 0.7243 (t60) REVERT: H 110 PHE cc_start: 0.7764 (m-10) cc_final: 0.7388 (m-10) REVERT: H 207 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7634 (mm-40) REVERT: H 223 PHE cc_start: 0.7460 (m-80) cc_final: 0.7046 (m-80) REVERT: H 270 LYS cc_start: 0.7226 (mmpt) cc_final: 0.6936 (mmtm) REVERT: I 60 ILE cc_start: 0.8876 (mp) cc_final: 0.8305 (mm) REVERT: I 66 ASP cc_start: 0.7593 (t70) cc_final: 0.7071 (t70) REVERT: I 79 VAL cc_start: 0.8188 (t) cc_final: 0.7470 (p) REVERT: I 86 ILE cc_start: 0.8580 (pt) cc_final: 0.7990 (mp) REVERT: I 98 GLU cc_start: 0.8151 (mp0) cc_final: 0.7719 (mp0) REVERT: I 100 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7963 (mtm-85) REVERT: I 113 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7637 (mmmm) REVERT: I 152 LEU cc_start: 0.7391 (pt) cc_final: 0.6434 (mp) REVERT: I 153 VAL cc_start: 0.8708 (p) cc_final: 0.8415 (m) REVERT: I 155 ARG cc_start: 0.8405 (tpt90) cc_final: 0.7563 (mmm160) REVERT: I 158 GLN cc_start: 0.8920 (tt0) cc_final: 0.8520 (tt0) REVERT: I 160 LEU cc_start: 0.8667 (tt) cc_final: 0.8445 (tt) REVERT: I 164 LEU cc_start: 0.8613 (mt) cc_final: 0.8311 (mt) REVERT: I 174 PHE cc_start: 0.7052 (t80) cc_final: 0.6835 (t80) REVERT: I 190 LYS cc_start: 0.7994 (mptt) cc_final: 0.7779 (mmtt) REVERT: I 198 MET cc_start: 0.8666 (ttm) cc_final: 0.8314 (tpp) REVERT: I 203 PHE cc_start: 0.8343 (t80) cc_final: 0.7963 (t80) REVERT: I 258 THR cc_start: 0.8782 (p) cc_final: 0.8558 (p) REVERT: I 261 TYR cc_start: 0.7283 (m-10) cc_final: 0.7053 (m-10) REVERT: J 13 ASN cc_start: 0.7066 (m-40) cc_final: 0.6821 (m110) REVERT: J 40 CYS cc_start: 0.7297 (t) cc_final: 0.6915 (t) REVERT: J 62 HIS cc_start: 0.7531 (t-90) cc_final: 0.6994 (t-90) REVERT: J 63 TRP cc_start: 0.7699 (m100) cc_final: 0.6202 (m100) REVERT: J 64 GLN cc_start: 0.7007 (tp40) cc_final: 0.5461 (mm-40) REVERT: J 70 TYR cc_start: 0.8496 (t80) cc_final: 0.7691 (t80) REVERT: J 71 GLU cc_start: 0.7986 (pp20) cc_final: 0.7505 (pp20) REVERT: J 82 ASN cc_start: 0.8033 (p0) cc_final: 0.7778 (p0) REVERT: J 86 ILE cc_start: 0.8984 (pt) cc_final: 0.8154 (mm) REVERT: J 92 LYS cc_start: 0.8934 (tptp) cc_final: 0.8512 (tptp) REVERT: J 100 ARG cc_start: 0.8589 (ptp90) cc_final: 0.8230 (ptt-90) REVERT: J 102 GLN cc_start: 0.8596 (mp10) cc_final: 0.8078 (mp10) REVERT: J 104 MET cc_start: 0.8352 (tpp) cc_final: 0.7660 (tpp) REVERT: J 106 TRP cc_start: 0.8480 (t60) cc_final: 0.8241 (t60) REVERT: J 116 GLN cc_start: 0.7500 (tm-30) cc_final: 0.6571 (tm-30) REVERT: J 131 LEU cc_start: 0.8649 (tt) cc_final: 0.8321 (tt) REVERT: J 139 HIS cc_start: 0.8568 (t70) cc_final: 0.8083 (t70) REVERT: J 154 GLU cc_start: 0.8186 (mp0) cc_final: 0.7814 (pm20) REVERT: J 165 GLU cc_start: 0.8297 (tp30) cc_final: 0.7853 (tp30) REVERT: J 178 LEU cc_start: 0.9247 (mm) cc_final: 0.8847 (mm) REVERT: J 189 ARG cc_start: 0.7189 (mtm-85) cc_final: 0.6737 (ptp-170) REVERT: J 198 MET cc_start: 0.8153 (tpt) cc_final: 0.7842 (tpp) REVERT: J 204 ASN cc_start: 0.8412 (m110) cc_final: 0.7528 (p0) REVERT: J 205 LYS cc_start: 0.8496 (tptp) cc_final: 0.7947 (tptp) REVERT: J 208 GLN cc_start: 0.8062 (pt0) cc_final: 0.7687 (pt0) REVERT: K 22 LEU cc_start: 0.8375 (mm) cc_final: 0.8089 (mm) REVERT: K 34 GLU cc_start: 0.8682 (pt0) cc_final: 0.8264 (pp20) REVERT: K 35 ASP cc_start: 0.8634 (m-30) cc_final: 0.8392 (m-30) REVERT: K 109 MET cc_start: 0.8256 (tpp) cc_final: 0.7087 (ptp) REVERT: K 110 PHE cc_start: 0.8023 (m-80) cc_final: 0.7289 (m-80) REVERT: K 190 LYS cc_start: 0.6478 (mttm) cc_final: 0.6188 (mmmt) REVERT: K 208 GLN cc_start: 0.8646 (tt0) cc_final: 0.7923 (mt0) REVERT: K 245 TRP cc_start: 0.8096 (m-90) cc_final: 0.7660 (m-90) REVERT: L 209 ARG cc_start: 0.8736 (mmp-170) cc_final: 0.8519 (mmp-170) REVERT: L 223 PHE cc_start: 0.5713 (p90) cc_final: 0.5288 (p90) REVERT: L 224 CYS cc_start: 0.7072 (p) cc_final: 0.6855 (p) REVERT: L 226 TYR cc_start: 0.7067 (p90) cc_final: 0.6053 (p90) REVERT: L 254 LYS cc_start: 0.8303 (tmtt) cc_final: 0.7718 (tppt) REVERT: L 262 LEU cc_start: 0.8253 (mm) cc_final: 0.7927 (mm) REVERT: L 266 ASN cc_start: 0.8232 (m110) cc_final: 0.7985 (m110) REVERT: L 269 VAL cc_start: 0.7700 (m) cc_final: 0.7455 (m) REVERT: M 7 LEU cc_start: 0.8363 (tt) cc_final: 0.7575 (tt) REVERT: M 10 GLU cc_start: 0.8009 (tp30) cc_final: 0.7622 (tp30) REVERT: M 11 GLU cc_start: 0.8316 (mp0) cc_final: 0.7995 (mp0) REVERT: M 16 HIS cc_start: 0.7788 (m-70) cc_final: 0.7281 (m170) REVERT: M 18 ASP cc_start: 0.7664 (t70) cc_final: 0.7308 (t70) REVERT: M 22 LEU cc_start: 0.8036 (pp) cc_final: 0.7818 (pp) REVERT: M 36 ILE cc_start: 0.8575 (mt) cc_final: 0.8312 (mt) REVERT: M 39 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7736 (tm-30) REVERT: M 109 MET cc_start: 0.8760 (tmm) cc_final: 0.8109 (ttt) REVERT: M 130 LEU cc_start: 0.8128 (mt) cc_final: 0.7827 (mt) REVERT: M 133 LYS cc_start: 0.8794 (ptpp) cc_final: 0.8478 (pttp) REVERT: M 154 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8707 (mm-30) REVERT: M 158 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7838 (tm-30) REVERT: M 159 THR cc_start: 0.8660 (m) cc_final: 0.8044 (p) REVERT: M 174 PHE cc_start: 0.7359 (t80) cc_final: 0.7000 (t80) REVERT: M 178 LEU cc_start: 0.8867 (mt) cc_final: 0.8248 (mt) REVERT: M 195 THR cc_start: 0.8314 (m) cc_final: 0.8000 (p) REVERT: M 202 ILE cc_start: 0.8722 (mm) cc_final: 0.8321 (mm) REVERT: M 205 LYS cc_start: 0.9002 (mtmm) cc_final: 0.8333 (mtmm) REVERT: M 206 GLU cc_start: 0.8567 (pt0) cc_final: 0.8070 (pt0) REVERT: M 207 GLN cc_start: 0.8538 (mm110) cc_final: 0.8259 (mm110) REVERT: M 209 ARG cc_start: 0.8764 (tmt170) cc_final: 0.8388 (ttp80) REVERT: M 224 CYS cc_start: 0.5721 (p) cc_final: 0.5504 (p) REVERT: N 23 HIS cc_start: 0.7781 (t70) cc_final: 0.7512 (t70) REVERT: N 65 VAL cc_start: 0.7530 (t) cc_final: 0.7265 (p) REVERT: N 104 MET cc_start: 0.8192 (ptm) cc_final: 0.7528 (ppp) REVERT: N 157 HIS cc_start: 0.7470 (m90) cc_final: 0.7201 (m90) REVERT: N 202 ILE cc_start: 0.8307 (mt) cc_final: 0.8052 (mt) REVERT: N 203 PHE cc_start: 0.7806 (t80) cc_final: 0.7126 (t80) REVERT: N 206 GLU cc_start: 0.7889 (pp20) cc_final: 0.7455 (pp20) REVERT: N 213 GLN cc_start: 0.8868 (mt0) cc_final: 0.8371 (mt0) REVERT: N 233 HIS cc_start: 0.7730 (m90) cc_final: 0.7404 (m-70) REVERT: N 236 GLU cc_start: 0.7790 (mp0) cc_final: 0.7414 (mp0) REVERT: N 242 GLN cc_start: 0.7747 (tt0) cc_final: 0.7168 (pp30) REVERT: N 243 VAL cc_start: 0.8549 (t) cc_final: 0.8036 (p) REVERT: N 244 LEU cc_start: 0.8371 (tt) cc_final: 0.8118 (tt) REVERT: N 256 ARG cc_start: 0.8361 (ttm110) cc_final: 0.7746 (ttm110) REVERT: N 270 LYS cc_start: 0.8044 (mptt) cc_final: 0.7771 (mptt) REVERT: O 48 MET cc_start: -0.1493 (ppp) cc_final: -0.1904 (ppp) REVERT: O 115 LEU cc_start: 0.8692 (tp) cc_final: 0.8469 (tp) REVERT: O 132 MET cc_start: 0.8094 (tmm) cc_final: 0.7547 (tmm) REVERT: O 152 LEU cc_start: 0.8719 (tp) cc_final: 0.8369 (tp) REVERT: O 157 HIS cc_start: 0.9069 (p90) cc_final: 0.8803 (p90) REVERT: O 158 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8829 (tp-100) REVERT: O 193 LEU cc_start: 0.8741 (mm) cc_final: 0.8478 (mm) REVERT: O 199 ASP cc_start: 0.8678 (m-30) cc_final: 0.8311 (m-30) REVERT: O 205 LYS cc_start: 0.9265 (mmtm) cc_final: 0.8967 (mmtm) REVERT: O 208 GLN cc_start: 0.8733 (tm130) cc_final: 0.8481 (tm-30) REVERT: O 209 ARG cc_start: 0.8816 (ptm-80) cc_final: 0.8524 (ptm-80) REVERT: O 211 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8228 (tp40) REVERT: P 87 TYR cc_start: 0.8713 (t80) cc_final: 0.8383 (t80) REVERT: P 104 MET cc_start: 0.9091 (mmp) cc_final: 0.8526 (mmp) REVERT: P 106 TRP cc_start: 0.8479 (t60) cc_final: 0.8193 (t60) REVERT: P 109 MET cc_start: 0.7538 (mmm) cc_final: 0.6943 (mmm) REVERT: P 132 MET cc_start: 0.6712 (tmm) cc_final: 0.6204 (tmm) REVERT: P 170 MET cc_start: 0.7537 (mtt) cc_final: 0.7043 (mpp) REVERT: P 172 ASN cc_start: 0.8827 (m-40) cc_final: 0.8526 (p0) REVERT: P 207 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7848 (mm-40) REVERT: P 223 PHE cc_start: 0.6727 (m-80) cc_final: 0.6460 (m-80) REVERT: P 233 HIS cc_start: 0.6612 (m-70) cc_final: 0.6331 (m-70) outliers start: 1 outliers final: 1 residues processed: 1151 average time/residue: 0.2131 time to fit residues: 385.5047 Evaluate side-chains 1074 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1073 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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: 0.8980 chunk 8 optimal weight: 0.0270 chunk 262 optimal weight: 0.6980 chunk 193 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 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** 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** E 204 ASN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 HIS M 69 HIS N 158 GLN ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.196838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.149728 restraints weight = 70226.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155528 restraints weight = 43533.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.159587 restraints weight = 30345.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.162454 restraints weight = 22832.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.164436 restraints weight = 18303.727| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34119 Z= 0.161 Angle : 0.764 15.605 46515 Z= 0.408 Chirality : 0.051 0.476 5006 Planarity : 0.005 0.075 5714 Dihedral : 14.941 171.405 5007 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.45 (0.13), residues: 3851 helix: 0.72 (0.12), residues: 1863 sheet: -0.53 (0.18), residues: 816 loop : -1.65 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 209 TYR 0.017 0.001 TYR N 134 PHE 0.029 0.002 PHE N 201 TRP 0.047 0.002 TRP O 63 HIS 0.017 0.001 HIS G 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (34119) covalent geometry : angle 0.76420 / 0.41 (46515) hydrogen bonds : bond 0.04216 / 2.89 ( 1746) hydrogen bonds : angle 5.51344 / 3.98 ( 5114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8088.59 seconds wall clock time: 140 minutes 2.02 seconds (8402.02 seconds total)