Starting phenix.real_space_refine on Mon Sep 14 20:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpp_14860/09_2026/7zpp_14860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpp_14860/09_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_14860/09_2026/7zpp_14860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpp_14860/09_2026/7zpp_14860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zpp_14860/09_2026/7zpp_14860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpp_14860/09_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-2.2.1-6174/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: 7.79, per 1000 atoms: 0.23 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 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: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 18 through 27 removed outlier: 3.652A pdb=" N LEU A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 196 through 209 Processing helix chain 'A' and resid 209 through 216 removed outlier: 4.211A pdb=" N GLN A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 146 through 168 removed outlier: 3.714A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 196 through 216 Processing helix chain 'C' and resid 3 through 16 removed outlier: 4.118A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 146 through 168 removed outlier: 3.774A pdb=" N LEU C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 Processing helix chain 'C' and resid 196 through 219 removed outlier: 3.684A pdb=" N ILE C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 125 through 135 Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 173 through 187 Processing helix chain 'D' and resid 196 through 219 Processing helix chain 'E' and resid 1 through 3 No H-bonds generated for 'chain 'E' and resid 1 through 3' Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 95 through 110 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 125 through 136 Processing helix chain 'E' and resid 146 through 168 Processing helix chain 'E' and resid 173 through 187 Processing helix chain 'E' and resid 196 through 219 Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 18 through 27 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 40 through 46 removed outlier: 3.562A pdb=" N GLN F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 109 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 146 through 168 Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 196 through 218 Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'G' and resid 120 through 125 Processing helix chain 'G' and resid 125 through 136 Processing helix chain 'G' and resid 146 through 168 removed outlier: 3.658A pdb=" N LEU G 152 " --> pdb=" O GLN G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 187 Processing helix chain 'G' and resid 196 through 219 removed outlier: 3.722A pdb=" N ILE G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER G 214 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS G 217 " --> pdb=" O GLN G 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 120 through 125 Processing helix chain 'H' and resid 125 through 136 Processing helix chain 'H' and resid 146 through 168 removed outlier: 4.286A pdb=" N LEU H 152 " --> pdb=" O GLN H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 187 Processing helix chain 'H' and resid 196 through 208 Processing helix chain 'H' and resid 209 through 219 removed outlier: 4.444A pdb=" N GLN H 213 " --> pdb=" O ARG H 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 18 through 27 removed outlier: 3.652A pdb=" N LEU I 22 " --> pdb=" O ASP I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 40 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 120 through 125 Processing helix chain 'I' and resid 125 through 135 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 168 Processing helix chain 'I' and resid 169 through 171 No H-bonds generated for 'chain 'I' and resid 169 through 171' Processing helix chain 'I' and resid 173 through 187 Processing helix chain 'I' and resid 196 through 209 Processing helix chain 'I' and resid 209 through 216 removed outlier: 4.211A pdb=" N GLN I 213 " --> pdb=" O ARG I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 219 No H-bonds generated for 'chain 'I' and resid 217 through 219' Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 29 through 40 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 120 through 125 Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 146 through 168 removed outlier: 3.714A pdb=" N LEU J 152 " --> pdb=" O GLN J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 171 No H-bonds generated for 'chain 'J' and resid 169 through 171' Processing helix chain 'J' and resid 173 through 187 Processing helix chain 'J' and resid 196 through 216 Processing helix chain 'K' and resid 3 through 16 removed outlier: 4.118A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 40 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 95 through 110 Processing helix chain 'K' and resid 120 through 125 Processing helix chain 'K' and resid 125 through 136 Processing helix chain 'K' and resid 146 through 168 removed outlier: 3.775A pdb=" N LEU K 152 " --> pdb=" O GLN K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 187 Processing helix chain 'K' and resid 196 through 219 removed outlier: 3.682A pdb=" N ILE K 210 " --> pdb=" O GLU K 206 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 110 Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 125 through 135 Processing helix chain 'L' and resid 146 through 168 Processing helix chain 'L' and resid 173 through 187 Processing helix chain 'L' and resid 196 through 219 Processing helix chain 'M' and resid 4 through 16 Processing helix chain 'M' and resid 18 through 27 Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 95 through 110 Processing helix chain 'M' and resid 120 through 125 Processing helix chain 'M' and resid 125 through 136 Processing helix chain 'M' and resid 146 through 168 Processing helix chain 'M' and resid 173 through 187 Processing helix chain 'M' and resid 196 through 219 Processing helix chain 'M' and resid 267 through 269 No H-bonds generated for 'chain 'M' and resid 267 through 269' Processing helix chain 'N' and resid 5 through 16 Processing helix chain 'N' and resid 18 through 27 Processing helix chain 'N' and resid 29 through 40 Processing helix chain 'N' and resid 40 through 46 removed outlier: 3.562A pdb=" N GLN N 44 " --> pdb=" O CYS N 40 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN N 46 " --> pdb=" O VAL N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 109 Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 125 through 136 Processing helix chain 'N' and resid 146 through 168 Processing helix chain 'N' and resid 169 through 171 No H-bonds generated for 'chain 'N' and resid 169 through 171' Processing helix chain 'N' and resid 173 through 187 Processing helix chain 'N' and resid 196 through 218 Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 18 through 27 Processing helix chain 'O' and resid 29 through 40 Processing helix chain 'O' and resid 40 through 46 Processing helix chain 'O' and resid 95 through 110 Processing helix chain 'O' and resid 120 through 125 Processing helix chain 'O' and resid 125 through 136 Processing helix chain 'O' and resid 146 through 168 removed outlier: 3.658A pdb=" N LEU O 152 " --> pdb=" O GLN O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 187 Processing helix chain 'O' and resid 196 through 219 removed outlier: 3.722A pdb=" N ILE O 210 " --> pdb=" O GLU O 206 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER O 214 " --> pdb=" O ILE O 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER O 216 " --> pdb=" O GLN O 212 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS O 217 " --> pdb=" O GLN O 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 110 Processing helix chain 'P' and resid 120 through 125 Processing helix chain 'P' and resid 125 through 136 Processing helix chain 'P' and resid 146 through 168 removed outlier: 4.286A pdb=" N LEU P 152 " --> pdb=" O GLN P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 187 Processing helix chain 'P' and resid 196 through 208 Processing helix chain 'P' and resid 209 through 219 removed outlier: 4.444A pdb=" N GLN P 213 " --> pdb=" O ARG P 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.756A pdb=" N VAL A 77 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 79 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 64 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP A 63 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 224 removed outlier: 4.581A pdb=" N ARG A 222 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 246 removed outlier: 3.827A pdb=" N TRP A 245 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 264 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 260 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.546A pdb=" N GLU B 89 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 75 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 68 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TRP B 63 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 243 removed outlier: 5.058A pdb=" N GLY B 239 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR B 226 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG B 222 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 223 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 246 removed outlier: 3.775A pdb=" N TRP B 245 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 253 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 260 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 86 through 91 removed outlier: 3.804A pdb=" N ILE C 74 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 77 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP C 63 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 140 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.365A pdb=" N CYS C 224 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 223 " --> pdb=" O ILE C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 229 through 230 Processing sheet with id=AB2, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.605A pdb=" N TRP C 245 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.522A pdb=" N ILE D 74 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.855A pdb=" N VAL D 77 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP D 63 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 241 through 242 removed outlier: 3.544A pdb=" N PHE D 223 " --> pdb=" O ILE D 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 245 through 246 removed outlier: 4.241A pdb=" N TRP D 245 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 252 " --> pdb=" O TRP D 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR E 68 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR E 68 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TRP E 63 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 238 through 242 removed outlier: 6.109A pdb=" N CYS E 224 " --> pdb=" O PRO E 240 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE E 223 " --> pdb=" O ILE E 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 229 through 230 Processing sheet with id=AC2, first strand: chain 'E' and resid 245 through 246 removed outlier: 4.235A pdb=" N TRP E 245 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 68 through 70 removed outlier: 3.753A pdb=" N ILE F 74 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 68 through 70 removed outlier: 6.081A pdb=" N TRP F 63 " --> pdb=" O GLN F 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.800A pdb=" N ARG F 260 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 264 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 251 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS F 254 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL F 243 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 226 " --> pdb=" O GLN F 238 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS F 224 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AC7, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR G 87 " --> pdb=" O TRP G 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 74 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR G 87 " --> pdb=" O TRP G 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR G 68 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL G 77 " --> pdb=" O ASP G 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP G 66 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP G 63 " --> pdb=" O GLN G 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 86 through 87 removed outlier: 3.556A pdb=" N ILE H 74 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 86 through 87 removed outlier: 3.766A pdb=" N THR H 68 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL H 77 " --> pdb=" O ASP H 66 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP H 66 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP H 63 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 115 " --> pdb=" O GLU H 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR H 140 " --> pdb=" O LEU H 115 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 238 through 242 removed outlier: 6.237A pdb=" N CYS H 224 " --> pdb=" O PRO H 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 270 " --> pdb=" O TYR H 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AD4, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.883A pdb=" N TRP H 245 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 252 " --> pdb=" O TRP H 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 86 through 90 removed outlier: 3.757A pdb=" N VAL I 77 " --> pdb=" O ASP I 66 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP I 66 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL I 79 " --> pdb=" O GLN I 64 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN I 64 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP I 63 " --> pdb=" O GLN I 116 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 222 through 224 removed outlier: 4.581A pdb=" N ARG I 222 " --> pdb=" O VAL I 243 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 229 through 230 Processing sheet with id=AD8, first strand: chain 'I' and resid 245 through 246 removed outlier: 3.826A pdb=" N TRP I 245 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE I 264 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG I 260 " --> pdb=" O ASP I 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.547A pdb=" N GLU J 89 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE J 75 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR J 68 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP J 63 " --> pdb=" O GLN J 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 238 through 243 removed outlier: 5.059A pdb=" N GLY J 239 " --> pdb=" O TYR J 226 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N TYR J 226 " --> pdb=" O GLY J 239 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG J 222 " --> pdb=" O VAL J 243 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE J 223 " --> pdb=" O ILE J 272 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 245 through 246 removed outlier: 3.775A pdb=" N TRP J 245 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL J 253 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 260 " --> pdb=" O ASP J 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 86 through 91 removed outlier: 3.802A pdb=" N ILE K 74 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL K 77 " --> pdb=" O ASP K 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP K 63 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR K 140 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 238 through 242 removed outlier: 6.365A pdb=" N CYS K 224 " --> pdb=" O PRO K 240 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE K 223 " --> pdb=" O ILE K 272 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 229 through 230 Processing sheet with id=AE6, first strand: chain 'K' and resid 245 through 246 removed outlier: 3.605A pdb=" N TRP K 245 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.522A pdb=" N ILE L 74 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.854A pdb=" N VAL L 77 " --> pdb=" O ASP L 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP L 63 " --> pdb=" O GLN L 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 241 through 242 removed outlier: 3.545A pdb=" N PHE L 223 " --> pdb=" O ILE L 272 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 245 through 246 removed outlier: 4.241A pdb=" N TRP L 245 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL L 252 " --> pdb=" O TRP L 245 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR M 68 " --> pdb=" O ILE M 75 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR M 68 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP M 63 " --> pdb=" O GLN M 116 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 238 through 242 removed outlier: 6.109A pdb=" N CYS M 224 " --> pdb=" O PRO M 240 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE M 223 " --> pdb=" O ILE M 272 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 229 through 230 Processing sheet with id=AF6, first strand: chain 'M' and resid 245 through 246 removed outlier: 4.235A pdb=" N TRP M 245 " --> pdb=" O VAL M 252 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 68 through 70 removed outlier: 3.752A pdb=" N ILE N 74 " --> pdb=" O VAL N 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 68 through 70 removed outlier: 6.081A pdb=" N TRP N 63 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 260 through 265 removed outlier: 3.800A pdb=" N ARG N 260 " --> pdb=" O ASP N 255 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE N 264 " --> pdb=" O ILE N 251 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE N 251 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS N 254 " --> pdb=" O VAL N 243 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL N 243 " --> pdb=" O LYS N 254 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR N 226 " --> pdb=" O GLN N 238 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS N 224 " --> pdb=" O PRO N 240 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 229 through 230 Processing sheet with id=AG2, first strand: chain 'O' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR O 87 " --> pdb=" O TRP O 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE O 74 " --> pdb=" O VAL O 91 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR O 87 " --> pdb=" O TRP O 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR O 68 " --> pdb=" O ILE O 75 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL O 77 " --> pdb=" O ASP O 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP O 66 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP O 63 " --> pdb=" O GLN O 116 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 86 through 87 removed outlier: 3.556A pdb=" N ILE P 74 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 86 through 87 removed outlier: 3.766A pdb=" N THR P 68 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL P 77 " --> pdb=" O ASP P 66 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP P 66 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TRP P 63 " --> pdb=" O GLN P 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU P 115 " --> pdb=" O GLU P 138 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR P 140 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 238 through 242 removed outlier: 6.237A pdb=" N CYS P 224 " --> pdb=" O PRO P 240 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS P 270 " --> pdb=" O TYR P 225 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 229 through 230 Processing sheet with id=AG8, first strand: chain 'P' and resid 245 through 246 removed outlier: 3.882A pdb=" N TRP P 245 " --> pdb=" O VAL P 252 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL P 252 " --> pdb=" O TRP P 245 " (cutoff:3.500A) 1714 hydrogen bonds defined for protein. 5010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 3.90 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: 2.900 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 35.190 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- 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 : 0.658 13.062 46515 Z= 0.387 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 0.65770 / 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 : 1.162 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: 0.2345 time to fit residues: 451.9350 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 : 1.197 ------------------------------------------------------------------------------- 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 = 0.4648 r_free = 0.4648 target = 0.209213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.163033 restraints weight = 72579.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.169067 restraints weight = 46479.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.173338 restraints weight = 32816.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.176397 restraints weight = 24841.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.178698 restraints weight = 19877.396| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34119 Z= 0.163 Angle : 0.698 13.016 46515 Z= 0.373 Chirality : 0.049 0.316 5006 Planarity : 0.005 0.089 5714 Dihedral : 14.422 168.522 5007 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 0.35 % Allowed : 3.64 % 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: 0.10 (0.13), residues: 3851 helix: 1.22 (0.12), residues: 1871 sheet: -0.49 (0.17), residues: 890 loop : -1.36 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 256 TYR 0.043 0.002 TYR E 70 PHE 0.043 0.002 PHE K 174 TRP 0.034 0.002 TRP H 78 HIS 0.023 0.002 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (34119) covalent geometry : angle 0.69850 / 0.37 (46515) hydrogen bonds : bond 0.04547 / 3.06 ( 1746) hydrogen bonds : angle 5.43106 / 3.90 ( 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 1168 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1156 time to evaluate : 1.244 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8725 (mm) cc_final: 0.8484 (mm) REVERT: A 62 HIS cc_start: 0.7949 (t70) cc_final: 0.7683 (t70) REVERT: A 64 GLN cc_start: 0.6588 (pm20) cc_final: 0.6193 (pm20) REVERT: A 76 LEU cc_start: 0.7502 (mp) cc_final: 0.7273 (mm) REVERT: A 79 VAL cc_start: 0.7343 (t) cc_final: 0.6813 (m) REVERT: A 92 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8478 (mtpp) REVERT: A 100 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7457 (mtm180) REVERT: A 107 TYR cc_start: 0.8443 (t80) cc_final: 0.8157 (t80) REVERT: A 118 ASP cc_start: 0.7633 (p0) cc_final: 0.7350 (p0) REVERT: A 132 MET cc_start: 0.7770 (mmm) cc_final: 0.7521 (mmm) REVERT: A 143 ILE cc_start: 0.7775 (pt) cc_final: 0.7328 (pt) REVERT: A 146 ASN cc_start: 0.8013 (m110) cc_final: 0.7447 (m-40) REVERT: A 153 VAL cc_start: 0.8996 (m) cc_final: 0.8791 (m) REVERT: A 155 ARG cc_start: 0.8507 (tpt90) cc_final: 0.7495 (mmm160) REVERT: A 158 GLN cc_start: 0.8868 (tt0) cc_final: 0.8557 (tt0) REVERT: A 164 LEU cc_start: 0.8137 (mt) cc_final: 0.7900 (mt) REVERT: A 203 PHE cc_start: 0.8292 (t80) cc_final: 0.7971 (t80) REVERT: A 208 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 254 LYS cc_start: 0.8289 (pptt) cc_final: 0.7445 (ttpp) REVERT: A 260 ARG cc_start: 0.7338 (ptm160) cc_final: 0.7058 (ptm160) REVERT: B 15 TRP cc_start: 0.7776 (m100) cc_final: 0.7377 (m100) REVERT: B 42 VAL cc_start: 0.3066 (t) cc_final: 0.2730 (t) REVERT: B 63 TRP cc_start: 0.7784 (m100) cc_final: 0.6306 (m100) REVERT: B 64 GLN cc_start: 0.6574 (tp40) cc_final: 0.5848 (tp40) REVERT: B 65 VAL cc_start: 0.8679 (t) cc_final: 0.8452 (t) REVERT: B 75 ILE cc_start: 0.7739 (pt) cc_final: 0.7430 (mp) REVERT: B 92 LYS cc_start: 0.8709 (tppt) cc_final: 0.8263 (tptp) REVERT: B 101 VAL cc_start: 0.9013 (t) cc_final: 0.8783 (t) REVERT: B 104 MET cc_start: 0.8476 (mmp) cc_final: 0.8166 (mmp) REVERT: B 129 GLN cc_start: 0.8478 (pt0) cc_final: 0.8066 (pt0) REVERT: B 131 LEU cc_start: 0.8888 (tt) cc_final: 0.8681 (tt) REVERT: B 132 MET cc_start: 0.8378 (mmp) cc_final: 0.8140 (mmt) REVERT: B 137 ILE cc_start: 0.8480 (tt) cc_final: 0.8217 (tt) REVERT: B 161 LYS cc_start: 0.9096 (ptpt) cc_final: 0.8889 (ptpt) REVERT: B 164 LEU cc_start: 0.8746 (tp) cc_final: 0.8499 (tp) REVERT: B 165 GLU cc_start: 0.7671 (tp30) cc_final: 0.7392 (tp30) REVERT: B 178 LEU cc_start: 0.8962 (mm) cc_final: 0.8540 (mm) REVERT: B 198 MET cc_start: 0.8096 (tpt) cc_final: 0.7649 (tpp) REVERT: B 204 ASN cc_start: 0.7402 (p0) cc_final: 0.7038 (p0) REVERT: B 208 GLN cc_start: 0.8042 (pt0) cc_final: 0.7790 (pt0) REVERT: C 7 LEU cc_start: 0.8732 (tt) cc_final: 0.8511 (tt) REVERT: C 18 ASP cc_start: 0.8736 (t70) cc_final: 0.8485 (t70) REVERT: C 30 ARG cc_start: 0.9004 (ttt180) cc_final: 0.8711 (ttp80) REVERT: C 110 PHE cc_start: 0.7696 (m-80) cc_final: 0.7384 (m-80) REVERT: C 132 MET cc_start: 0.8185 (ppp) cc_final: 0.7719 (ppp) REVERT: C 206 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: C 209 ARG cc_start: 0.8422 (ptt90) cc_final: 0.7980 (ptt90) REVERT: D 63 TRP cc_start: 0.5252 (m100) cc_final: 0.4958 (m100) REVERT: D 86 ILE cc_start: 0.6873 (pt) cc_final: 0.6635 (mm) REVERT: D 203 PHE cc_start: 0.7849 (t80) cc_final: 0.7584 (t80) REVERT: D 218 GLN cc_start: 0.8404 (mm110) cc_final: 0.7900 (mm110) REVERT: D 223 PHE cc_start: 0.6331 (p90) cc_final: 0.5829 (p90) REVERT: D 226 TYR cc_start: 0.6602 (p90) cc_final: 0.6069 (p90) REVERT: D 254 LYS cc_start: 0.7708 (ttmm) cc_final: 0.7437 (tppt) REVERT: E 7 LEU cc_start: 0.7746 (tt) cc_final: 0.7498 (tt) REVERT: E 9 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7962 (mm-30) REVERT: E 10 GLU cc_start: 0.8090 (tp30) cc_final: 0.7801 (tp30) REVERT: E 13 ASN cc_start: 0.8768 (m110) cc_final: 0.8481 (m110) REVERT: E 18 ASP cc_start: 0.7367 (t70) cc_final: 0.7163 (t70) REVERT: E 36 ILE cc_start: 0.8132 (mt) cc_final: 0.7781 (tp) REVERT: E 87 TYR cc_start: 0.7103 (t80) cc_final: 0.6572 (t80) REVERT: E 110 PHE cc_start: 0.7678 (m-80) cc_final: 0.6880 (m-10) REVERT: E 150 GLN cc_start: 0.7601 (mm110) cc_final: 0.7293 (mm-40) REVERT: E 159 THR cc_start: 0.8598 (m) cc_final: 0.7976 (p) REVERT: E 199 ASP cc_start: 0.8393 (m-30) cc_final: 0.7612 (m-30) REVERT: E 236 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8464 (mm-30) REVERT: F 23 HIS cc_start: 0.7752 (t70) cc_final: 0.7473 (t70) REVERT: F 86 ILE cc_start: 0.6653 (pt) cc_final: 0.5925 (mm) REVERT: F 183 ILE cc_start: 0.5947 (mt) cc_final: 0.5736 (mt) REVERT: F 199 ASP cc_start: 0.8519 (m-30) cc_final: 0.8266 (m-30) REVERT: F 202 ILE cc_start: 0.8319 (mt) cc_final: 0.7959 (mt) REVERT: F 203 PHE cc_start: 0.7635 (t80) cc_final: 0.6847 (t80) REVERT: F 206 GLU cc_start: 0.7994 (pp20) cc_final: 0.7740 (pp20) REVERT: F 208 GLN cc_start: 0.8555 (tt0) cc_final: 0.8137 (tm-30) REVERT: F 233 HIS cc_start: 0.7549 (m90) cc_final: 0.7244 (m90) REVERT: F 236 GLU cc_start: 0.7834 (pm20) cc_final: 0.7516 (mp0) REVERT: F 243 VAL cc_start: 0.8057 (t) cc_final: 0.7438 (m) REVERT: F 244 LEU cc_start: 0.7782 (tt) cc_final: 0.7532 (tt) REVERT: F 256 ARG cc_start: 0.8309 (ttm110) cc_final: 0.7893 (ttm110) REVERT: F 260 ARG cc_start: 0.7101 (mtm110) cc_final: 0.6839 (mtm110) REVERT: F 270 LYS cc_start: 0.7863 (mttt) cc_final: 0.7288 (mttt) REVERT: G 10 GLU cc_start: 0.5632 (pt0) cc_final: 0.5294 (pt0) REVERT: G 48 MET cc_start: -0.0468 (ppp) cc_final: -0.1244 (ppp) REVERT: G 85 LEU cc_start: 0.7168 (tp) cc_final: 0.6780 (tp) REVERT: G 110 PHE cc_start: 0.7514 (m-80) cc_final: 0.7098 (m-80) REVERT: G 131 LEU cc_start: 0.9229 (mt) cc_final: 0.9015 (mt) REVERT: G 158 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8825 (pp30) REVERT: G 160 LEU cc_start: 0.8413 (pp) cc_final: 0.8203 (pp) REVERT: G 197 PRO cc_start: 0.8144 (Cg_exo) cc_final: 0.7796 (Cg_endo) REVERT: G 201 PHE cc_start: 0.8773 (t80) cc_final: 0.8286 (t80) REVERT: G 205 LYS cc_start: 0.9197 (mmtm) cc_final: 0.8948 (mmtp) REVERT: H 62 HIS cc_start: 0.7440 (t-90) cc_final: 0.6896 (t-170) REVERT: H 78 TRP cc_start: 0.5869 (m-10) cc_final: 0.5349 (m-10) REVERT: H 87 TYR cc_start: 0.8040 (t80) cc_final: 0.7649 (t80) REVERT: H 101 VAL cc_start: 0.8769 (p) cc_final: 0.8538 (p) REVERT: H 104 MET cc_start: 0.9129 (mmp) cc_final: 0.8534 (mmp) REVERT: H 109 MET cc_start: 0.8107 (tpt) cc_final: 0.7876 (tpt) REVERT: H 110 PHE cc_start: 0.7984 (m-10) cc_final: 0.7497 (m-10) REVERT: H 132 MET cc_start: 0.6113 (tmm) cc_final: 0.5841 (tmm) REVERT: H 164 LEU cc_start: 0.9167 (mm) cc_final: 0.8929 (pp) REVERT: I 60 ILE cc_start: 0.8499 (mt) cc_final: 0.8286 (mp) REVERT: I 79 VAL cc_start: 0.7575 (t) cc_final: 0.7121 (p) REVERT: I 92 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8462 (mtpp) REVERT: I 100 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7502 (mtm180) REVERT: I 101 VAL cc_start: 0.9299 (t) cc_final: 0.9061 (p) REVERT: I 104 MET cc_start: 0.8246 (ttm) cc_final: 0.8043 (ttm) 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: 0.7560 (p0) REVERT: I 132 MET cc_start: 0.7980 (mmm) cc_final: 0.7670 (mmm) REVERT: I 146 ASN cc_start: 0.7930 (m110) cc_final: 0.7130 (m-40) REVERT: I 158 GLN cc_start: 0.8969 (tt0) cc_final: 0.8683 (tt0) REVERT: I 164 LEU cc_start: 0.8313 (mt) cc_final: 0.8073 (mt) REVERT: I 203 PHE cc_start: 0.8423 (t80) cc_final: 0.7976 (t80) REVERT: I 208 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7771 (tm-30) REVERT: J 42 VAL cc_start: 0.4504 (t) cc_final: 0.4266 (t) REVERT: J 63 TRP cc_start: 0.7741 (m100) cc_final: 0.6487 (m100) REVERT: J 64 GLN cc_start: 0.6770 (tp40) cc_final: 0.5975 (tp40) REVERT: J 70 TYR cc_start: 0.7243 (t80) cc_final: 0.6487 (t80) REVERT: J 73 LYS cc_start: 0.7870 (mttt) cc_final: 0.7046 (mtmt) REVERT: J 86 ILE cc_start: 0.8657 (pt) cc_final: 0.7914 (mm) REVERT: J 92 LYS cc_start: 0.8789 (tptp) cc_final: 0.8448 (tptp) REVERT: J 101 VAL cc_start: 0.9081 (t) cc_final: 0.8821 (t) REVERT: J 104 MET cc_start: 0.8222 (tpp) cc_final: 0.7597 (tpp) REVERT: J 131 LEU cc_start: 0.8621 (tt) cc_final: 0.8272 (tt) REVERT: J 137 ILE cc_start: 0.8210 (tt) cc_final: 0.7980 (tt) REVERT: J 138 GLU cc_start: 0.7726 (tp30) cc_final: 0.7452 (tp30) REVERT: J 160 LEU cc_start: 0.8698 (tt) cc_final: 0.8354 (tt) REVERT: J 161 LYS cc_start: 0.9016 (ptpt) cc_final: 0.8643 (ptpt) REVERT: J 162 ASN cc_start: 0.8941 (m110) cc_final: 0.8661 (m-40) REVERT: J 174 PHE cc_start: 0.6799 (t80) cc_final: 0.6391 (t80) REVERT: J 178 LEU cc_start: 0.8995 (mm) cc_final: 0.8751 (mm) REVERT: J 184 THR cc_start: 0.8968 (p) cc_final: 0.8510 (p) REVERT: J 186 ASN cc_start: 0.7598 (m-40) cc_final: 0.7008 (m110) REVERT: J 189 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.6285 (mtm110) REVERT: J 198 MET cc_start: 0.8032 (tpt) cc_final: 0.7744 (tpp) REVERT: J 204 ASN cc_start: 0.7890 (m110) cc_final: 0.7265 (m110) REVERT: J 205 LYS cc_start: 0.8248 (tptp) cc_final: 0.7768 (tptp) REVERT: J 208 GLN cc_start: 0.7954 (pt0) cc_final: 0.7648 (pt0) REVERT: K 7 LEU cc_start: 0.8625 (tt) cc_final: 0.8405 (tt) REVERT: K 15 TRP cc_start: 0.8003 (m100) cc_final: 0.7607 (m100) REVERT: K 40 CYS cc_start: 0.8284 (m) cc_final: 0.7679 (p) REVERT: K 109 MET cc_start: 0.8033 (tpp) cc_final: 0.7182 (ptp) REVERT: K 110 PHE cc_start: 0.7419 (m-80) cc_final: 0.6969 (m-80) REVERT: K 132 MET cc_start: 0.7217 (ppp) cc_final: 0.6616 (ppp) REVERT: K 193 LEU cc_start: 0.7602 (mt) cc_final: 0.7022 (mm) REVERT: K 206 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: K 245 TRP cc_start: 0.8087 (m100) cc_final: 0.7874 (m100) REVERT: L 63 TRP cc_start: 0.6244 (m100) cc_final: 0.5918 (m100) REVERT: L 86 ILE cc_start: 0.6307 (pt) cc_final: 0.6081 (mm) REVERT: L 226 TYR cc_start: 0.6840 (p90) cc_final: 0.6054 (p90) REVERT: L 248 ASP cc_start: 0.8137 (p0) cc_final: 0.7901 (p0) REVERT: L 259 ASP cc_start: 0.8522 (m-30) cc_final: 0.8145 (m-30) REVERT: L 269 VAL cc_start: 0.7939 (m) cc_final: 0.7737 (m) REVERT: M 7 LEU cc_start: 0.7703 (tt) cc_final: 0.7459 (tt) REVERT: M 12 HIS cc_start: 0.7980 (t-90) cc_final: 0.7409 (t-170) REVERT: M 18 ASP cc_start: 0.7227 (t70) cc_final: 0.6814 (t70) REVERT: M 22 LEU cc_start: 0.7958 (pp) cc_final: 0.7668 (pp) REVERT: M 76 LEU cc_start: 0.7169 (tp) cc_final: 0.6357 (tp) REVERT: M 87 TYR cc_start: 0.7204 (t80) cc_final: 0.6642 (t80) REVERT: M 109 MET cc_start: 0.8430 (tmm) cc_final: 0.8137 (tmm) REVERT: M 158 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7334 (tm-30) REVERT: M 159 THR cc_start: 0.8656 (m) cc_final: 0.7896 (p) REVERT: M 162 ASN cc_start: 0.8086 (m-40) cc_final: 0.7825 (m110) REVERT: M 199 ASP cc_start: 0.8555 (m-30) cc_final: 0.7652 (m-30) REVERT: M 202 ILE cc_start: 0.9022 (mm) cc_final: 0.8701 (mm) REVERT: M 204 ASN cc_start: 0.8368 (t0) cc_final: 0.8159 (t0) REVERT: N 23 HIS cc_start: 0.7612 (t70) cc_final: 0.7401 (t70) REVERT: N 65 VAL cc_start: 0.7267 (t) cc_final: 0.6909 (p) REVERT: N 104 MET cc_start: 0.8272 (ptm) cc_final: 0.7926 (ptm) REVERT: N 110 PHE cc_start: 0.8050 (m-80) cc_final: 0.7239 (m-10) REVERT: N 162 ASN cc_start: 0.8169 (m110) cc_final: 0.7950 (m110) REVERT: N 203 PHE cc_start: 0.7640 (t80) cc_final: 0.6779 (t80) REVERT: N 205 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7695 (mtmm) REVERT: N 206 GLU cc_start: 0.7741 (pp20) cc_final: 0.7471 (pp20) REVERT: N 208 GLN cc_start: 0.8406 (tt0) cc_final: 0.8090 (tm-30) REVERT: N 213 GLN cc_start: 0.8777 (mt0) cc_final: 0.8455 (mt0) REVERT: N 230 LYS cc_start: 0.8117 (mttt) cc_final: 0.7831 (tptp) REVERT: N 233 HIS cc_start: 0.7703 (m90) cc_final: 0.7307 (m-70) REVERT: N 242 GLN cc_start: 0.7709 (tt0) cc_final: 0.7013 (pp30) REVERT: N 243 VAL cc_start: 0.8178 (t) cc_final: 0.7309 (m) REVERT: N 244 LEU cc_start: 0.8120 (tt) cc_final: 0.7722 (tt) REVERT: N 256 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7640 (ttm110) REVERT: N 267 LYS cc_start: 0.8681 (ptmt) cc_final: 0.7598 (mmtt) REVERT: O 48 MET cc_start: -0.2088 (ppp) cc_final: -0.2994 (ppp) REVERT: O 104 MET cc_start: 0.7999 (pmm) cc_final: 0.7758 (pmm) REVERT: O 110 PHE cc_start: 0.8043 (m-80) cc_final: 0.7645 (m-80) REVERT: O 132 MET cc_start: 0.8177 (tmm) cc_final: 0.7839 (tmm) REVERT: O 201 PHE cc_start: 0.8757 (t80) cc_final: 0.7752 (t80) REVERT: O 205 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8848 (mmtp) REVERT: O 208 GLN cc_start: 0.8574 (tm130) cc_final: 0.8279 (tm-30) REVERT: O 209 ARG cc_start: 0.8648 (ptm-80) cc_final: 0.8272 (ptm-80) REVERT: O 211 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8203 (tp40) REVERT: P 101 VAL cc_start: 0.9143 (p) cc_final: 0.8831 (p) REVERT: P 104 MET cc_start: 0.9143 (mmp) cc_final: 0.8735 (mmp) REVERT: P 132 MET cc_start: 0.5922 (tmm) cc_final: 0.5604 (tmm) REVERT: P 170 MET cc_start: 0.7335 (mtt) cc_final: 0.6910 (mpp) REVERT: P 222 ARG cc_start: 0.5818 (mtp85) cc_final: 0.5478 (mmm-85) REVERT: P 230 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6939 (mmtm) REVERT: P 254 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7982 (tppt) outliers start: 12 outliers final: 1 residues processed: 1164 average time/residue: 0.2340 time to fit residues: 429.6602 Evaluate side-chains 1072 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1069 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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: 0.9980 chunk 80 optimal weight: 4.9990 chunk 237 optimal weight: 0.0470 chunk 175 optimal weight: 6.9990 chunk 376 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 311 optimal weight: 0.0070 overall best weight: 0.5496 ------------------------------------------------------------------------------- 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 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 208 GLN G 211 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 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.207307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.161034 restraints weight = 71869.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.166968 restraints weight = 46273.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.171155 restraints weight = 32784.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.174287 restraints weight = 24762.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.176538 restraints weight = 19806.439| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34119 Z= 0.156 Angle : 0.675 12.653 46515 Z= 0.362 Chirality : 0.048 0.295 5006 Planarity : 0.005 0.089 5714 Dihedral : 14.605 169.013 5007 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.22 % 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: -0.02 (0.13), residues: 3851 helix: 1.14 (0.12), residues: 1865 sheet: -0.60 (0.17), residues: 935 loop : -1.41 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 100 TYR 0.023 0.001 TYR J 70 PHE 0.028 0.002 PHE K 174 TRP 0.033 0.002 TRP P 78 HIS 0.016 0.002 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (34119) covalent geometry : angle 0.67490 / 0.36 (46515) hydrogen bonds : bond 0.04253 / 2.86 ( 1746) hydrogen bonds : angle 5.41510 / 3.89 ( 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 1142 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1136 time to evaluate : 1.168 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: A 48 MET cc_start: 0.4867 (mmm) cc_final: 0.4099 (mmm) REVERT: A 60 ILE cc_start: 0.8743 (mm) cc_final: 0.8445 (mm) REVERT: A 62 HIS cc_start: 0.7871 (t70) cc_final: 0.7543 (t70) REVERT: A 79 VAL cc_start: 0.7565 (t) cc_final: 0.7009 (p) REVERT: A 92 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8510 (mtpp) REVERT: A 100 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7508 (mtm180) REVERT: A 107 TYR cc_start: 0.8478 (t80) cc_final: 0.8160 (t80) REVERT: A 113 LYS cc_start: 0.7825 (mmmm) cc_final: 0.7564 (mmmm) REVERT: A 132 MET cc_start: 0.7984 (mmm) cc_final: 0.7750 (mmm) REVERT: A 135 LEU cc_start: 0.8753 (mt) cc_final: 0.8512 (mt) REVERT: A 143 ILE cc_start: 0.7860 (pt) cc_final: 0.7323 (pt) REVERT: A 146 ASN cc_start: 0.8040 (m110) cc_final: 0.7078 (m-40) REVERT: A 155 ARG cc_start: 0.8562 (tpt90) cc_final: 0.7597 (mmm160) REVERT: A 158 GLN cc_start: 0.8931 (tt0) cc_final: 0.8546 (tt0) REVERT: A 159 THR cc_start: 0.8469 (m) cc_final: 0.8268 (p) REVERT: A 201 PHE cc_start: 0.7999 (t80) cc_final: 0.7690 (t80) REVERT: A 203 PHE cc_start: 0.8314 (t80) cc_final: 0.7938 (t80) REVERT: A 208 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 226 TYR cc_start: 0.6081 (p90) cc_final: 0.5546 (p90) REVERT: A 258 THR cc_start: 0.8693 (p) cc_final: 0.8450 (p) REVERT: A 260 ARG cc_start: 0.7421 (ptm160) cc_final: 0.7129 (ptm160) REVERT: B 15 TRP cc_start: 0.7940 (m100) cc_final: 0.7492 (m100) REVERT: B 40 CYS cc_start: 0.7301 (t) cc_final: 0.6850 (p) REVERT: B 63 TRP cc_start: 0.7930 (m100) cc_final: 0.6106 (m100) REVERT: B 64 GLN cc_start: 0.6862 (tp40) cc_final: 0.6366 (mm-40) REVERT: B 65 VAL cc_start: 0.8631 (t) cc_final: 0.8287 (t) REVERT: B 75 ILE cc_start: 0.7809 (pt) cc_final: 0.7530 (mp) REVERT: B 89 GLU cc_start: 0.7728 (tt0) cc_final: 0.7528 (tt0) REVERT: B 92 LYS cc_start: 0.8720 (tppt) cc_final: 0.8424 (tppp) REVERT: B 101 VAL cc_start: 0.8989 (t) cc_final: 0.8727 (t) REVERT: B 102 GLN cc_start: 0.8432 (mp10) cc_final: 0.8222 (mm-40) REVERT: B 104 MET cc_start: 0.8607 (mmp) cc_final: 0.8239 (mmp) REVERT: B 105 LYS cc_start: 0.9090 (mtpp) cc_final: 0.8811 (mtpp) REVERT: B 129 GLN cc_start: 0.8472 (pt0) cc_final: 0.8096 (pt0) REVERT: B 132 MET cc_start: 0.8446 (mmp) cc_final: 0.8221 (mmt) REVERT: B 137 ILE cc_start: 0.8494 (tt) cc_final: 0.8124 (tt) REVERT: B 139 HIS cc_start: 0.8109 (t70) cc_final: 0.7894 (t70) REVERT: B 165 GLU cc_start: 0.8002 (tp30) cc_final: 0.7561 (tp30) REVERT: B 170 MET cc_start: 0.8463 (tpt) cc_final: 0.8257 (tpt) REVERT: B 178 LEU cc_start: 0.9025 (mm) cc_final: 0.8647 (mm) REVERT: B 198 MET cc_start: 0.8124 (tpt) cc_final: 0.7720 (tpp) REVERT: B 204 ASN cc_start: 0.7601 (p0) cc_final: 0.7313 (p0) REVERT: C 7 LEU cc_start: 0.8731 (tt) cc_final: 0.8489 (tt) REVERT: C 35 ASP cc_start: 0.8628 (m-30) cc_final: 0.8421 (m-30) REVERT: C 110 PHE cc_start: 0.7553 (m-80) cc_final: 0.7192 (m-80) REVERT: C 132 MET cc_start: 0.8219 (ppp) cc_final: 0.7784 (ppp) REVERT: C 209 ARG cc_start: 0.8526 (ptt90) cc_final: 0.7933 (ptt90) REVERT: D 203 PHE cc_start: 0.7944 (t80) cc_final: 0.7651 (t80) REVERT: D 218 GLN cc_start: 0.8437 (mm110) cc_final: 0.7940 (mm110) REVERT: D 223 PHE cc_start: 0.6480 (p90) cc_final: 0.6059 (p90) REVERT: D 226 TYR cc_start: 0.6917 (p90) cc_final: 0.6203 (p90) REVERT: D 244 LEU cc_start: 0.8162 (mt) cc_final: 0.7656 (pp) REVERT: D 254 LYS cc_start: 0.7769 (ttmm) cc_final: 0.7357 (tppt) REVERT: D 268 ASP cc_start: 0.7121 (t70) cc_final: 0.6878 (t70) REVERT: E 10 GLU cc_start: 0.8187 (tp30) cc_final: 0.7770 (tp30) REVERT: E 12 HIS cc_start: 0.7974 (t70) cc_final: 0.7493 (t70) REVERT: E 13 ASN cc_start: 0.8770 (m110) cc_final: 0.8550 (m110) REVERT: E 15 TRP cc_start: 0.8720 (m-10) cc_final: 0.8486 (m-10) REVERT: E 18 ASP cc_start: 0.7482 (t70) cc_final: 0.7213 (t70) REVERT: E 22 LEU cc_start: 0.8136 (pp) cc_final: 0.7879 (pp) REVERT: E 87 TYR cc_start: 0.7166 (t80) cc_final: 0.5769 (t80) REVERT: E 89 GLU cc_start: 0.7717 (pm20) cc_final: 0.5798 (mp0) REVERT: E 110 PHE cc_start: 0.7392 (m-80) cc_final: 0.7186 (m-10) REVERT: E 150 GLN cc_start: 0.7945 (mm110) cc_final: 0.7005 (mm-40) REVERT: E 159 THR cc_start: 0.8575 (m) cc_final: 0.7996 (p) REVERT: E 178 LEU cc_start: 0.8949 (mt) cc_final: 0.8501 (mt) REVERT: E 199 ASP cc_start: 0.8397 (m-30) cc_final: 0.7607 (m-30) REVERT: E 207 GLN cc_start: 0.8486 (mm110) cc_final: 0.8178 (mm-40) REVERT: E 236 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8522 (mm-30) REVERT: F 23 HIS cc_start: 0.7748 (t70) cc_final: 0.7512 (t70) REVERT: F 86 ILE cc_start: 0.6731 (pt) cc_final: 0.6024 (mm) REVERT: F 154 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7354 (mm-30) REVERT: F 157 HIS cc_start: 0.7219 (m90) cc_final: 0.6697 (m90) REVERT: F 162 ASN cc_start: 0.8697 (m-40) cc_final: 0.8486 (m110) REVERT: F 199 ASP cc_start: 0.8507 (m-30) cc_final: 0.8295 (m-30) REVERT: F 203 PHE cc_start: 0.7813 (t80) cc_final: 0.6944 (t80) REVERT: F 205 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7574 (mtmm) REVERT: F 206 GLU cc_start: 0.8192 (pp20) cc_final: 0.7930 (pp20) REVERT: F 230 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7765 (mmmm) REVERT: F 233 HIS cc_start: 0.7635 (m90) cc_final: 0.7253 (m90) REVERT: F 236 GLU cc_start: 0.8006 (pm20) cc_final: 0.7595 (mp0) REVERT: F 242 GLN cc_start: 0.7539 (tt0) cc_final: 0.6559 (pp30) REVERT: F 243 VAL cc_start: 0.8111 (t) cc_final: 0.7038 (m) REVERT: F 244 LEU cc_start: 0.7983 (tt) cc_final: 0.7496 (tt) REVERT: F 256 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8007 (ttm110) REVERT: F 260 ARG cc_start: 0.6936 (mtm110) cc_final: 0.6731 (ttp-110) REVERT: F 267 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8122 (pttt) REVERT: G 48 MET cc_start: -0.0296 (ppp) cc_final: -0.1164 (ppp) REVERT: G 62 HIS cc_start: 0.7321 (t70) cc_final: 0.7000 (t70) REVERT: G 85 LEU cc_start: 0.7236 (tp) cc_final: 0.6844 (tp) REVERT: G 110 PHE cc_start: 0.7597 (m-80) cc_final: 0.7142 (m-80) REVERT: G 131 LEU cc_start: 0.9231 (mt) cc_final: 0.9018 (mt) REVERT: G 197 PRO cc_start: 0.8430 (Cg_exo) cc_final: 0.8082 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8943 (m-30) cc_final: 0.8715 (m-30) REVERT: G 201 PHE cc_start: 0.8883 (t80) cc_final: 0.8039 (t80) REVERT: G 205 LYS cc_start: 0.9252 (mmtm) cc_final: 0.9028 (mmtp) REVERT: H 62 HIS cc_start: 0.7454 (t-90) cc_final: 0.6914 (t-170) REVERT: H 78 TRP cc_start: 0.6353 (m-10) cc_final: 0.5973 (m-10) REVERT: H 87 TYR cc_start: 0.8268 (t80) cc_final: 0.7787 (t80) REVERT: H 101 VAL cc_start: 0.8844 (p) cc_final: 0.8608 (p) REVERT: H 104 MET cc_start: 0.9145 (mmp) cc_final: 0.8540 (mmp) REVERT: H 109 MET cc_start: 0.8084 (tpt) cc_final: 0.7858 (tpt) REVERT: H 110 PHE cc_start: 0.8015 (m-10) cc_final: 0.7547 (m-10) REVERT: H 164 LEU cc_start: 0.9153 (mm) cc_final: 0.8879 (pp) REVERT: H 223 PHE cc_start: 0.6990 (m-80) cc_final: 0.6584 (m-10) REVERT: H 254 LYS cc_start: 0.8232 (mmmm) cc_final: 0.8019 (mmmm) REVERT: H 267 LYS cc_start: 0.7117 (ptmm) cc_final: 0.6528 (tmtt) REVERT: H 271 PHE cc_start: 0.6595 (p90) cc_final: 0.6320 (p90) REVERT: H 272 ILE cc_start: 0.7718 (mm) cc_final: 0.7478 (mm) REVERT: I 79 VAL cc_start: 0.7736 (t) cc_final: 0.7286 (p) REVERT: I 92 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8489 (mtpp) REVERT: I 97 GLN cc_start: 0.7657 (pm20) cc_final: 0.7132 (pm20) REVERT: I 98 GLU cc_start: 0.8227 (mp0) cc_final: 0.7895 (mp0) REVERT: I 100 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7436 (mtm-85) REVERT: I 104 MET cc_start: 0.8549 (ttm) cc_final: 0.8241 (ttm) REVERT: I 105 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8196 (mtmm) REVERT: I 118 ASP cc_start: 0.7776 (p0) cc_final: 0.7477 (p0) REVERT: I 132 MET cc_start: 0.8106 (mmm) cc_final: 0.7846 (mmm) REVERT: I 146 ASN cc_start: 0.7866 (m110) cc_final: 0.7076 (m-40) REVERT: I 158 GLN cc_start: 0.9071 (tt0) cc_final: 0.8130 (pt0) REVERT: I 164 LEU cc_start: 0.8424 (mt) cc_final: 0.8164 (mt) REVERT: I 203 PHE cc_start: 0.8455 (t80) cc_final: 0.7953 (t80) REVERT: I 208 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7844 (tm-30) REVERT: I 222 ARG cc_start: 0.5365 (mtp-110) cc_final: 0.5127 (mtm110) REVERT: I 254 LYS cc_start: 0.7365 (tptt) cc_final: 0.7163 (tptt) REVERT: I 258 THR cc_start: 0.8516 (p) cc_final: 0.8314 (p) REVERT: I 260 ARG cc_start: 0.7102 (ptm160) cc_final: 0.6816 (ptm160) REVERT: J 40 CYS cc_start: 0.7162 (t) cc_final: 0.6737 (p) REVERT: J 63 TRP cc_start: 0.7782 (m100) cc_final: 0.6213 (m100) REVERT: J 64 GLN cc_start: 0.6932 (tp40) cc_final: 0.6520 (mm-40) REVERT: J 65 VAL cc_start: 0.8801 (t) cc_final: 0.8405 (t) REVERT: J 86 ILE cc_start: 0.8700 (pt) cc_final: 0.7903 (mm) REVERT: J 89 GLU cc_start: 0.7806 (tt0) cc_final: 0.7458 (tt0) REVERT: J 92 LYS cc_start: 0.8744 (tptp) cc_final: 0.8412 (tptp) REVERT: J 100 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8058 (mtm-85) REVERT: J 101 VAL cc_start: 0.9078 (t) cc_final: 0.8795 (t) REVERT: J 104 MET cc_start: 0.8281 (tpp) cc_final: 0.7606 (tpp) REVERT: J 116 GLN cc_start: 0.7078 (tm-30) cc_final: 0.6826 (tm-30) REVERT: J 131 LEU cc_start: 0.8608 (tt) cc_final: 0.8216 (tt) REVERT: J 138 GLU cc_start: 0.7756 (tp30) cc_final: 0.7441 (tp30) REVERT: J 139 HIS cc_start: 0.8490 (t70) cc_final: 0.8175 (t70) REVERT: J 162 ASN cc_start: 0.8969 (m110) cc_final: 0.8700 (m-40) REVERT: J 178 LEU cc_start: 0.9050 (mm) cc_final: 0.8756 (mm) REVERT: J 184 THR cc_start: 0.8931 (p) cc_final: 0.8632 (p) REVERT: J 186 ASN cc_start: 0.7713 (m-40) cc_final: 0.7235 (m-40) REVERT: J 198 MET cc_start: 0.8081 (tpt) cc_final: 0.7764 (tpp) REVERT: J 204 ASN cc_start: 0.8200 (m110) cc_final: 0.7586 (m110) REVERT: J 205 LYS cc_start: 0.8318 (tptp) cc_final: 0.7805 (tptp) REVERT: J 208 GLN cc_start: 0.7955 (pt0) cc_final: 0.7708 (pt0) REVERT: K 7 LEU cc_start: 0.8684 (tt) cc_final: 0.8481 (tt) REVERT: K 14 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8354 (mmtm) REVERT: K 15 TRP cc_start: 0.8065 (m100) cc_final: 0.7583 (m100) REVERT: K 18 ASP cc_start: 0.8782 (t70) cc_final: 0.8578 (t70) REVERT: K 34 GLU cc_start: 0.8793 (pt0) cc_final: 0.8267 (pp20) REVERT: K 35 ASP cc_start: 0.8731 (m-30) cc_final: 0.8405 (m-30) REVERT: K 40 CYS cc_start: 0.8346 (m) cc_final: 0.7709 (p) REVERT: K 132 MET cc_start: 0.7397 (ppp) cc_final: 0.7152 (ppp) REVERT: K 193 LEU cc_start: 0.7704 (mt) cc_final: 0.7112 (mm) REVERT: L 63 TRP cc_start: 0.6072 (m100) cc_final: 0.5652 (m100) REVERT: L 86 ILE cc_start: 0.6319 (pt) cc_final: 0.6099 (mm) REVERT: L 223 PHE cc_start: 0.6238 (p90) cc_final: 0.5908 (p90) REVERT: L 226 TYR cc_start: 0.7145 (p90) cc_final: 0.6125 (p90) REVERT: M 13 ASN cc_start: 0.8850 (m110) cc_final: 0.8602 (m110) REVERT: M 18 ASP cc_start: 0.7484 (t70) cc_final: 0.7132 (t70) REVERT: M 22 LEU cc_start: 0.8017 (pp) cc_final: 0.7776 (pp) REVERT: M 78 TRP cc_start: 0.6141 (m100) cc_final: 0.5703 (m100) REVERT: M 87 TYR cc_start: 0.7417 (t80) cc_final: 0.6839 (t80) REVERT: M 109 MET cc_start: 0.8358 (tmm) cc_final: 0.8149 (tmm) REVERT: M 154 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8780 (mm-30) REVERT: M 155 ARG cc_start: 0.8579 (ttt180) cc_final: 0.8251 (mtt90) REVERT: M 158 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7460 (tm-30) REVERT: M 159 THR cc_start: 0.8663 (m) cc_final: 0.7923 (p) REVERT: M 162 ASN cc_start: 0.8134 (m-40) cc_final: 0.7914 (m110) REVERT: M 199 ASP cc_start: 0.8594 (m-30) cc_final: 0.7711 (m-30) REVERT: M 209 ARG cc_start: 0.8929 (tmt170) cc_final: 0.8592 (ttp80) REVERT: N 11 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: N 23 HIS cc_start: 0.7646 (t70) cc_final: 0.7369 (t70) REVERT: N 65 VAL cc_start: 0.7563 (t) cc_final: 0.7207 (p) REVERT: N 98 GLU cc_start: 0.7680 (mp0) cc_final: 0.7405 (mp0) REVERT: N 104 MET cc_start: 0.8301 (ptm) cc_final: 0.7973 (ptm) REVERT: N 110 PHE cc_start: 0.8062 (m-80) cc_final: 0.7394 (m-80) REVERT: N 203 PHE cc_start: 0.7901 (t80) cc_final: 0.7446 (t80) REVERT: N 208 GLN cc_start: 0.8480 (tt0) cc_final: 0.8166 (tm-30) REVERT: N 213 GLN cc_start: 0.8866 (mt0) cc_final: 0.8408 (mt0) REVERT: N 233 HIS cc_start: 0.7720 (m90) cc_final: 0.7259 (m-70) REVERT: N 242 GLN cc_start: 0.7827 (tt0) cc_final: 0.7168 (pp30) REVERT: N 243 VAL cc_start: 0.8269 (t) cc_final: 0.7538 (m) REVERT: N 244 LEU cc_start: 0.8253 (tt) cc_final: 0.7941 (tt) REVERT: N 256 ARG cc_start: 0.8443 (ttm110) cc_final: 0.7758 (ttm110) REVERT: N 270 LYS cc_start: 0.7690 (mptt) cc_final: 0.6721 (mmtm) REVERT: O 40 CYS cc_start: 0.5884 (t) cc_final: 0.5627 (t) REVERT: O 48 MET cc_start: -0.1315 (ppp) cc_final: -0.1762 (ppp) REVERT: O 104 MET cc_start: 0.7999 (pmm) cc_final: 0.7785 (pmm) REVERT: O 110 PHE cc_start: 0.8173 (m-80) cc_final: 0.7814 (m-80) REVERT: O 132 MET cc_start: 0.8161 (tmm) cc_final: 0.7718 (tmm) REVERT: O 193 LEU cc_start: 0.8749 (mm) cc_final: 0.8494 (mm) REVERT: O 201 PHE cc_start: 0.8800 (t80) cc_final: 0.7951 (t80) REVERT: O 205 LYS cc_start: 0.9161 (mmtm) cc_final: 0.8861 (mmtp) REVERT: O 208 GLN cc_start: 0.8723 (tm130) cc_final: 0.8461 (tm-30) REVERT: O 209 ARG cc_start: 0.8760 (ptm-80) cc_final: 0.8385 (ptm-80) REVERT: O 211 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8265 (tp40) REVERT: P 87 TYR cc_start: 0.8704 (t80) cc_final: 0.8214 (t80) REVERT: P 101 VAL cc_start: 0.9066 (p) cc_final: 0.8842 (p) REVERT: P 104 MET cc_start: 0.9214 (mmp) cc_final: 0.8805 (mmp) REVERT: P 106 TRP cc_start: 0.8460 (t60) cc_final: 0.8080 (t60) REVERT: P 132 MET cc_start: 0.6257 (tmm) cc_final: 0.5663 (tmm) REVERT: P 170 MET cc_start: 0.7359 (mtt) cc_final: 0.6948 (mpp) REVERT: P 222 ARG cc_start: 0.6069 (mtp85) cc_final: 0.5814 (mmm-85) REVERT: P 230 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6858 (mmtm) REVERT: P 254 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8056 (tppt) outliers start: 6 outliers final: 2 residues processed: 1137 average time/residue: 0.2337 time to fit residues: 417.8533 Evaluate side-chains 1065 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1062 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 374 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 227 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 302 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 338 optimal weight: 0.0970 chunk 207 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 266 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 102 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS 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** ** I 44 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 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 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.205126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.158473 restraints weight = 71093.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.164416 restraints weight = 45544.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.168623 restraints weight = 32152.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.171694 restraints weight = 24425.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.173832 restraints weight = 19576.852| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34119 Z= 0.153 Angle : 0.674 12.860 46515 Z= 0.361 Chirality : 0.048 0.313 5006 Planarity : 0.005 0.061 5714 Dihedral : 14.708 169.225 5007 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 0.18 % Allowed : 3.10 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 3851 helix: 1.07 (0.12), residues: 1863 sheet: -0.63 (0.17), residues: 907 loop : -1.44 (0.17), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 155 TYR 0.025 0.001 TYR M 70 PHE 0.028 0.002 PHE D 203 TRP 0.036 0.002 TRP O 63 HIS 0.021 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (34119) covalent geometry : angle 0.67390 / 0.36 (46515) hydrogen bonds : bond 0.04076 / 2.77 ( 1746) hydrogen bonds : angle 5.31653 / 3.81 ( 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 1148 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1142 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TRP cc_start: 0.6553 (m-10) cc_final: 0.5931 (m100) REVERT: A 60 ILE cc_start: 0.8627 (mm) cc_final: 0.8339 (mm) REVERT: A 62 HIS cc_start: 0.7903 (t70) cc_final: 0.7487 (t70) REVERT: A 64 GLN cc_start: 0.6392 (pm20) cc_final: 0.6107 (pm20) REVERT: A 79 VAL cc_start: 0.7824 (t) cc_final: 0.7295 (p) REVERT: A 92 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8508 (mtpp) REVERT: A 100 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7538 (mtm180) REVERT: A 105 LYS cc_start: 0.9203 (mtpp) cc_final: 0.8921 (mtpp) REVERT: A 107 TYR cc_start: 0.8466 (t80) cc_final: 0.8168 (t80) REVERT: A 113 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7597 (mmmm) REVERT: A 116 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 118 ASP cc_start: 0.7607 (p0) cc_final: 0.7400 (p0) REVERT: A 129 GLN cc_start: 0.8003 (tt0) cc_final: 0.7614 (tt0) REVERT: A 132 MET cc_start: 0.7974 (mmm) cc_final: 0.7710 (mmm) REVERT: A 135 LEU cc_start: 0.8754 (mt) cc_final: 0.8493 (mt) REVERT: A 146 ASN cc_start: 0.7991 (m110) cc_final: 0.7414 (m-40) REVERT: A 155 ARG cc_start: 0.8522 (tpt90) cc_final: 0.7681 (mmm160) REVERT: A 158 GLN cc_start: 0.8920 (tt0) cc_final: 0.8567 (tt0) REVERT: A 164 LEU cc_start: 0.8243 (mt) cc_final: 0.7966 (mt) REVERT: A 201 PHE cc_start: 0.8118 (t80) cc_final: 0.7852 (t80) REVERT: A 203 PHE cc_start: 0.8290 (t80) cc_final: 0.7912 (t80) REVERT: A 208 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 223 PHE cc_start: 0.6647 (m-80) cc_final: 0.6244 (m-10) REVERT: A 226 TYR cc_start: 0.5950 (p90) cc_final: 0.4261 (p90) REVERT: A 242 GLN cc_start: 0.6260 (tp-100) cc_final: 0.6053 (tp-100) REVERT: A 254 LYS cc_start: 0.8309 (tmmt) cc_final: 0.7868 (ttpp) REVERT: A 260 ARG cc_start: 0.7249 (ptm160) cc_final: 0.7047 (ptm160) REVERT: B 15 TRP cc_start: 0.7898 (m100) cc_final: 0.7415 (m100) REVERT: B 40 CYS cc_start: 0.7411 (t) cc_final: 0.6909 (p) REVERT: B 63 TRP cc_start: 0.7937 (m100) cc_final: 0.6295 (m100) REVERT: B 64 GLN cc_start: 0.7127 (tp40) cc_final: 0.6285 (mm-40) REVERT: B 65 VAL cc_start: 0.8633 (t) cc_final: 0.8247 (t) REVERT: B 70 TYR cc_start: 0.7844 (t80) cc_final: 0.7409 (t80) REVERT: B 75 ILE cc_start: 0.7823 (pt) cc_final: 0.7567 (mp) REVERT: B 86 ILE cc_start: 0.8677 (pt) cc_final: 0.8201 (mm) REVERT: B 89 GLU cc_start: 0.7842 (tt0) cc_final: 0.7626 (tt0) REVERT: B 92 LYS cc_start: 0.8678 (tppt) cc_final: 0.8377 (tppp) REVERT: B 104 MET cc_start: 0.8611 (mmp) cc_final: 0.8372 (mmp) REVERT: B 116 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6752 (tm-30) REVERT: B 132 MET cc_start: 0.8484 (mmp) cc_final: 0.8260 (mmt) REVERT: B 137 ILE cc_start: 0.8474 (tt) cc_final: 0.8054 (tt) REVERT: B 139 HIS cc_start: 0.8095 (t70) cc_final: 0.7842 (t70) REVERT: B 165 GLU cc_start: 0.7846 (tp30) cc_final: 0.7547 (tp30) REVERT: B 170 MET cc_start: 0.8431 (tpt) cc_final: 0.8224 (tpt) REVERT: B 178 LEU cc_start: 0.9055 (mm) cc_final: 0.8697 (mm) REVERT: B 198 MET cc_start: 0.8158 (tpt) cc_final: 0.7734 (tpp) REVERT: B 204 ASN cc_start: 0.7662 (p0) cc_final: 0.7295 (p0) REVERT: C 28 ILE cc_start: 0.8072 (tp) cc_final: 0.7785 (tp) REVERT: C 35 ASP cc_start: 0.8592 (m-30) cc_final: 0.8385 (m-30) REVERT: C 110 PHE cc_start: 0.7772 (m-80) cc_final: 0.7487 (m-80) REVERT: C 132 MET cc_start: 0.8259 (ppp) cc_final: 0.7832 (ppp) REVERT: C 161 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8775 (tmmt) REVERT: C 199 ASP cc_start: 0.8894 (m-30) cc_final: 0.8659 (m-30) REVERT: C 209 ARG cc_start: 0.8484 (ptt90) cc_final: 0.7903 (ptt90) REVERT: D 203 PHE cc_start: 0.7888 (t80) cc_final: 0.7665 (t80) REVERT: D 223 PHE cc_start: 0.6331 (p90) cc_final: 0.5898 (p90) REVERT: D 226 TYR cc_start: 0.6881 (p90) cc_final: 0.6181 (p90) REVERT: D 244 LEU cc_start: 0.8281 (mt) cc_final: 0.7657 (pp) REVERT: D 254 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7588 (tptt) REVERT: D 268 ASP cc_start: 0.7106 (t70) cc_final: 0.6886 (t70) REVERT: E 10 GLU cc_start: 0.8041 (tp30) cc_final: 0.7503 (tp30) REVERT: E 15 TRP cc_start: 0.8677 (m-10) cc_final: 0.8435 (m-10) REVERT: E 100 ARG cc_start: 0.8733 (ptp90) cc_final: 0.8278 (ptp-170) REVERT: E 133 LYS cc_start: 0.9070 (ptpp) cc_final: 0.8410 (pttm) REVERT: E 150 GLN cc_start: 0.8023 (mm110) cc_final: 0.7111 (mm-40) REVERT: E 159 THR cc_start: 0.8563 (m) cc_final: 0.7953 (p) REVERT: E 178 LEU cc_start: 0.8908 (mt) cc_final: 0.8391 (mt) REVERT: E 199 ASP cc_start: 0.8402 (m-30) cc_final: 0.7594 (m-30) REVERT: E 201 PHE cc_start: 0.8307 (t80) cc_final: 0.7812 (t80) REVERT: E 205 LYS cc_start: 0.8960 (mttt) cc_final: 0.8400 (mmtp) REVERT: E 242 GLN cc_start: 0.6442 (pp30) cc_final: 0.6040 (pp30) REVERT: F 23 HIS cc_start: 0.7779 (t70) cc_final: 0.7451 (t70) REVERT: F 82 ASN cc_start: 0.8318 (m110) cc_final: 0.7976 (m110) REVERT: F 104 MET cc_start: 0.7956 (ptm) cc_final: 0.7424 (ppp) REVERT: F 199 ASP cc_start: 0.8533 (m-30) cc_final: 0.8231 (m-30) REVERT: F 203 PHE cc_start: 0.7747 (t80) cc_final: 0.7273 (t80) REVERT: F 205 LYS cc_start: 0.8511 (mtmm) cc_final: 0.7857 (mtmm) REVERT: F 208 GLN cc_start: 0.8524 (tt0) cc_final: 0.8085 (tm-30) REVERT: F 230 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7860 (mmmm) REVERT: F 233 HIS cc_start: 0.7600 (m90) cc_final: 0.7262 (m90) REVERT: F 236 GLU cc_start: 0.7987 (pm20) cc_final: 0.7562 (mp0) REVERT: F 242 GLN cc_start: 0.7252 (tt0) cc_final: 0.6422 (pp30) REVERT: F 243 VAL cc_start: 0.8267 (t) cc_final: 0.7057 (m) REVERT: F 244 LEU cc_start: 0.7922 (tt) cc_final: 0.7538 (tt) REVERT: F 256 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7964 (ttm110) REVERT: F 267 LYS cc_start: 0.8675 (ptmt) cc_final: 0.8191 (pttt) REVERT: G 48 MET cc_start: -0.0276 (ppp) cc_final: -0.1151 (ppp) REVERT: G 62 HIS cc_start: 0.7419 (t70) cc_final: 0.7042 (t70) REVERT: G 85 LEU cc_start: 0.7175 (tp) cc_final: 0.6718 (tp) REVERT: G 104 MET cc_start: 0.7859 (pmm) cc_final: 0.7641 (pmm) REVERT: G 110 PHE cc_start: 0.7654 (m-80) cc_final: 0.7242 (m-80) REVERT: G 131 LEU cc_start: 0.9257 (mt) cc_final: 0.9011 (mt) REVERT: G 155 ARG cc_start: 0.9137 (mtp-110) cc_final: 0.8637 (ptp-110) REVERT: G 171 PHE cc_start: 0.7690 (m-10) cc_final: 0.7482 (m-80) REVERT: G 197 PRO cc_start: 0.8484 (Cg_exo) cc_final: 0.8151 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8932 (m-30) cc_final: 0.8602 (m-30) REVERT: H 62 HIS cc_start: 0.7648 (t-90) cc_final: 0.7045 (t-170) REVERT: H 78 TRP cc_start: 0.6749 (m-10) cc_final: 0.6480 (m-10) REVERT: H 87 TYR cc_start: 0.8361 (t80) cc_final: 0.7865 (t80) REVERT: H 101 VAL cc_start: 0.8834 (p) cc_final: 0.8621 (p) REVERT: H 104 MET cc_start: 0.9065 (mmp) cc_final: 0.8481 (mmp) REVERT: H 106 TRP cc_start: 0.8371 (t60) cc_final: 0.7942 (t60) REVERT: H 109 MET cc_start: 0.7981 (tpt) cc_final: 0.7737 (tpt) REVERT: H 110 PHE cc_start: 0.8129 (m-10) cc_final: 0.7811 (m-10) REVERT: H 199 ASP cc_start: 0.7876 (m-30) cc_final: 0.7664 (m-30) REVERT: H 207 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7810 (mm-40) REVERT: I 60 ILE cc_start: 0.8919 (mp) cc_final: 0.8609 (mp) REVERT: I 79 VAL cc_start: 0.7738 (t) cc_final: 0.7279 (p) REVERT: I 92 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8568 (mtpp) REVERT: I 97 GLN cc_start: 0.7705 (pm20) cc_final: 0.7245 (pm20) REVERT: I 98 GLU cc_start: 0.8190 (mp0) cc_final: 0.7934 (mp0) REVERT: I 100 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7597 (mtm-85) REVERT: I 118 ASP cc_start: 0.7807 (p0) cc_final: 0.7383 (p0) REVERT: I 146 ASN cc_start: 0.7728 (m110) cc_final: 0.7099 (m110) REVERT: I 155 ARG cc_start: 0.8352 (tpt90) cc_final: 0.7700 (mmm160) REVERT: I 158 GLN cc_start: 0.9055 (tt0) cc_final: 0.8681 (tt0) REVERT: I 178 LEU cc_start: 0.8037 (tp) cc_final: 0.7556 (tp) REVERT: I 184 THR cc_start: 0.8302 (m) cc_final: 0.7964 (p) REVERT: I 198 MET cc_start: 0.8414 (ttm) cc_final: 0.8167 (ttm) REVERT: I 201 PHE cc_start: 0.8292 (t80) cc_final: 0.8069 (t80) REVERT: I 203 PHE cc_start: 0.8243 (t80) cc_final: 0.7823 (t80) REVERT: I 208 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7880 (tm-30) REVERT: I 209 ARG cc_start: 0.7282 (tpp80) cc_final: 0.6883 (tpp80) REVERT: I 222 ARG cc_start: 0.5402 (mtp-110) cc_final: 0.4952 (mtm110) REVERT: I 260 ARG cc_start: 0.7039 (ptm160) cc_final: 0.6638 (ptm160) REVERT: J 40 CYS cc_start: 0.7157 (t) cc_final: 0.6774 (p) REVERT: J 62 HIS cc_start: 0.7392 (t-90) cc_final: 0.7117 (t-90) REVERT: J 63 TRP cc_start: 0.7917 (m100) cc_final: 0.6359 (m100) REVERT: J 64 GLN cc_start: 0.7131 (tp40) cc_final: 0.6351 (mm110) REVERT: J 65 VAL cc_start: 0.8812 (t) cc_final: 0.8396 (t) REVERT: J 86 ILE cc_start: 0.8805 (pt) cc_final: 0.8071 (mm) REVERT: J 89 GLU cc_start: 0.7719 (tt0) cc_final: 0.7435 (tt0) REVERT: J 92 LYS cc_start: 0.8766 (tptp) cc_final: 0.8402 (tptp) REVERT: J 101 VAL cc_start: 0.9100 (t) cc_final: 0.8839 (t) REVERT: J 104 MET cc_start: 0.8220 (tpp) cc_final: 0.7491 (tpp) REVERT: J 116 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6879 (tm-30) REVERT: J 131 LEU cc_start: 0.8838 (tt) cc_final: 0.8433 (tt) REVERT: J 138 GLU cc_start: 0.7791 (tp30) cc_final: 0.7515 (tp30) REVERT: J 139 HIS cc_start: 0.8466 (t70) cc_final: 0.8139 (t70) REVERT: J 178 LEU cc_start: 0.9009 (mm) cc_final: 0.8592 (mm) REVERT: J 186 ASN cc_start: 0.7736 (m-40) cc_final: 0.7102 (m110) REVERT: J 204 ASN cc_start: 0.8293 (m110) cc_final: 0.7229 (p0) REVERT: J 205 LYS cc_start: 0.8254 (tptp) cc_final: 0.7656 (tptp) REVERT: J 208 GLN cc_start: 0.8087 (pt0) cc_final: 0.7719 (pt0) REVERT: K 14 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8284 (mmtm) REVERT: K 34 GLU cc_start: 0.8781 (pt0) cc_final: 0.8334 (pp20) REVERT: K 35 ASP cc_start: 0.8660 (m-30) cc_final: 0.8288 (m-30) REVERT: K 40 CYS cc_start: 0.8301 (m) cc_final: 0.7712 (p) REVERT: K 132 MET cc_start: 0.7458 (ppp) cc_final: 0.7221 (ppp) REVERT: L 86 ILE cc_start: 0.6601 (pt) cc_final: 0.6164 (mm) REVERT: L 209 ARG cc_start: 0.8726 (mmp-170) cc_final: 0.8463 (mmm160) REVERT: L 226 TYR cc_start: 0.6670 (p90) cc_final: 0.5918 (p90) REVERT: L 254 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7275 (tmtt) REVERT: L 256 ARG cc_start: 0.7678 (tmm160) cc_final: 0.7469 (ttp80) REVERT: M 7 LEU cc_start: 0.8037 (tt) cc_final: 0.7736 (tt) REVERT: M 13 ASN cc_start: 0.8783 (m110) cc_final: 0.8528 (m110) REVERT: M 18 ASP cc_start: 0.7523 (t70) cc_final: 0.7152 (t70) REVERT: M 76 LEU cc_start: 0.7272 (tp) cc_final: 0.6960 (tp) REVERT: M 87 TYR cc_start: 0.7345 (t80) cc_final: 0.6865 (t80) REVERT: M 154 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8735 (mm-30) REVERT: M 155 ARG cc_start: 0.8572 (ttt180) cc_final: 0.8256 (mtt90) REVERT: M 158 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7356 (tm-30) REVERT: M 159 THR cc_start: 0.8659 (m) cc_final: 0.7871 (p) REVERT: M 162 ASN cc_start: 0.8078 (m-40) cc_final: 0.7848 (m110) REVERT: M 174 PHE cc_start: 0.6977 (t80) cc_final: 0.6742 (t80) REVERT: M 178 LEU cc_start: 0.8800 (mt) cc_final: 0.8552 (mt) REVERT: M 199 ASP cc_start: 0.8562 (m-30) cc_final: 0.7609 (m-30) REVERT: M 202 ILE cc_start: 0.8887 (mm) cc_final: 0.8668 (mm) REVERT: M 207 GLN cc_start: 0.8477 (mm110) cc_final: 0.8179 (mm110) REVERT: M 209 ARG cc_start: 0.8847 (tmt170) cc_final: 0.8413 (ttp80) REVERT: N 23 HIS cc_start: 0.7638 (t70) cc_final: 0.7390 (t70) REVERT: N 65 VAL cc_start: 0.7600 (t) cc_final: 0.7247 (p) REVERT: N 104 MET cc_start: 0.8091 (ptm) cc_final: 0.7680 (ptm) REVERT: N 110 PHE cc_start: 0.7980 (m-80) cc_final: 0.7549 (m-80) REVERT: N 162 ASN cc_start: 0.8616 (m-40) cc_final: 0.8271 (m110) REVERT: N 203 PHE cc_start: 0.7711 (t80) cc_final: 0.7281 (t80) REVERT: N 208 GLN cc_start: 0.8461 (tt0) cc_final: 0.8221 (tm-30) REVERT: N 213 GLN cc_start: 0.8784 (mt0) cc_final: 0.8182 (mt0) REVERT: N 230 LYS cc_start: 0.8207 (mttt) cc_final: 0.7428 (ttpp) REVERT: N 233 HIS cc_start: 0.7691 (m90) cc_final: 0.7363 (m-70) REVERT: N 242 GLN cc_start: 0.7775 (tt0) cc_final: 0.7156 (pp30) REVERT: N 243 VAL cc_start: 0.8331 (t) cc_final: 0.7570 (m) REVERT: N 244 LEU cc_start: 0.8227 (tt) cc_final: 0.7967 (tt) REVERT: N 256 ARG cc_start: 0.8350 (ttm110) cc_final: 0.7673 (ttm110) REVERT: N 258 THR cc_start: 0.8582 (p) cc_final: 0.8314 (p) REVERT: N 270 LYS cc_start: 0.7745 (mptt) cc_final: 0.6940 (mptt) REVERT: O 40 CYS cc_start: 0.5653 (t) cc_final: 0.5407 (t) REVERT: O 48 MET cc_start: -0.1385 (ppp) cc_final: -0.1830 (ppp) REVERT: O 62 HIS cc_start: 0.6736 (p-80) cc_final: 0.6296 (p-80) REVERT: O 104 MET cc_start: 0.8032 (pmm) cc_final: 0.7796 (pmm) REVERT: O 110 PHE cc_start: 0.8298 (m-80) cc_final: 0.7590 (m-80) REVERT: O 115 LEU cc_start: 0.8834 (tp) cc_final: 0.8572 (tp) REVERT: O 132 MET cc_start: 0.8151 (tmm) cc_final: 0.7630 (tmm) REVERT: O 155 ARG cc_start: 0.9196 (mtm110) cc_final: 0.8789 (ptp-110) REVERT: O 193 LEU cc_start: 0.8702 (mm) cc_final: 0.8409 (mm) REVERT: O 199 ASP cc_start: 0.8842 (m-30) cc_final: 0.8571 (m-30) REVERT: O 201 PHE cc_start: 0.8757 (t80) cc_final: 0.7848 (t80) REVERT: O 205 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8877 (mmtp) REVERT: O 208 GLN cc_start: 0.8593 (tm130) cc_final: 0.8331 (tm-30) REVERT: O 209 ARG cc_start: 0.8754 (ptm-80) cc_final: 0.8394 (ptm-80) REVERT: O 211 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8205 (tp40) REVERT: P 87 TYR cc_start: 0.8716 (t80) cc_final: 0.8310 (t80) REVERT: P 101 VAL cc_start: 0.9163 (p) cc_final: 0.8926 (p) REVERT: P 104 MET cc_start: 0.9181 (mmp) cc_final: 0.8759 (mmp) REVERT: P 106 TRP cc_start: 0.8452 (t60) cc_final: 0.8108 (t60) REVERT: P 132 MET cc_start: 0.6408 (tmm) cc_final: 0.5798 (tmm) REVERT: P 137 ILE cc_start: 0.8040 (mm) cc_final: 0.7808 (mm) REVERT: P 170 MET cc_start: 0.7405 (mtt) cc_final: 0.6933 (mpp) REVERT: P 172 ASN cc_start: 0.8746 (m-40) cc_final: 0.8372 (p0) REVERT: P 230 LYS cc_start: 0.7352 (mmmt) cc_final: 0.7121 (mmtm) REVERT: P 254 LYS cc_start: 0.8701 (mtpp) cc_final: 0.7935 (tppt) outliers start: 6 outliers final: 1 residues processed: 1143 average time/residue: 0.2343 time to fit residues: 419.5438 Evaluate side-chains 1049 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1048 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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: 0.9990 chunk 135 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 311 optimal weight: 0.0000 chunk 67 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 357 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 E 139 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** 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 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 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN L 158 GLN M 69 HIS M 204 ASN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 102 GLN O 158 GLN O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.202717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156255 restraints weight = 71453.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.161989 restraints weight = 45688.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.166099 restraints weight = 32356.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.169070 restraints weight = 24582.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.171193 restraints weight = 19714.368| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 34119 Z= 0.159 Angle : 0.696 13.398 46515 Z= 0.374 Chirality : 0.049 0.276 5006 Planarity : 0.005 0.064 5714 Dihedral : 14.780 169.629 5007 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 0.24 % Allowed : 2.66 % Favored : 97.10 % 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: -0.20 (0.13), residues: 3851 helix: 0.96 (0.12), residues: 1859 sheet: -0.66 (0.17), residues: 867 loop : -1.39 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 222 TYR 0.019 0.001 TYR M 70 PHE 0.032 0.002 PHE D 203 TRP 0.058 0.002 TRP D 63 HIS 0.021 0.001 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (34119) covalent geometry : angle 0.69597 / 0.37 (46515) hydrogen bonds : bond 0.04173 / 2.84 ( 1746) hydrogen bonds : angle 5.40100 / 3.90 ( 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 1144 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1136 time to evaluate : 1.204 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 15 TRP cc_start: 0.6575 (m-10) cc_final: 0.5779 (m100) REVERT: A 60 ILE cc_start: 0.8748 (mm) cc_final: 0.8401 (mm) REVERT: A 62 HIS cc_start: 0.7844 (t70) cc_final: 0.7491 (t70) REVERT: A 64 GLN cc_start: 0.6435 (pm20) cc_final: 0.6053 (pm20) REVERT: A 79 VAL cc_start: 0.7871 (t) cc_final: 0.7359 (p) REVERT: A 92 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8610 (mtpp) REVERT: A 100 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7537 (mtm-85) REVERT: A 107 TYR cc_start: 0.8531 (t80) cc_final: 0.8263 (t80) REVERT: A 113 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7624 (mmmm) REVERT: A 132 MET cc_start: 0.8045 (mmm) cc_final: 0.7576 (mmm) REVERT: A 146 ASN cc_start: 0.8051 (m110) cc_final: 0.7344 (m-40) REVERT: A 155 ARG cc_start: 0.8586 (tpt90) cc_final: 0.7673 (mmm160) REVERT: A 158 GLN cc_start: 0.8880 (tt0) cc_final: 0.8509 (tt0) REVERT: A 164 LEU cc_start: 0.8254 (mt) cc_final: 0.7975 (mt) REVERT: A 201 PHE cc_start: 0.8208 (t80) cc_final: 0.7940 (t80) REVERT: A 203 PHE cc_start: 0.8311 (t80) cc_final: 0.7936 (t80) REVERT: A 208 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 226 TYR cc_start: 0.6071 (p90) cc_final: 0.5752 (p90) REVERT: A 254 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8103 (ttpp) REVERT: A 258 THR cc_start: 0.8797 (p) cc_final: 0.8522 (p) REVERT: B 15 TRP cc_start: 0.7909 (m100) cc_final: 0.7412 (m100) REVERT: B 40 CYS cc_start: 0.7481 (t) cc_final: 0.6932 (p) REVERT: B 63 TRP cc_start: 0.7946 (m100) cc_final: 0.6418 (m100) REVERT: B 64 GLN cc_start: 0.7111 (tp40) cc_final: 0.6168 (mm-40) REVERT: B 65 VAL cc_start: 0.8664 (t) cc_final: 0.8200 (t) REVERT: B 70 TYR cc_start: 0.7748 (t80) cc_final: 0.7417 (t80) REVERT: B 75 ILE cc_start: 0.7892 (pt) cc_final: 0.7644 (mp) REVERT: B 86 ILE cc_start: 0.8740 (pt) cc_final: 0.8125 (mm) REVERT: B 89 GLU cc_start: 0.7773 (tt0) cc_final: 0.7519 (tt0) REVERT: B 92 LYS cc_start: 0.8712 (tppt) cc_final: 0.8418 (tppp) REVERT: B 101 VAL cc_start: 0.8982 (t) cc_final: 0.8625 (t) REVERT: B 102 GLN cc_start: 0.8457 (mp10) cc_final: 0.8153 (mm-40) REVERT: B 104 MET cc_start: 0.8626 (mmp) cc_final: 0.8364 (mmp) REVERT: B 116 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6776 (tm-30) REVERT: B 132 MET cc_start: 0.8572 (mmp) cc_final: 0.8320 (mmt) REVERT: B 137 ILE cc_start: 0.8484 (tt) cc_final: 0.7817 (tt) REVERT: B 138 GLU cc_start: 0.7908 (tp30) cc_final: 0.7660 (tp30) REVERT: B 139 HIS cc_start: 0.8461 (t70) cc_final: 0.7927 (t70) REVERT: B 165 GLU cc_start: 0.7906 (tp30) cc_final: 0.7592 (tp30) REVERT: B 178 LEU cc_start: 0.9095 (mm) cc_final: 0.8658 (mm) REVERT: B 198 MET cc_start: 0.8097 (tpt) cc_final: 0.7678 (tpp) REVERT: C 28 ILE cc_start: 0.8075 (tp) cc_final: 0.7671 (tp) REVERT: C 35 ASP cc_start: 0.8578 (m-30) cc_final: 0.8014 (m-30) REVERT: C 110 PHE cc_start: 0.7773 (m-80) cc_final: 0.7540 (m-80) REVERT: C 132 MET cc_start: 0.8298 (ppp) cc_final: 0.7876 (ppp) REVERT: C 190 LYS cc_start: 0.6405 (mttm) cc_final: 0.6068 (mmmt) REVERT: C 199 ASP cc_start: 0.8850 (m-30) cc_final: 0.8635 (m-30) REVERT: C 209 ARG cc_start: 0.8568 (ptt90) cc_final: 0.8089 (ptt90) REVERT: C 244 LEU cc_start: 0.8315 (mm) cc_final: 0.7509 (mm) REVERT: C 245 TRP cc_start: 0.8186 (m-90) cc_final: 0.7830 (m-90) REVERT: D 203 PHE cc_start: 0.7688 (t80) cc_final: 0.7442 (t80) REVERT: D 218 GLN cc_start: 0.8475 (mm110) cc_final: 0.7911 (mm110) REVERT: D 223 PHE cc_start: 0.6372 (p90) cc_final: 0.5796 (p90) REVERT: D 226 TYR cc_start: 0.6598 (p90) cc_final: 0.6155 (p90) REVERT: D 254 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7652 (tptm) REVERT: D 263 VAL cc_start: 0.8202 (m) cc_final: 0.7993 (t) REVERT: D 268 ASP cc_start: 0.7024 (t70) cc_final: 0.6824 (t70) REVERT: E 10 GLU cc_start: 0.8087 (tp30) cc_final: 0.7560 (tp30) REVERT: E 15 TRP cc_start: 0.8578 (m-10) cc_final: 0.8078 (m-10) REVERT: E 16 HIS cc_start: 0.7800 (m-70) cc_final: 0.7500 (m170) REVERT: E 18 ASP cc_start: 0.7530 (t70) cc_final: 0.7323 (t70) REVERT: E 97 GLN cc_start: 0.7866 (pm20) cc_final: 0.7553 (pm20) REVERT: E 100 ARG cc_start: 0.8759 (ptp90) cc_final: 0.8401 (ptt-90) REVERT: E 101 VAL cc_start: 0.8850 (t) cc_final: 0.8590 (t) REVERT: E 138 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7454 (tm-30) REVERT: E 150 GLN cc_start: 0.7923 (mm110) cc_final: 0.7275 (mm-40) REVERT: E 158 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7590 (tm-30) REVERT: E 159 THR cc_start: 0.8543 (m) cc_final: 0.7920 (p) REVERT: E 178 LEU cc_start: 0.8932 (mt) cc_final: 0.8707 (mt) REVERT: E 199 ASP cc_start: 0.8390 (m-30) cc_final: 0.7532 (m-30) REVERT: E 201 PHE cc_start: 0.8262 (t80) cc_final: 0.7894 (t80) REVERT: E 204 ASN cc_start: 0.8582 (t0) cc_final: 0.8373 (t0) REVERT: E 205 LYS cc_start: 0.8889 (mttt) cc_final: 0.8379 (mmtp) REVERT: E 224 CYS cc_start: 0.5078 (p) cc_final: 0.4702 (p) REVERT: F 15 TRP cc_start: 0.6879 (m100) cc_final: 0.6267 (m100) REVERT: F 23 HIS cc_start: 0.7812 (t70) cc_final: 0.7484 (t70) REVERT: F 104 MET cc_start: 0.7939 (ptm) cc_final: 0.7446 (ppp) REVERT: F 105 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8762 (mttt) REVERT: F 199 ASP cc_start: 0.8480 (m-30) cc_final: 0.8151 (m-30) REVERT: F 202 ILE cc_start: 0.8195 (mt) cc_final: 0.7994 (mt) REVERT: F 205 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8324 (mtmt) REVERT: F 230 LYS cc_start: 0.8376 (mmmt) cc_final: 0.7882 (mmmm) REVERT: F 233 HIS cc_start: 0.7594 (m90) cc_final: 0.7336 (m90) REVERT: F 236 GLU cc_start: 0.7937 (pm20) cc_final: 0.7624 (pm20) REVERT: F 242 GLN cc_start: 0.7230 (tt0) cc_final: 0.6554 (pp30) REVERT: F 243 VAL cc_start: 0.8375 (t) cc_final: 0.7138 (m) REVERT: F 244 LEU cc_start: 0.7997 (tt) cc_final: 0.7608 (tt) REVERT: F 256 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7937 (ttm110) REVERT: G 48 MET cc_start: -0.0488 (ppp) cc_final: -0.1303 (ppp) REVERT: G 62 HIS cc_start: 0.7399 (t70) cc_final: 0.6915 (t70) REVERT: G 85 LEU cc_start: 0.7143 (tp) cc_final: 0.6634 (tp) REVERT: G 104 MET cc_start: 0.7842 (pmm) cc_final: 0.7630 (pmm) REVERT: G 110 PHE cc_start: 0.7869 (m-80) cc_final: 0.7480 (m-80) REVERT: G 131 LEU cc_start: 0.9279 (mt) cc_final: 0.9016 (mt) REVERT: G 153 VAL cc_start: 0.8190 (t) cc_final: 0.7855 (t) REVERT: G 164 LEU cc_start: 0.8188 (pp) cc_final: 0.7843 (pp) REVERT: G 183 ILE cc_start: 0.7434 (mt) cc_final: 0.7146 (mt) REVERT: G 197 PRO cc_start: 0.8614 (Cg_exo) cc_final: 0.8357 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8953 (m-30) cc_final: 0.8543 (m-30) REVERT: G 201 PHE cc_start: 0.8710 (t80) cc_final: 0.8019 (t80) REVERT: G 202 ILE cc_start: 0.8810 (mt) cc_final: 0.8606 (mt) REVERT: G 205 LYS cc_start: 0.9288 (mmtm) cc_final: 0.9063 (mmtp) REVERT: H 62 HIS cc_start: 0.7707 (t-90) cc_final: 0.7107 (t-170) REVERT: H 78 TRP cc_start: 0.6971 (m-10) cc_final: 0.6576 (m-10) REVERT: H 87 TYR cc_start: 0.8421 (t80) cc_final: 0.7925 (t80) REVERT: H 101 VAL cc_start: 0.8866 (p) cc_final: 0.8624 (p) REVERT: H 104 MET cc_start: 0.9068 (mmp) cc_final: 0.8452 (mmp) REVERT: H 109 MET cc_start: 0.7997 (tpt) cc_final: 0.7302 (tpt) REVERT: H 110 PHE cc_start: 0.8160 (m-10) cc_final: 0.7677 (m-10) REVERT: H 207 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7824 (mm-40) REVERT: H 222 ARG cc_start: 0.6496 (mmm160) cc_final: 0.6295 (mmm160) REVERT: H 223 PHE cc_start: 0.7183 (m-80) cc_final: 0.6944 (m-80) REVERT: I 66 ASP cc_start: 0.7340 (t70) cc_final: 0.6883 (t70) REVERT: I 79 VAL cc_start: 0.7984 (t) cc_final: 0.7533 (p) REVERT: I 90 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7572 (tmm-80) REVERT: I 92 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8367 (mtpp) REVERT: I 97 GLN cc_start: 0.7883 (pm20) cc_final: 0.7632 (pm20) REVERT: I 98 GLU cc_start: 0.8149 (mp0) cc_final: 0.7821 (mp0) REVERT: I 100 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7600 (mtm-85) REVERT: I 118 ASP cc_start: 0.7705 (p0) cc_final: 0.7320 (p0) REVERT: I 132 MET cc_start: 0.8190 (mmm) cc_final: 0.7871 (mmm) REVERT: I 143 ILE cc_start: 0.8467 (tp) cc_final: 0.7885 (tp) REVERT: I 146 ASN cc_start: 0.7979 (m110) cc_final: 0.7313 (m110) REVERT: I 155 ARG cc_start: 0.8313 (tpt90) cc_final: 0.7645 (mmm160) REVERT: I 158 GLN cc_start: 0.9047 (tt0) cc_final: 0.8696 (tt0) REVERT: I 161 LYS cc_start: 0.8644 (tptt) cc_final: 0.8441 (tptt) REVERT: I 164 LEU cc_start: 0.8463 (mt) cc_final: 0.8223 (mt) REVERT: I 184 THR cc_start: 0.8355 (m) cc_final: 0.8079 (p) REVERT: I 198 MET cc_start: 0.8423 (ttm) cc_final: 0.8182 (tpp) REVERT: I 203 PHE cc_start: 0.8254 (t80) cc_final: 0.7838 (t80) REVERT: I 208 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7929 (tm-30) REVERT: I 209 ARG cc_start: 0.7296 (tpp80) cc_final: 0.6904 (tpp80) REVERT: I 222 ARG cc_start: 0.5640 (mtp-110) cc_final: 0.5125 (mtm110) REVERT: I 253 VAL cc_start: 0.7303 (t) cc_final: 0.7028 (m) REVERT: I 264 ILE cc_start: 0.7871 (mm) cc_final: 0.7597 (mm) REVERT: J 40 CYS cc_start: 0.7176 (t) cc_final: 0.6760 (p) REVERT: J 62 HIS cc_start: 0.7219 (t-90) cc_final: 0.6929 (t-90) REVERT: J 63 TRP cc_start: 0.7849 (m100) cc_final: 0.6031 (m100) REVERT: J 64 GLN cc_start: 0.7162 (tp40) cc_final: 0.6321 (mm110) REVERT: J 65 VAL cc_start: 0.8749 (t) cc_final: 0.8417 (t) REVERT: J 71 GLU cc_start: 0.7802 (pp20) cc_final: 0.7572 (pp20) REVERT: J 86 ILE cc_start: 0.8887 (pt) cc_final: 0.8074 (mm) REVERT: J 92 LYS cc_start: 0.8800 (tptp) cc_final: 0.8426 (tptp) REVERT: J 100 ARG cc_start: 0.8561 (mpp80) cc_final: 0.8318 (ptp-170) REVERT: J 101 VAL cc_start: 0.8999 (t) cc_final: 0.8746 (t) REVERT: J 104 MET cc_start: 0.8185 (tpp) cc_final: 0.7463 (tpp) REVERT: J 116 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6986 (tm-30) REVERT: J 131 LEU cc_start: 0.8846 (tt) cc_final: 0.8428 (tt) REVERT: J 138 GLU cc_start: 0.7758 (tp30) cc_final: 0.7535 (tp30) REVERT: J 139 HIS cc_start: 0.8527 (t70) cc_final: 0.8160 (t70) REVERT: J 178 LEU cc_start: 0.9062 (mm) cc_final: 0.8676 (mm) REVERT: J 186 ASN cc_start: 0.7716 (m-40) cc_final: 0.7170 (m-40) REVERT: J 204 ASN cc_start: 0.8267 (m110) cc_final: 0.7244 (p0) REVERT: J 205 LYS cc_start: 0.8280 (tptp) cc_final: 0.7654 (tptp) REVERT: J 208 GLN cc_start: 0.8093 (pt0) cc_final: 0.7741 (pt0) REVERT: K 40 CYS cc_start: 0.8314 (m) cc_final: 0.7745 (p) REVERT: K 110 PHE cc_start: 0.7724 (m-80) cc_final: 0.7458 (m-80) REVERT: K 132 MET cc_start: 0.7551 (ppp) cc_final: 0.7309 (ppp) REVERT: K 222 ARG cc_start: 0.7340 (ttt-90) cc_final: 0.7085 (tmt170) REVERT: L 86 ILE cc_start: 0.6628 (pt) cc_final: 0.6337 (mm) REVERT: L 209 ARG cc_start: 0.8593 (mmp-170) cc_final: 0.8317 (mmm160) REVERT: L 223 PHE cc_start: 0.6002 (p90) cc_final: 0.5632 (p90) REVERT: L 226 TYR cc_start: 0.7115 (p90) cc_final: 0.6164 (p90) REVERT: L 254 LYS cc_start: 0.8407 (tmtt) cc_final: 0.7737 (tppt) REVERT: L 263 VAL cc_start: 0.7928 (m) cc_final: 0.7725 (t) REVERT: L 269 VAL cc_start: 0.7729 (m) cc_final: 0.7497 (m) REVERT: M 7 LEU cc_start: 0.8161 (tt) cc_final: 0.7325 (tt) REVERT: M 11 GLU cc_start: 0.8225 (mp0) cc_final: 0.7888 (mp0) REVERT: M 18 ASP cc_start: 0.7582 (t70) cc_final: 0.7198 (t70) REVERT: M 63 TRP cc_start: 0.7176 (m100) cc_final: 0.6623 (m100) REVERT: M 76 LEU cc_start: 0.7489 (tp) cc_final: 0.7194 (tp) REVERT: M 87 TYR cc_start: 0.7436 (t80) cc_final: 0.6872 (t80) REVERT: M 109 MET cc_start: 0.8248 (tmm) cc_final: 0.8030 (tmm) REVERT: M 154 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8734 (mm-30) REVERT: M 155 ARG cc_start: 0.8576 (ttt180) cc_final: 0.8289 (mtt90) REVERT: M 158 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7347 (tm-30) REVERT: M 159 THR cc_start: 0.8657 (m) cc_final: 0.7866 (p) REVERT: M 162 ASN cc_start: 0.8127 (m-40) cc_final: 0.7871 (m110) REVERT: M 178 LEU cc_start: 0.8799 (mt) cc_final: 0.8563 (mt) REVERT: M 199 ASP cc_start: 0.8664 (m-30) cc_final: 0.7709 (m-30) REVERT: M 202 ILE cc_start: 0.8780 (mm) cc_final: 0.8286 (mm) REVERT: M 205 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8214 (mtmm) REVERT: M 206 GLU cc_start: 0.8626 (pt0) cc_final: 0.8113 (pt0) REVERT: M 207 GLN cc_start: 0.8499 (mm110) cc_final: 0.8246 (mm110) REVERT: M 209 ARG cc_start: 0.8817 (tmt170) cc_final: 0.8395 (ttp80) REVERT: N 23 HIS cc_start: 0.7687 (t70) cc_final: 0.7422 (t70) REVERT: N 65 VAL cc_start: 0.7549 (t) cc_final: 0.7073 (p) REVERT: N 104 MET cc_start: 0.8149 (ptm) cc_final: 0.7796 (ptm) REVERT: N 110 PHE cc_start: 0.8036 (m-80) cc_final: 0.7811 (m-80) REVERT: N 154 GLU cc_start: 0.7968 (mp0) cc_final: 0.7703 (mp0) REVERT: N 162 ASN cc_start: 0.8611 (m-40) cc_final: 0.8392 (m110) REVERT: N 203 PHE cc_start: 0.7633 (t80) cc_final: 0.7221 (t80) REVERT: N 205 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7885 (ptpp) REVERT: N 208 GLN cc_start: 0.8468 (tt0) cc_final: 0.8195 (tm-30) REVERT: N 210 ILE cc_start: 0.8321 (pt) cc_final: 0.8098 (pt) REVERT: N 213 GLN cc_start: 0.8786 (mt0) cc_final: 0.8128 (mt0) REVERT: N 230 LYS cc_start: 0.8266 (mttt) cc_final: 0.7562 (mppt) REVERT: N 233 HIS cc_start: 0.7719 (m90) cc_final: 0.7130 (m-70) REVERT: N 242 GLN cc_start: 0.7793 (tt0) cc_final: 0.7192 (pp30) REVERT: N 243 VAL cc_start: 0.8502 (t) cc_final: 0.7489 (m) REVERT: N 244 LEU cc_start: 0.8227 (tt) cc_final: 0.7978 (tt) REVERT: N 256 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7680 (ttm110) REVERT: O 40 CYS cc_start: 0.5656 (t) cc_final: 0.5427 (t) REVERT: O 48 MET cc_start: -0.1433 (ppp) cc_final: -0.1853 (ppp) REVERT: O 104 MET cc_start: 0.8058 (pmm) cc_final: 0.7717 (pmm) REVERT: O 110 PHE cc_start: 0.8014 (m-80) cc_final: 0.7728 (m-10) REVERT: O 115 LEU cc_start: 0.8822 (tp) cc_final: 0.8579 (tp) REVERT: O 132 MET cc_start: 0.8145 (tmm) cc_final: 0.7776 (tmm) REVERT: O 154 GLU cc_start: 0.9017 (pp20) cc_final: 0.8571 (pp20) REVERT: O 155 ARG cc_start: 0.9099 (mtm110) cc_final: 0.8874 (ptp-110) REVERT: O 157 HIS cc_start: 0.8947 (p90) cc_final: 0.8687 (p90) REVERT: O 193 LEU cc_start: 0.8734 (mm) cc_final: 0.8472 (mm) REVERT: O 199 ASP cc_start: 0.8865 (m-30) cc_final: 0.8546 (m-30) REVERT: O 201 PHE cc_start: 0.8726 (t80) cc_final: 0.7959 (t80) REVERT: O 205 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8913 (mmtp) REVERT: O 208 GLN cc_start: 0.8642 (tm130) cc_final: 0.8351 (tm-30) REVERT: O 209 ARG cc_start: 0.8810 (ptm-80) cc_final: 0.8467 (ptm-80) REVERT: O 211 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8143 (tp40) REVERT: P 87 TYR cc_start: 0.8649 (t80) cc_final: 0.8342 (t80) REVERT: P 101 VAL cc_start: 0.9166 (p) cc_final: 0.8925 (p) REVERT: P 104 MET cc_start: 0.9170 (mmp) cc_final: 0.8653 (mmp) REVERT: P 106 TRP cc_start: 0.8500 (t60) cc_final: 0.8147 (t60) REVERT: P 132 MET cc_start: 0.6387 (tmm) cc_final: 0.5817 (tmm) REVERT: P 137 ILE cc_start: 0.8142 (mm) cc_final: 0.7930 (mm) REVERT: P 170 MET cc_start: 0.7440 (mtt) cc_final: 0.6959 (mpp) REVERT: P 172 ASN cc_start: 0.8778 (m-40) cc_final: 0.8439 (p0) REVERT: P 230 LYS cc_start: 0.7367 (mmmt) cc_final: 0.7133 (mmtm) outliers start: 8 outliers final: 3 residues processed: 1140 average time/residue: 0.2327 time to fit residues: 417.5231 Evaluate side-chains 1065 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1062 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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: 0.9990 chunk 74 optimal weight: 0.6980 chunk 373 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 120 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 356 optimal weight: 0.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN L 158 GLN M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 62 HIS O 102 GLN O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.202275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.155432 restraints weight = 70735.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.161122 restraints weight = 45267.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.165282 restraints weight = 32173.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.168249 restraints weight = 24460.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.170372 restraints weight = 19652.525| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 34119 Z= 0.155 Angle : 0.693 13.652 46515 Z= 0.370 Chirality : 0.049 0.269 5006 Planarity : 0.005 0.125 5714 Dihedral : 14.796 169.691 5007 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 0.09 % Allowed : 2.25 % Favored : 97.66 % 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: 1.00 (0.12), residues: 1870 sheet: -0.63 (0.17), residues: 879 loop : -1.46 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 155 TYR 0.054 0.001 TYR O 70 PHE 0.048 0.002 PHE K 26 TRP 0.060 0.002 TRP F 237 HIS 0.022 0.001 HIS G 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (34119) covalent geometry : angle 0.69310 / 0.37 (46515) hydrogen bonds : bond 0.04067 / 2.79 ( 1746) hydrogen bonds : angle 5.40170 / 3.90 ( 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 1148 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1145 time to evaluate : 1.201 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 15 TRP cc_start: 0.6625 (m-10) cc_final: 0.5577 (m100) REVERT: A 60 ILE cc_start: 0.8724 (mm) cc_final: 0.8291 (mm) REVERT: A 62 HIS cc_start: 0.7790 (t70) cc_final: 0.7417 (t70) REVERT: A 64 GLN cc_start: 0.6451 (pm20) cc_final: 0.5764 (pm20) REVERT: A 66 ASP cc_start: 0.7273 (t70) cc_final: 0.6901 (t70) REVERT: A 79 VAL cc_start: 0.7909 (t) cc_final: 0.7266 (p) REVERT: A 82 ASN cc_start: 0.8228 (t0) cc_final: 0.7935 (p0) REVERT: A 92 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8346 (mtpp) REVERT: A 97 GLN cc_start: 0.7647 (pm20) cc_final: 0.7237 (pm20) REVERT: A 100 ARG cc_start: 0.8118 (mtt90) cc_final: 0.7637 (mtm-85) REVERT: A 107 TYR cc_start: 0.8407 (t80) cc_final: 0.8048 (t80) REVERT: A 113 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7649 (mmmm) REVERT: A 118 ASP cc_start: 0.7519 (p0) cc_final: 0.7249 (p0) REVERT: A 129 GLN cc_start: 0.7871 (tt0) cc_final: 0.7552 (tt0) REVERT: A 135 LEU cc_start: 0.8790 (mt) cc_final: 0.8415 (mt) REVERT: A 146 ASN cc_start: 0.8128 (m110) cc_final: 0.7352 (m-40) REVERT: A 152 LEU cc_start: 0.7452 (pt) cc_final: 0.6386 (mp) REVERT: A 153 VAL cc_start: 0.8976 (m) cc_final: 0.8718 (m) REVERT: A 155 ARG cc_start: 0.8616 (tpt90) cc_final: 0.7720 (mmm160) REVERT: A 158 GLN cc_start: 0.8866 (tt0) cc_final: 0.8467 (tt0) REVERT: A 161 LYS cc_start: 0.8686 (tptt) cc_final: 0.8458 (tptt) REVERT: A 201 PHE cc_start: 0.8263 (t80) cc_final: 0.7986 (t80) REVERT: A 203 PHE cc_start: 0.8306 (t80) cc_final: 0.7876 (t80) REVERT: A 208 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7610 (tm-30) REVERT: A 226 TYR cc_start: 0.6170 (p90) cc_final: 0.5865 (p90) REVERT: A 254 LYS cc_start: 0.8551 (tmmt) cc_final: 0.8284 (ttpp) REVERT: B 15 TRP cc_start: 0.7901 (m100) cc_final: 0.7400 (m100) REVERT: B 40 CYS cc_start: 0.7417 (t) cc_final: 0.6905 (p) REVERT: B 63 TRP cc_start: 0.7892 (m100) cc_final: 0.6157 (m100) REVERT: B 64 GLN cc_start: 0.7073 (tp40) cc_final: 0.6503 (mm110) REVERT: B 65 VAL cc_start: 0.8661 (t) cc_final: 0.8250 (t) REVERT: B 70 TYR cc_start: 0.7929 (t80) cc_final: 0.7470 (t80) REVERT: B 75 ILE cc_start: 0.7923 (pt) cc_final: 0.7645 (mp) REVERT: B 86 ILE cc_start: 0.8783 (pt) cc_final: 0.8059 (mm) REVERT: B 87 TYR cc_start: 0.8188 (t80) cc_final: 0.7977 (t80) REVERT: B 92 LYS cc_start: 0.8726 (tppt) cc_final: 0.8183 (tptp) REVERT: B 101 VAL cc_start: 0.8945 (t) cc_final: 0.8668 (t) REVERT: B 102 GLN cc_start: 0.8490 (mp10) cc_final: 0.8219 (mm-40) REVERT: B 104 MET cc_start: 0.8635 (mmp) cc_final: 0.8336 (mmp) REVERT: B 105 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8715 (mtpp) REVERT: B 129 GLN cc_start: 0.8437 (pt0) cc_final: 0.8061 (pt0) REVERT: B 132 MET cc_start: 0.8608 (mmp) cc_final: 0.8340 (mmt) REVERT: B 137 ILE cc_start: 0.8580 (tt) cc_final: 0.7835 (tt) REVERT: B 138 GLU cc_start: 0.7887 (tp30) cc_final: 0.7644 (tp30) REVERT: B 139 HIS cc_start: 0.8476 (t70) cc_final: 0.7943 (t70) REVERT: B 165 GLU cc_start: 0.7895 (tp30) cc_final: 0.7569 (tp30) REVERT: B 178 LEU cc_start: 0.9169 (mm) cc_final: 0.8775 (mm) REVERT: B 198 MET cc_start: 0.8058 (tpt) cc_final: 0.7639 (tpp) REVERT: B 204 ASN cc_start: 0.7951 (p0) cc_final: 0.7440 (p0) REVERT: B 208 GLN cc_start: 0.8609 (mt0) cc_final: 0.8374 (mt0) REVERT: C 28 ILE cc_start: 0.8084 (tp) cc_final: 0.7670 (tp) REVERT: C 110 PHE cc_start: 0.7802 (m-80) cc_final: 0.7544 (m-80) REVERT: C 161 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8708 (ttpp) REVERT: C 186 ASN cc_start: 0.7924 (m-40) cc_final: 0.7688 (m110) REVERT: C 190 LYS cc_start: 0.6409 (mttm) cc_final: 0.6045 (mmmt) REVERT: C 199 ASP cc_start: 0.8802 (m-30) cc_final: 0.8531 (m-30) REVERT: C 206 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: C 209 ARG cc_start: 0.8476 (ptt90) cc_final: 0.8150 (ptt90) REVERT: C 244 LEU cc_start: 0.8228 (mm) cc_final: 0.7450 (mm) REVERT: C 245 TRP cc_start: 0.8196 (m-90) cc_final: 0.7827 (m-90) REVERT: D 218 GLN cc_start: 0.8466 (mm110) cc_final: 0.7914 (mm110) REVERT: D 226 TYR cc_start: 0.7028 (p90) cc_final: 0.6171 (p90) REVERT: D 254 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7680 (tptm) REVERT: D 262 LEU cc_start: 0.7716 (mp) cc_final: 0.7477 (mp) REVERT: D 263 VAL cc_start: 0.8208 (m) cc_final: 0.7952 (t) REVERT: E 10 GLU cc_start: 0.8009 (tp30) cc_final: 0.7431 (tp30) REVERT: E 15 TRP cc_start: 0.8615 (m-10) cc_final: 0.8400 (m-10) REVERT: E 16 HIS cc_start: 0.7968 (m-70) cc_final: 0.7590 (m170) REVERT: E 87 TYR cc_start: 0.7064 (t80) cc_final: 0.6248 (t80) REVERT: E 138 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7394 (tm-30) REVERT: E 150 GLN cc_start: 0.8103 (mm110) cc_final: 0.7536 (mm110) REVERT: E 159 THR cc_start: 0.8571 (m) cc_final: 0.7940 (p) REVERT: E 178 LEU cc_start: 0.8939 (mt) cc_final: 0.8715 (mt) REVERT: E 199 ASP cc_start: 0.8377 (m-30) cc_final: 0.7583 (m-30) REVERT: E 201 PHE cc_start: 0.8291 (t80) cc_final: 0.7898 (t80) REVERT: E 205 LYS cc_start: 0.8876 (mttt) cc_final: 0.8447 (mmtp) REVERT: E 224 CYS cc_start: 0.5869 (p) cc_final: 0.5413 (p) REVERT: E 242 GLN cc_start: 0.5951 (pp30) cc_final: 0.5443 (pp30) REVERT: F 23 HIS cc_start: 0.7572 (t70) cc_final: 0.7224 (t70) REVERT: F 65 VAL cc_start: 0.7099 (t) cc_final: 0.6844 (p) REVERT: F 80 GLU cc_start: 0.6672 (tm-30) cc_final: 0.6293 (tm-30) REVERT: F 104 MET cc_start: 0.7974 (ptm) cc_final: 0.7453 (ppp) REVERT: F 105 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8830 (mttt) REVERT: F 158 GLN cc_start: 0.9186 (mt0) cc_final: 0.8508 (pt0) REVERT: F 208 GLN cc_start: 0.8544 (tt0) cc_final: 0.8056 (tm-30) REVERT: F 230 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7936 (mmmm) REVERT: F 233 HIS cc_start: 0.7624 (m90) cc_final: 0.7337 (m90) REVERT: F 236 GLU cc_start: 0.7797 (pm20) cc_final: 0.7568 (mp0) REVERT: F 242 GLN cc_start: 0.7235 (tt0) cc_final: 0.6562 (pp30) REVERT: F 243 VAL cc_start: 0.8391 (t) cc_final: 0.7179 (m) REVERT: F 244 LEU cc_start: 0.8073 (tt) cc_final: 0.7672 (tt) REVERT: F 256 ARG cc_start: 0.8349 (ttm110) cc_final: 0.7945 (ttm110) REVERT: G 48 MET cc_start: -0.0474 (ppp) cc_final: -0.1319 (ppp) REVERT: G 62 HIS cc_start: 0.7329 (t70) cc_final: 0.6949 (t70) REVERT: G 104 MET cc_start: 0.7844 (pmm) cc_final: 0.7607 (pmm) REVERT: G 110 PHE cc_start: 0.8024 (m-80) cc_final: 0.7253 (m-80) REVERT: G 131 LEU cc_start: 0.9284 (mt) cc_final: 0.9028 (mt) REVERT: G 161 LYS cc_start: 0.9216 (tptt) cc_final: 0.8679 (tptt) REVERT: G 170 MET cc_start: 0.7598 (mmp) cc_final: 0.7369 (mmp) REVERT: G 171 PHE cc_start: 0.6947 (m-80) cc_final: 0.6525 (m-80) REVERT: G 197 PRO cc_start: 0.8561 (Cg_exo) cc_final: 0.8357 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8932 (m-30) cc_final: 0.8473 (m-30) REVERT: G 209 ARG cc_start: 0.8869 (ttp80) cc_final: 0.8266 (ttp80) REVERT: G 210 ILE cc_start: 0.8556 (pt) cc_final: 0.7915 (pt) REVERT: H 78 TRP cc_start: 0.6877 (m-10) cc_final: 0.6557 (m-10) REVERT: H 87 TYR cc_start: 0.8460 (t80) cc_final: 0.7982 (t80) REVERT: H 95 THR cc_start: 0.5236 (t) cc_final: 0.5025 (p) REVERT: H 101 VAL cc_start: 0.8861 (p) cc_final: 0.8617 (p) REVERT: H 104 MET cc_start: 0.9092 (mmp) cc_final: 0.8485 (mmp) REVERT: H 106 TRP cc_start: 0.8455 (t60) cc_final: 0.7879 (t60) REVERT: H 110 PHE cc_start: 0.7809 (m-10) cc_final: 0.7567 (m-10) REVERT: H 207 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7716 (mm-40) REVERT: H 223 PHE cc_start: 0.7156 (m-80) cc_final: 0.6929 (m-80) REVERT: I 66 ASP cc_start: 0.7567 (t70) cc_final: 0.7141 (t70) REVERT: I 79 VAL cc_start: 0.8032 (t) cc_final: 0.7483 (p) REVERT: I 86 ILE cc_start: 0.8404 (pt) cc_final: 0.7683 (mp) REVERT: I 92 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8574 (mtpp) REVERT: I 97 GLN cc_start: 0.7835 (pm20) cc_final: 0.7591 (pm20) REVERT: I 98 GLU cc_start: 0.8173 (mp0) cc_final: 0.7774 (mp0) REVERT: I 100 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7624 (mtm-85) REVERT: I 118 ASP cc_start: 0.7633 (p0) cc_final: 0.7290 (p0) REVERT: I 132 MET cc_start: 0.8300 (mmm) cc_final: 0.7978 (mmm) REVERT: I 143 ILE cc_start: 0.8489 (tp) cc_final: 0.7872 (tp) REVERT: I 146 ASN cc_start: 0.8113 (m110) cc_final: 0.7399 (m110) REVERT: I 155 ARG cc_start: 0.8298 (tpt90) cc_final: 0.7617 (mmm160) REVERT: I 158 GLN cc_start: 0.9049 (tt0) cc_final: 0.8615 (tt0) REVERT: I 159 THR cc_start: 0.8600 (p) cc_final: 0.8245 (m) REVERT: I 164 LEU cc_start: 0.8501 (mt) cc_final: 0.8243 (mt) REVERT: I 183 ILE cc_start: 0.8852 (mt) cc_final: 0.8608 (mt) REVERT: I 198 MET cc_start: 0.8509 (ttm) cc_final: 0.8217 (tpp) REVERT: I 201 PHE cc_start: 0.8380 (t80) cc_final: 0.8168 (t80) REVERT: I 203 PHE cc_start: 0.8239 (t80) cc_final: 0.7840 (t80) REVERT: I 208 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7945 (tm-30) REVERT: I 209 ARG cc_start: 0.7393 (tpp80) cc_final: 0.7015 (tpp80) REVERT: I 253 VAL cc_start: 0.7311 (t) cc_final: 0.7042 (m) REVERT: I 254 LYS cc_start: 0.8340 (tptp) cc_final: 0.7963 (tppt) REVERT: I 264 ILE cc_start: 0.7985 (mm) cc_final: 0.7689 (mm) REVERT: J 40 CYS cc_start: 0.7164 (t) cc_final: 0.6706 (p) REVERT: J 62 HIS cc_start: 0.7262 (t-90) cc_final: 0.6883 (t-90) REVERT: J 63 TRP cc_start: 0.7761 (m100) cc_final: 0.5955 (m100) REVERT: J 64 GLN cc_start: 0.7139 (tp40) cc_final: 0.6271 (mm110) REVERT: J 65 VAL cc_start: 0.8723 (t) cc_final: 0.8382 (t) REVERT: J 86 ILE cc_start: 0.8919 (pt) cc_final: 0.8132 (mm) REVERT: J 92 LYS cc_start: 0.8808 (tptp) cc_final: 0.8436 (tptp) REVERT: J 100 ARG cc_start: 0.8641 (mpp80) cc_final: 0.8379 (mtt90) REVERT: J 104 MET cc_start: 0.8194 (tpp) cc_final: 0.7558 (tpp) REVERT: J 116 GLN cc_start: 0.7325 (tm-30) cc_final: 0.7044 (tm-30) REVERT: J 131 LEU cc_start: 0.8838 (tt) cc_final: 0.8476 (tt) REVERT: J 138 GLU cc_start: 0.7765 (tp30) cc_final: 0.7531 (tp30) REVERT: J 139 HIS cc_start: 0.8492 (t70) cc_final: 0.8176 (t70) REVERT: J 178 LEU cc_start: 0.9075 (mm) cc_final: 0.8700 (mm) REVERT: J 186 ASN cc_start: 0.7772 (m-40) cc_final: 0.7212 (m-40) REVERT: J 204 ASN cc_start: 0.8314 (m110) cc_final: 0.7223 (p0) REVERT: J 205 LYS cc_start: 0.8278 (tptp) cc_final: 0.7728 (tptp) REVERT: J 208 GLN cc_start: 0.8112 (pt0) cc_final: 0.7735 (pt0) REVERT: K 15 TRP cc_start: 0.8203 (m100) cc_final: 0.7696 (m100) REVERT: K 22 LEU cc_start: 0.8640 (mm) cc_final: 0.8036 (mm) REVERT: K 34 GLU cc_start: 0.8745 (pt0) cc_final: 0.8314 (pp20) REVERT: K 35 ASP cc_start: 0.8703 (m-30) cc_final: 0.8402 (m-30) REVERT: K 40 CYS cc_start: 0.8288 (m) cc_final: 0.7732 (p) REVERT: K 132 MET cc_start: 0.7494 (ppp) cc_final: 0.7275 (ppp) REVERT: K 190 LYS cc_start: 0.6493 (mttm) cc_final: 0.5990 (mmmt) REVERT: K 208 GLN cc_start: 0.8546 (tt0) cc_final: 0.7828 (mt0) REVERT: K 212 GLN cc_start: 0.7715 (mp10) cc_final: 0.7103 (mp10) REVERT: K 222 ARG cc_start: 0.7573 (ttt-90) cc_final: 0.7373 (tmt170) REVERT: L 86 ILE cc_start: 0.6935 (pt) cc_final: 0.6666 (mm) REVERT: L 209 ARG cc_start: 0.8672 (mmp-170) cc_final: 0.8438 (mmp-170) REVERT: L 223 PHE cc_start: 0.6040 (p90) cc_final: 0.5836 (p90) REVERT: L 226 TYR cc_start: 0.6682 (p90) cc_final: 0.6050 (p90) REVERT: L 254 LYS cc_start: 0.8336 (tmtt) cc_final: 0.7757 (tppt) REVERT: L 263 VAL cc_start: 0.8039 (m) cc_final: 0.7798 (t) REVERT: L 269 VAL cc_start: 0.7730 (m) cc_final: 0.7471 (m) REVERT: M 18 ASP cc_start: 0.7672 (t70) cc_final: 0.7386 (t70) REVERT: M 36 ILE cc_start: 0.8575 (mt) cc_final: 0.8345 (mt) REVERT: M 63 TRP cc_start: 0.7091 (m100) cc_final: 0.6361 (m100) REVERT: M 76 LEU cc_start: 0.7192 (tp) cc_final: 0.6927 (tp) REVERT: M 78 TRP cc_start: 0.5934 (m100) cc_final: 0.5514 (m100) REVERT: M 87 TYR cc_start: 0.7430 (t80) cc_final: 0.6764 (t80) REVERT: M 154 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8714 (mm-30) REVERT: M 155 ARG cc_start: 0.8569 (ttt180) cc_final: 0.8273 (mtt90) REVERT: M 158 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7358 (tm-30) REVERT: M 159 THR cc_start: 0.8804 (m) cc_final: 0.8186 (p) REVERT: M 162 ASN cc_start: 0.8148 (m-40) cc_final: 0.7892 (m110) REVERT: M 178 LEU cc_start: 0.8805 (mt) cc_final: 0.8558 (mt) REVERT: M 199 ASP cc_start: 0.8651 (m-30) cc_final: 0.7704 (m-30) REVERT: M 202 ILE cc_start: 0.8792 (mm) cc_final: 0.8253 (mm) REVERT: M 205 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8450 (mtmm) REVERT: M 206 GLU cc_start: 0.8606 (pt0) cc_final: 0.8127 (pt0) REVERT: M 207 GLN cc_start: 0.8498 (mm110) cc_final: 0.8227 (mm110) REVERT: M 209 ARG cc_start: 0.8829 (tmt170) cc_final: 0.8393 (ttp80) REVERT: N 23 HIS cc_start: 0.7728 (t70) cc_final: 0.7453 (t70) REVERT: N 65 VAL cc_start: 0.7525 (t) cc_final: 0.7258 (p) REVERT: N 104 MET cc_start: 0.8155 (ptm) cc_final: 0.7743 (ptm) REVERT: N 170 MET cc_start: 0.7070 (mpp) cc_final: 0.6822 (mpp) REVERT: N 203 PHE cc_start: 0.7755 (t80) cc_final: 0.7351 (t80) REVERT: N 208 GLN cc_start: 0.8481 (tt0) cc_final: 0.8219 (tm-30) REVERT: N 210 ILE cc_start: 0.8291 (pt) cc_final: 0.8079 (pt) REVERT: N 213 GLN cc_start: 0.8756 (mt0) cc_final: 0.8134 (mt0) REVERT: N 233 HIS cc_start: 0.7732 (m90) cc_final: 0.7366 (m-70) REVERT: N 242 GLN cc_start: 0.7852 (tt0) cc_final: 0.7213 (pp30) REVERT: N 243 VAL cc_start: 0.8492 (t) cc_final: 0.7507 (m) REVERT: N 244 LEU cc_start: 0.8298 (tt) cc_final: 0.8020 (tt) REVERT: N 256 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7707 (ttm110) REVERT: O 40 CYS cc_start: 0.5702 (t) cc_final: 0.5489 (t) REVERT: O 48 MET cc_start: -0.1440 (ppp) cc_final: -0.1891 (ppp) REVERT: O 71 GLU cc_start: 0.6683 (mp0) cc_final: 0.6474 (tp30) REVERT: O 110 PHE cc_start: 0.8146 (m-80) cc_final: 0.7839 (m-10) REVERT: O 132 MET cc_start: 0.8141 (tmm) cc_final: 0.7745 (tmm) REVERT: O 154 GLU cc_start: 0.9025 (pp20) cc_final: 0.8533 (pp20) REVERT: O 155 ARG cc_start: 0.9155 (mtm110) cc_final: 0.8728 (ptp-110) REVERT: O 157 HIS cc_start: 0.9056 (p90) cc_final: 0.8735 (p90) REVERT: O 193 LEU cc_start: 0.8723 (mm) cc_final: 0.8479 (mm) REVERT: O 199 ASP cc_start: 0.8861 (m-30) cc_final: 0.8537 (m-30) REVERT: O 201 PHE cc_start: 0.8754 (t80) cc_final: 0.7956 (t80) REVERT: O 205 LYS cc_start: 0.9235 (mmtm) cc_final: 0.8913 (mmtp) REVERT: O 209 ARG cc_start: 0.8764 (ptm-80) cc_final: 0.8352 (ptm-80) REVERT: P 87 TYR cc_start: 0.8653 (t80) cc_final: 0.8298 (t80) REVERT: P 101 VAL cc_start: 0.9144 (p) cc_final: 0.8903 (p) REVERT: P 104 MET cc_start: 0.9166 (mmp) cc_final: 0.8640 (mmp) REVERT: P 106 TRP cc_start: 0.8444 (t60) cc_final: 0.8077 (t60) REVERT: P 132 MET cc_start: 0.6668 (tmm) cc_final: 0.6082 (tmm) REVERT: P 137 ILE cc_start: 0.8177 (mm) cc_final: 0.7892 (mm) REVERT: P 170 MET cc_start: 0.7443 (mtt) cc_final: 0.6970 (mpp) REVERT: P 172 ASN cc_start: 0.8796 (m-40) cc_final: 0.8457 (p0) REVERT: P 230 LYS cc_start: 0.7414 (mmmt) cc_final: 0.7171 (mmtm) REVERT: P 254 LYS cc_start: 0.8612 (mtpp) cc_final: 0.7771 (tppt) outliers start: 3 outliers final: 1 residues processed: 1148 average time/residue: 0.2327 time to fit residues: 421.0324 Evaluate side-chains 1055 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1053 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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: 0.0770 chunk 178 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- 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 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 238 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 62 HIS ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN J 157 HIS J 158 GLN J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN L 186 ASN M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN N 186 ASN O 102 GLN O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.199110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.152656 restraints weight = 71000.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.158375 restraints weight = 45029.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.162354 restraints weight = 31668.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.165254 restraints weight = 23997.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.167251 restraints weight = 19262.863| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34119 Z= 0.178 Angle : 0.723 13.786 46515 Z= 0.391 Chirality : 0.050 0.238 5006 Planarity : 0.005 0.091 5714 Dihedral : 14.859 170.598 5007 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 0.03 % Allowed : 1.89 % 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: -0.28 (0.13), residues: 3851 helix: 0.93 (0.12), residues: 1859 sheet: -0.71 (0.17), residues: 855 loop : -1.49 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 222 TYR 0.034 0.001 TYR G 70 PHE 0.033 0.002 PHE N 201 TRP 0.039 0.002 TRP F 78 HIS 0.017 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (34119) covalent geometry : angle 0.72280 / 0.39 (46515) hydrogen bonds : bond 0.04224 / 2.90 ( 1746) hydrogen bonds : angle 5.55696 / 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 1143 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1142 time to evaluate : 1.214 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: A 15 TRP cc_start: 0.6879 (m-10) cc_final: 0.5819 (m100) REVERT: A 60 ILE cc_start: 0.8689 (mm) cc_final: 0.8281 (mm) REVERT: A 66 ASP cc_start: 0.7420 (t70) cc_final: 0.7018 (t70) REVERT: A 79 VAL cc_start: 0.8074 (t) cc_final: 0.7567 (p) REVERT: A 81 THR cc_start: 0.8690 (p) cc_final: 0.8400 (t) REVERT: A 90 ARG cc_start: 0.8054 (tmm-80) cc_final: 0.7651 (tmm-80) REVERT: A 92 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8318 (mtpp) REVERT: A 97 GLN cc_start: 0.7877 (pm20) cc_final: 0.7606 (pm20) REVERT: A 100 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7542 (mtm-85) REVERT: A 107 TYR cc_start: 0.8432 (t80) cc_final: 0.8085 (t80) REVERT: A 113 LYS cc_start: 0.7985 (mmmm) cc_final: 0.7695 (mmmm) REVERT: A 129 GLN cc_start: 0.7896 (tt0) cc_final: 0.7597 (tt0) REVERT: A 131 LEU cc_start: 0.8704 (pp) cc_final: 0.8428 (pp) REVERT: A 132 MET cc_start: 0.8090 (mmm) cc_final: 0.7608 (mmm) REVERT: A 135 LEU cc_start: 0.8860 (mt) cc_final: 0.8541 (mt) REVERT: A 155 ARG cc_start: 0.8571 (tpt90) cc_final: 0.7454 (mmm160) REVERT: A 158 GLN cc_start: 0.8856 (tt0) cc_final: 0.8484 (tt0) REVERT: A 164 LEU cc_start: 0.8340 (mt) cc_final: 0.8083 (mt) REVERT: A 175 GLU cc_start: 0.8302 (pm20) cc_final: 0.7960 (pm20) REVERT: A 190 LYS cc_start: 0.7847 (ptpp) cc_final: 0.6646 (mtpt) REVERT: A 198 MET cc_start: 0.8406 (ttm) cc_final: 0.8181 (ttm) REVERT: A 201 PHE cc_start: 0.8476 (t80) cc_final: 0.8275 (t80) REVERT: A 203 PHE cc_start: 0.8489 (t80) cc_final: 0.8073 (t80) REVERT: A 223 PHE cc_start: 0.6575 (m-10) cc_final: 0.6362 (m-10) REVERT: A 226 TYR cc_start: 0.6347 (p90) cc_final: 0.5979 (p90) REVERT: A 254 LYS cc_start: 0.8424 (tmmt) cc_final: 0.8072 (ttpp) REVERT: A 258 THR cc_start: 0.8801 (p) cc_final: 0.8540 (p) REVERT: B 13 ASN cc_start: 0.6994 (m110) cc_final: 0.6564 (m110) REVERT: B 15 TRP cc_start: 0.7923 (m100) cc_final: 0.7414 (m100) REVERT: B 40 CYS cc_start: 0.7500 (t) cc_final: 0.6927 (p) REVERT: B 63 TRP cc_start: 0.7853 (m100) cc_final: 0.6154 (m100) REVERT: B 64 GLN cc_start: 0.7083 (tp40) cc_final: 0.6585 (mm110) REVERT: B 65 VAL cc_start: 0.8620 (t) cc_final: 0.8208 (t) REVERT: B 70 TYR cc_start: 0.8179 (t80) cc_final: 0.7805 (t80) REVERT: B 75 ILE cc_start: 0.7961 (pt) cc_final: 0.7744 (mp) REVERT: B 86 ILE cc_start: 0.8864 (pt) cc_final: 0.8090 (mm) REVERT: B 87 TYR cc_start: 0.8216 (t80) cc_final: 0.8006 (t80) REVERT: B 89 GLU cc_start: 0.7715 (tt0) cc_final: 0.7169 (tt0) REVERT: B 92 LYS cc_start: 0.8773 (tppt) cc_final: 0.8163 (tptp) REVERT: B 101 VAL cc_start: 0.8985 (t) cc_final: 0.8655 (t) REVERT: B 102 GLN cc_start: 0.8691 (mp10) cc_final: 0.8285 (mm-40) REVERT: B 104 MET cc_start: 0.8701 (mmp) cc_final: 0.8337 (mmp) REVERT: B 129 GLN cc_start: 0.8463 (pt0) cc_final: 0.8081 (pt0) REVERT: B 131 LEU cc_start: 0.9073 (tt) cc_final: 0.8822 (tt) REVERT: B 132 MET cc_start: 0.8625 (mmp) cc_final: 0.8366 (mmt) REVERT: B 137 ILE cc_start: 0.8608 (tt) cc_final: 0.7791 (tt) REVERT: B 138 GLU cc_start: 0.7847 (tp30) cc_final: 0.7531 (tp30) REVERT: B 139 HIS cc_start: 0.8491 (t70) cc_final: 0.7992 (t70) REVERT: B 164 LEU cc_start: 0.8941 (tp) cc_final: 0.8717 (tp) REVERT: B 165 GLU cc_start: 0.7992 (tp30) cc_final: 0.7674 (tp30) REVERT: B 178 LEU cc_start: 0.9211 (mm) cc_final: 0.8817 (mm) REVERT: B 189 ARG cc_start: 0.7115 (mtm-85) cc_final: 0.6433 (ptp-170) REVERT: B 198 MET cc_start: 0.8069 (tpt) cc_final: 0.7658 (tpp) REVERT: B 204 ASN cc_start: 0.8021 (p0) cc_final: 0.7693 (p0) REVERT: C 11 GLU cc_start: 0.8153 (tp30) cc_final: 0.6854 (tp30) REVERT: C 28 ILE cc_start: 0.8088 (tp) cc_final: 0.7636 (tp) REVERT: C 34 GLU cc_start: 0.8359 (pp20) cc_final: 0.7706 (pp20) REVERT: C 39 GLN cc_start: 0.8488 (tp40) cc_final: 0.7810 (tp40) REVERT: C 106 TRP cc_start: 0.6635 (t60) cc_final: 0.6379 (t60) REVERT: C 110 PHE cc_start: 0.7796 (m-80) cc_final: 0.7266 (m-80) REVERT: C 132 MET cc_start: 0.8293 (ppp) cc_final: 0.7842 (ppp) REVERT: C 162 ASN cc_start: 0.8898 (m-40) cc_final: 0.8358 (m-40) REVERT: C 190 LYS cc_start: 0.6592 (mttm) cc_final: 0.6253 (mmmt) REVERT: C 198 MET cc_start: 0.8535 (tpt) cc_final: 0.8163 (tpt) REVERT: C 199 ASP cc_start: 0.8809 (m-30) cc_final: 0.8503 (m-30) REVERT: C 202 ILE cc_start: 0.8362 (mt) cc_final: 0.8132 (mt) REVERT: C 208 GLN cc_start: 0.8512 (tt0) cc_final: 0.8129 (mt0) REVERT: C 209 ARG cc_start: 0.8583 (ptt90) cc_final: 0.8359 (ptt90) REVERT: C 244 LEU cc_start: 0.8256 (mm) cc_final: 0.7554 (mm) REVERT: D 205 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7078 (mmmt) REVERT: D 218 GLN cc_start: 0.8514 (mm110) cc_final: 0.7967 (mm110) REVERT: D 223 PHE cc_start: 0.6103 (p90) cc_final: 0.5656 (p90) REVERT: D 226 TYR cc_start: 0.7193 (p90) cc_final: 0.6185 (p90) REVERT: D 244 LEU cc_start: 0.8571 (mt) cc_final: 0.8256 (mt) REVERT: D 262 LEU cc_start: 0.7897 (mp) cc_final: 0.7657 (mp) REVERT: D 263 VAL cc_start: 0.8364 (m) cc_final: 0.8126 (t) REVERT: E 10 GLU cc_start: 0.7950 (tp30) cc_final: 0.7451 (tp30) REVERT: E 16 HIS cc_start: 0.7947 (m-70) cc_final: 0.7193 (m170) REVERT: E 97 GLN cc_start: 0.7927 (pm20) cc_final: 0.7710 (pm20) REVERT: E 100 ARG cc_start: 0.8827 (ptp90) cc_final: 0.8568 (ptp-170) REVERT: E 101 VAL cc_start: 0.8821 (t) cc_final: 0.8584 (t) REVERT: E 150 GLN cc_start: 0.8122 (mm110) cc_final: 0.7626 (mm-40) REVERT: E 158 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7540 (tm-30) REVERT: E 159 THR cc_start: 0.8532 (m) cc_final: 0.7885 (p) REVERT: E 178 LEU cc_start: 0.8984 (mt) cc_final: 0.8731 (mt) REVERT: F 23 HIS cc_start: 0.7548 (t70) cc_final: 0.7195 (t70) REVERT: F 65 VAL cc_start: 0.6839 (t) cc_final: 0.6416 (p) REVERT: F 104 MET cc_start: 0.8020 (ptm) cc_final: 0.7501 (ppp) REVERT: F 105 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8860 (mttt) REVERT: F 158 GLN cc_start: 0.8847 (mt0) cc_final: 0.8603 (mm110) REVERT: F 205 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8246 (mtmt) REVERT: F 206 GLU cc_start: 0.7930 (pm20) cc_final: 0.7648 (pm20) REVERT: F 208 GLN cc_start: 0.8576 (tt0) cc_final: 0.8101 (tm-30) REVERT: F 230 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8024 (mmmm) REVERT: F 237 TRP cc_start: 0.8414 (m100) cc_final: 0.8063 (m100) REVERT: F 242 GLN cc_start: 0.7340 (tt0) cc_final: 0.6687 (pp30) REVERT: F 243 VAL cc_start: 0.8422 (t) cc_final: 0.7260 (m) REVERT: F 244 LEU cc_start: 0.8170 (tt) cc_final: 0.7783 (tt) REVERT: F 256 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7947 (ttm110) REVERT: G 48 MET cc_start: -0.0463 (ppp) cc_final: -0.1307 (ppp) REVERT: G 62 HIS cc_start: 0.7526 (t70) cc_final: 0.6865 (t70) REVERT: G 104 MET cc_start: 0.7842 (pmm) cc_final: 0.7570 (pmm) REVERT: G 110 PHE cc_start: 0.7930 (m-80) cc_final: 0.7447 (m-10) REVERT: G 131 LEU cc_start: 0.9295 (mt) cc_final: 0.9045 (mt) REVERT: G 155 ARG cc_start: 0.9103 (ttm110) cc_final: 0.8900 (ttm170) REVERT: G 165 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8472 (mm-30) REVERT: G 170 MET cc_start: 0.7803 (mmp) cc_final: 0.7550 (mmp) REVERT: G 171 PHE cc_start: 0.6899 (m-80) cc_final: 0.6432 (m-80) REVERT: G 197 PRO cc_start: 0.8536 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8930 (m-30) cc_final: 0.8431 (m-30) REVERT: G 209 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8212 (ttp80) REVERT: G 210 ILE cc_start: 0.8570 (pt) cc_final: 0.7920 (pt) REVERT: H 78 TRP cc_start: 0.7009 (m-10) cc_final: 0.6685 (m-10) REVERT: H 87 TYR cc_start: 0.8484 (t80) cc_final: 0.8048 (t80) REVERT: H 101 VAL cc_start: 0.8831 (p) cc_final: 0.8611 (p) REVERT: H 104 MET cc_start: 0.9105 (mmp) cc_final: 0.8467 (mmp) REVERT: H 106 TRP cc_start: 0.8473 (t60) cc_final: 0.7959 (t60) REVERT: H 199 ASP cc_start: 0.8015 (m-30) cc_final: 0.7698 (m-30) REVERT: H 205 LYS cc_start: 0.8299 (mtmm) cc_final: 0.8096 (mtmt) REVERT: H 207 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7824 (mm-40) REVERT: H 223 PHE cc_start: 0.7253 (m-80) cc_final: 0.6750 (m-80) REVERT: H 238 GLN cc_start: 0.6822 (mm110) cc_final: 0.6570 (mm-40) REVERT: I 60 ILE cc_start: 0.8908 (mp) cc_final: 0.8322 (mm) REVERT: I 66 ASP cc_start: 0.7505 (t70) cc_final: 0.6977 (t70) REVERT: I 79 VAL cc_start: 0.8046 (t) cc_final: 0.7545 (p) REVERT: I 81 THR cc_start: 0.8692 (p) cc_final: 0.8425 (t) REVERT: I 86 ILE cc_start: 0.8515 (pt) cc_final: 0.7971 (mp) REVERT: I 92 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8535 (mtpp) REVERT: I 98 GLU cc_start: 0.8185 (mp0) cc_final: 0.7875 (mp0) REVERT: I 100 ARG cc_start: 0.8302 (mtt90) cc_final: 0.7767 (mtm-85) REVERT: I 102 GLN cc_start: 0.9106 (mm110) cc_final: 0.8762 (mm-40) REVERT: I 105 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8156 (mtmm) REVERT: I 118 ASP cc_start: 0.7688 (p0) cc_final: 0.7390 (p0) REVERT: I 129 GLN cc_start: 0.7800 (tt0) cc_final: 0.7583 (tt0) REVERT: I 143 ILE cc_start: 0.8598 (tp) cc_final: 0.8052 (tp) REVERT: I 146 ASN cc_start: 0.8151 (m110) cc_final: 0.7444 (m110) REVERT: I 155 ARG cc_start: 0.8318 (tpt90) cc_final: 0.7610 (mmm160) REVERT: I 158 GLN cc_start: 0.9024 (tt0) cc_final: 0.8614 (tt0) REVERT: I 159 THR cc_start: 0.8601 (p) cc_final: 0.8287 (m) REVERT: I 160 LEU cc_start: 0.8784 (tt) cc_final: 0.8491 (tt) REVERT: I 164 LEU cc_start: 0.8607 (mt) cc_final: 0.8300 (mt) REVERT: I 183 ILE cc_start: 0.9042 (mt) cc_final: 0.8829 (mt) REVERT: I 198 MET cc_start: 0.8493 (ttm) cc_final: 0.8281 (tpp) REVERT: I 203 PHE cc_start: 0.8334 (t80) cc_final: 0.7909 (t80) REVERT: I 208 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7969 (tm-30) REVERT: I 209 ARG cc_start: 0.7453 (tpp80) cc_final: 0.7042 (tpp80) REVERT: I 264 ILE cc_start: 0.7933 (mm) cc_final: 0.7599 (mm) REVERT: J 40 CYS cc_start: 0.7202 (t) cc_final: 0.6915 (t) REVERT: J 62 HIS cc_start: 0.7302 (t-90) cc_final: 0.7065 (t-90) REVERT: J 63 TRP cc_start: 0.7769 (m100) cc_final: 0.6135 (m100) REVERT: J 64 GLN cc_start: 0.7122 (tp40) cc_final: 0.6252 (tp40) REVERT: J 65 VAL cc_start: 0.8742 (t) cc_final: 0.8531 (t) REVERT: J 70 TYR cc_start: 0.8510 (t80) cc_final: 0.7860 (t80) REVERT: J 86 ILE cc_start: 0.8966 (pt) cc_final: 0.8232 (mm) REVERT: J 92 LYS cc_start: 0.8858 (tptp) cc_final: 0.8492 (tptp) REVERT: J 98 GLU cc_start: 0.8090 (pm20) cc_final: 0.7856 (pm20) REVERT: J 100 ARG cc_start: 0.8694 (mpp80) cc_final: 0.8247 (mtt180) REVERT: J 102 GLN cc_start: 0.8646 (mp10) cc_final: 0.8064 (mp10) REVERT: J 104 MET cc_start: 0.8242 (tpp) cc_final: 0.7667 (tpp) REVERT: J 131 LEU cc_start: 0.8767 (tt) cc_final: 0.8428 (tt) REVERT: J 132 MET cc_start: 0.8638 (mmp) cc_final: 0.8416 (mmt) REVERT: J 137 ILE cc_start: 0.8475 (tt) cc_final: 0.7958 (tt) REVERT: J 138 GLU cc_start: 0.7788 (tp30) cc_final: 0.7572 (tp30) REVERT: J 139 HIS cc_start: 0.8529 (t70) cc_final: 0.8071 (t70) REVERT: J 178 LEU cc_start: 0.9128 (mm) cc_final: 0.8712 (mm) REVERT: J 201 PHE cc_start: 0.9083 (t80) cc_final: 0.8629 (t80) REVERT: J 204 ASN cc_start: 0.8130 (m110) cc_final: 0.7294 (p0) REVERT: J 207 GLN cc_start: 0.8187 (mp10) cc_final: 0.7825 (mt0) REVERT: J 208 GLN cc_start: 0.8077 (pt0) cc_final: 0.7782 (pt0) REVERT: K 10 GLU cc_start: 0.8611 (pp20) cc_final: 0.8274 (tm-30) REVERT: K 22 LEU cc_start: 0.8385 (mm) cc_final: 0.7914 (mm) REVERT: K 190 LYS cc_start: 0.6667 (mttm) cc_final: 0.6256 (mmmt) REVERT: L 223 PHE cc_start: 0.5970 (p90) cc_final: 0.5443 (p90) REVERT: L 224 CYS cc_start: 0.7099 (p) cc_final: 0.6885 (p) REVERT: L 226 TYR cc_start: 0.7189 (p90) cc_final: 0.6091 (p90) REVERT: L 254 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7686 (tppt) REVERT: L 263 VAL cc_start: 0.8132 (m) cc_final: 0.7882 (t) REVERT: L 269 VAL cc_start: 0.7743 (m) cc_final: 0.7470 (m) REVERT: M 18 ASP cc_start: 0.7767 (t70) cc_final: 0.7397 (t70) REVERT: M 36 ILE cc_start: 0.8607 (mt) cc_final: 0.8387 (mt) REVERT: M 63 TRP cc_start: 0.7251 (m100) cc_final: 0.6656 (m100) REVERT: M 87 TYR cc_start: 0.7483 (t80) cc_final: 0.6196 (t80) REVERT: M 89 GLU cc_start: 0.7261 (pm20) cc_final: 0.5333 (mp0) REVERT: M 130 LEU cc_start: 0.8184 (mt) cc_final: 0.7435 (mt) REVERT: M 133 LYS cc_start: 0.9088 (ptpp) cc_final: 0.8729 (mmtt) REVERT: M 155 ARG cc_start: 0.8583 (ttt180) cc_final: 0.8318 (mtt90) REVERT: M 158 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7380 (tm-30) REVERT: M 159 THR cc_start: 0.8691 (m) cc_final: 0.7890 (p) REVERT: M 178 LEU cc_start: 0.8811 (mt) cc_final: 0.8565 (mt) REVERT: M 199 ASP cc_start: 0.8673 (m-30) cc_final: 0.7726 (m-30) REVERT: M 202 ILE cc_start: 0.8790 (mm) cc_final: 0.8271 (mm) REVERT: M 205 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8605 (mtmm) REVERT: M 206 GLU cc_start: 0.8613 (pt0) cc_final: 0.8059 (pt0) REVERT: N 23 HIS cc_start: 0.7737 (t70) cc_final: 0.7481 (t70) REVERT: N 65 VAL cc_start: 0.7432 (t) cc_final: 0.7187 (p) REVERT: N 89 GLU cc_start: 0.6728 (tp30) cc_final: 0.6521 (tp30) REVERT: N 104 MET cc_start: 0.8144 (ptm) cc_final: 0.7815 (ptm) REVERT: N 105 LYS cc_start: 0.9234 (mtmm) cc_final: 0.8831 (mttt) REVERT: N 110 PHE cc_start: 0.8138 (m-80) cc_final: 0.7846 (m-80) REVERT: N 127 SER cc_start: 0.8604 (t) cc_final: 0.8327 (t) REVERT: N 158 GLN cc_start: 0.9105 (mp10) cc_final: 0.8823 (mp10) REVERT: N 162 ASN cc_start: 0.8657 (m110) cc_final: 0.8439 (m110) REVERT: N 203 PHE cc_start: 0.7981 (t80) cc_final: 0.7102 (t80) REVERT: N 205 LYS cc_start: 0.8443 (ptpp) cc_final: 0.7976 (mtmm) REVERT: N 206 GLU cc_start: 0.8363 (pp20) cc_final: 0.8031 (pp20) REVERT: N 208 GLN cc_start: 0.8474 (tt0) cc_final: 0.8222 (tm-30) REVERT: N 213 GLN cc_start: 0.8789 (mt0) cc_final: 0.8143 (mt0) REVERT: N 233 HIS cc_start: 0.7754 (m90) cc_final: 0.7366 (m-70) REVERT: N 242 GLN cc_start: 0.7729 (tt0) cc_final: 0.7129 (pp30) REVERT: N 243 VAL cc_start: 0.8537 (t) cc_final: 0.7955 (p) REVERT: N 244 LEU cc_start: 0.8355 (tt) cc_final: 0.8123 (tt) REVERT: N 256 ARG cc_start: 0.8388 (ttm110) cc_final: 0.7727 (ttm110) REVERT: N 270 LYS cc_start: 0.7903 (mptt) cc_final: 0.7291 (mmtp) REVERT: O 48 MET cc_start: -0.1481 (ppp) cc_final: -0.1918 (ppp) REVERT: O 85 LEU cc_start: 0.7428 (tp) cc_final: 0.7197 (tp) REVERT: O 110 PHE cc_start: 0.8146 (m-80) cc_final: 0.7811 (m-10) REVERT: O 132 MET cc_start: 0.8079 (tmm) cc_final: 0.7623 (tmm) REVERT: O 155 ARG cc_start: 0.9165 (mtm110) cc_final: 0.8871 (ptp-110) REVERT: O 199 ASP cc_start: 0.8862 (m-30) cc_final: 0.8518 (m-30) REVERT: O 201 PHE cc_start: 0.8806 (t80) cc_final: 0.7999 (t80) REVERT: O 205 LYS cc_start: 0.9258 (mmtm) cc_final: 0.8978 (mmtp) REVERT: O 208 GLN cc_start: 0.8683 (tm130) cc_final: 0.8483 (tm-30) REVERT: O 209 ARG cc_start: 0.8796 (ptm-80) cc_final: 0.8415 (ptm-80) REVERT: P 87 TYR cc_start: 0.8702 (t80) cc_final: 0.8394 (t80) REVERT: P 101 VAL cc_start: 0.9125 (p) cc_final: 0.8886 (p) REVERT: P 104 MET cc_start: 0.9160 (mmp) cc_final: 0.8640 (mmp) REVERT: P 106 TRP cc_start: 0.8480 (t60) cc_final: 0.8061 (t60) REVERT: P 115 LEU cc_start: 0.4609 (tp) cc_final: 0.4380 (tp) REVERT: P 132 MET cc_start: 0.6666 (tmm) cc_final: 0.6175 (tmm) REVERT: P 137 ILE cc_start: 0.8372 (mm) cc_final: 0.8133 (mm) REVERT: P 170 MET cc_start: 0.7882 (mtt) cc_final: 0.7345 (mpp) REVERT: P 172 ASN cc_start: 0.8813 (m-40) cc_final: 0.8465 (p0) REVERT: P 207 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7885 (mm-40) REVERT: P 222 ARG cc_start: 0.6199 (mmm-85) cc_final: 0.5464 (mmm160) REVERT: P 223 PHE cc_start: 0.6286 (m-80) cc_final: 0.5880 (m-80) REVERT: P 230 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7490 (mmtm) REVERT: P 272 ILE cc_start: 0.7672 (mp) cc_final: 0.7362 (mp) outliers start: 1 outliers final: 1 residues processed: 1142 average time/residue: 0.2300 time to fit residues: 414.9863 Evaluate side-chains 1075 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1074 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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: 5.9990 chunk 261 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 385 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ** 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 211 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 ** E 204 ASN ** 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 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** I 207 GLN J 158 GLN J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN O 211 GLN P 148 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.194981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148530 restraints weight = 71467.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154197 restraints weight = 44455.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158068 restraints weight = 31062.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160736 restraints weight = 23535.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.162840 restraints weight = 18994.664| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 34119 Z= 0.248 Angle : 0.784 15.159 46515 Z= 0.429 Chirality : 0.051 0.273 5006 Planarity : 0.006 0.108 5714 Dihedral : 14.975 171.658 5007 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 3851 helix: 0.68 (0.12), residues: 1867 sheet: -0.66 (0.18), residues: 822 loop : -1.68 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 222 TYR 0.025 0.002 TYR O 70 PHE 0.036 0.002 PHE H 201 TRP 0.057 0.003 TRP F 78 HIS 0.012 0.002 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.25 (34119) covalent geometry : angle 0.78394 / 0.43 (46515) hydrogen bonds : bond 0.04731 / 3.21 ( 1746) hydrogen bonds : angle 5.81483 / 4.20 ( 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 1165 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1165 time to evaluate : 1.289 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: A 60 ILE cc_start: 0.8704 (mm) cc_final: 0.8271 (mm) REVERT: A 62 HIS cc_start: 0.7745 (t70) cc_final: 0.7491 (t-170) REVERT: A 64 GLN cc_start: 0.6426 (pm20) cc_final: 0.6021 (pm20) REVERT: A 66 ASP cc_start: 0.7862 (t70) cc_final: 0.7354 (t70) REVERT: A 81 THR cc_start: 0.8712 (p) cc_final: 0.8394 (t) REVERT: A 90 ARG cc_start: 0.8120 (tmm-80) cc_final: 0.7755 (tmm-80) REVERT: A 92 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8342 (mtpp) REVERT: A 97 GLN cc_start: 0.8007 (pm20) cc_final: 0.7658 (pm20) REVERT: A 100 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7665 (mtm-85) REVERT: A 107 TYR cc_start: 0.8404 (t80) cc_final: 0.8176 (t80) REVERT: A 113 LYS cc_start: 0.8093 (mmmm) cc_final: 0.7756 (mmmm) REVERT: A 116 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7096 (tm-30) REVERT: A 118 ASP cc_start: 0.7597 (p0) cc_final: 0.7314 (p0) REVERT: A 129 GLN cc_start: 0.8054 (tt0) cc_final: 0.7775 (tt0) REVERT: A 131 LEU cc_start: 0.8890 (pp) cc_final: 0.8683 (pp) REVERT: A 132 MET cc_start: 0.8114 (mmm) cc_final: 0.7626 (mmm) REVERT: A 135 LEU cc_start: 0.8898 (mt) cc_final: 0.8635 (mt) REVERT: A 158 GLN cc_start: 0.8915 (tt0) cc_final: 0.8073 (pt0) REVERT: A 164 LEU cc_start: 0.8456 (mt) cc_final: 0.8203 (mt) REVERT: A 178 LEU cc_start: 0.8070 (tp) cc_final: 0.7632 (tp) REVERT: A 190 LYS cc_start: 0.8043 (ptpp) cc_final: 0.7154 (mtpp) REVERT: A 203 PHE cc_start: 0.8511 (t80) cc_final: 0.8084 (t80) REVERT: A 211 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7854 (tp-100) REVERT: A 226 TYR cc_start: 0.6508 (p90) cc_final: 0.6192 (p90) REVERT: A 254 LYS cc_start: 0.8442 (tmmt) cc_final: 0.8009 (ttpp) REVERT: B 15 TRP cc_start: 0.7762 (m100) cc_final: 0.7352 (m100) REVERT: B 40 CYS cc_start: 0.7534 (t) cc_final: 0.6972 (p) REVERT: B 63 TRP cc_start: 0.7836 (m100) cc_final: 0.5978 (m100) REVERT: B 64 GLN cc_start: 0.7139 (tp40) cc_final: 0.6608 (mm110) REVERT: B 65 VAL cc_start: 0.8667 (t) cc_final: 0.8271 (t) REVERT: B 70 TYR cc_start: 0.8358 (t80) cc_final: 0.7748 (t80) REVERT: B 75 ILE cc_start: 0.8023 (pt) cc_final: 0.7822 (mp) REVERT: B 82 ASN cc_start: 0.8086 (p0) cc_final: 0.7846 (p0) REVERT: B 86 ILE cc_start: 0.8908 (pt) cc_final: 0.8095 (mm) REVERT: B 89 GLU cc_start: 0.7824 (tt0) cc_final: 0.7188 (tt0) REVERT: B 90 ARG cc_start: 0.8776 (tpt-90) cc_final: 0.8019 (tpp80) REVERT: B 92 LYS cc_start: 0.8866 (tppt) cc_final: 0.8578 (tppp) REVERT: B 104 MET cc_start: 0.8741 (mmp) cc_final: 0.8249 (mmp) REVERT: B 129 GLN cc_start: 0.8475 (pt0) cc_final: 0.8107 (pt0) REVERT: B 131 LEU cc_start: 0.9112 (tt) cc_final: 0.8843 (tt) REVERT: B 132 MET cc_start: 0.8732 (mmp) cc_final: 0.8465 (mmt) REVERT: B 137 ILE cc_start: 0.8548 (tt) cc_final: 0.7722 (tt) REVERT: B 138 GLU cc_start: 0.7894 (tp30) cc_final: 0.7630 (tp30) REVERT: B 139 HIS cc_start: 0.8581 (t70) cc_final: 0.8065 (t70) REVERT: B 165 GLU cc_start: 0.8053 (tp30) cc_final: 0.7764 (tp30) REVERT: B 174 PHE cc_start: 0.7776 (t80) cc_final: 0.7358 (t80) REVERT: B 175 GLU cc_start: 0.8850 (pm20) cc_final: 0.8578 (mp0) REVERT: B 178 LEU cc_start: 0.9170 (mm) cc_final: 0.8774 (mm) REVERT: B 186 ASN cc_start: 0.8466 (m-40) cc_final: 0.8149 (m-40) REVERT: B 189 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6849 (ttp-110) REVERT: B 198 MET cc_start: 0.8122 (tpt) cc_final: 0.7764 (tpp) REVERT: C 5 ILE cc_start: 0.9313 (mt) cc_final: 0.9090 (mt) REVERT: C 11 GLU cc_start: 0.8328 (tp30) cc_final: 0.7549 (tp30) REVERT: C 28 ILE cc_start: 0.7754 (tp) cc_final: 0.7500 (tp) REVERT: C 38 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7657 (tp-100) REVERT: C 39 GLN cc_start: 0.8485 (tp40) cc_final: 0.7913 (tp40) REVERT: C 106 TRP cc_start: 0.6588 (t60) cc_final: 0.6294 (t60) REVERT: C 110 PHE cc_start: 0.7779 (m-80) cc_final: 0.7246 (m-80) REVERT: C 132 MET cc_start: 0.8425 (ppp) cc_final: 0.7959 (ppp) REVERT: C 162 ASN cc_start: 0.8966 (m-40) cc_final: 0.8604 (m-40) REVERT: C 190 LYS cc_start: 0.6720 (mttm) cc_final: 0.6395 (mmmt) REVERT: C 198 MET cc_start: 0.8657 (tpt) cc_final: 0.8059 (tpt) REVERT: C 199 ASP cc_start: 0.8896 (m-30) cc_final: 0.8556 (m-30) REVERT: C 202 ILE cc_start: 0.8411 (mt) cc_final: 0.8169 (mt) REVERT: C 208 GLN cc_start: 0.8836 (tt0) cc_final: 0.8340 (mt0) REVERT: C 244 LEU cc_start: 0.8168 (mm) cc_final: 0.7840 (mm) REVERT: D 205 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7106 (mmmt) REVERT: D 209 ARG cc_start: 0.8809 (tpm170) cc_final: 0.8442 (mmm160) REVERT: D 218 GLN cc_start: 0.8469 (mm110) cc_final: 0.7897 (mm110) REVERT: D 223 PHE cc_start: 0.6234 (p90) cc_final: 0.5767 (p90) REVERT: D 226 TYR cc_start: 0.7041 (p90) cc_final: 0.6056 (p90) REVERT: D 254 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8015 (ttmt) REVERT: D 262 LEU cc_start: 0.8077 (mp) cc_final: 0.7836 (mm) REVERT: D 263 VAL cc_start: 0.8592 (m) cc_final: 0.8357 (t) REVERT: E 16 HIS cc_start: 0.8076 (m-70) cc_final: 0.7117 (m170) REVERT: E 97 GLN cc_start: 0.8048 (pm20) cc_final: 0.7753 (pm20) REVERT: E 100 ARG cc_start: 0.8825 (ptp90) cc_final: 0.8380 (ptt-90) REVERT: E 150 GLN cc_start: 0.8189 (mm110) cc_final: 0.7531 (mm-40) REVERT: E 158 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7557 (tm-30) REVERT: E 159 THR cc_start: 0.8535 (m) cc_final: 0.7892 (p) REVERT: E 178 LEU cc_start: 0.8988 (mt) cc_final: 0.8763 (mt) REVERT: E 201 PHE cc_start: 0.8587 (t80) cc_final: 0.8156 (t80) REVERT: E 202 ILE cc_start: 0.8816 (mp) cc_final: 0.8596 (mp) REVERT: E 224 CYS cc_start: 0.6162 (p) cc_final: 0.5634 (p) REVERT: F 23 HIS cc_start: 0.7600 (t70) cc_final: 0.7271 (t70) REVERT: F 65 VAL cc_start: 0.6844 (t) cc_final: 0.6470 (p) REVERT: F 104 MET cc_start: 0.8155 (ptm) cc_final: 0.7555 (ppp) REVERT: F 131 LEU cc_start: 0.8501 (tp) cc_final: 0.8247 (mm) REVERT: F 158 GLN cc_start: 0.8836 (mt0) cc_final: 0.8521 (mm-40) REVERT: F 164 LEU cc_start: 0.8471 (mt) cc_final: 0.8254 (mt) REVERT: F 205 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8266 (mtmt) REVERT: F 208 GLN cc_start: 0.8407 (tt0) cc_final: 0.8194 (tm-30) REVERT: F 230 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7978 (mmmm) REVERT: F 231 ARG cc_start: 0.7859 (mpp-170) cc_final: 0.7362 (mpp-170) REVERT: F 233 HIS cc_start: 0.7799 (m-70) cc_final: 0.7572 (m-70) REVERT: F 237 TRP cc_start: 0.8438 (m100) cc_final: 0.7964 (m100) REVERT: F 242 GLN cc_start: 0.7494 (tt0) cc_final: 0.6887 (pp30) REVERT: F 243 VAL cc_start: 0.8507 (t) cc_final: 0.7430 (m) REVERT: F 244 LEU cc_start: 0.8332 (tt) cc_final: 0.7824 (tt) REVERT: F 256 ARG cc_start: 0.8371 (ttm110) cc_final: 0.7998 (ttm110) REVERT: G 48 MET cc_start: -0.0461 (ppp) cc_final: -0.1305 (ppp) REVERT: G 62 HIS cc_start: 0.7441 (t70) cc_final: 0.6695 (t70) REVERT: G 71 GLU cc_start: 0.7441 (tp30) cc_final: 0.7059 (tp30) REVERT: G 85 LEU cc_start: 0.7377 (tp) cc_final: 0.7044 (tp) REVERT: G 104 MET cc_start: 0.8085 (pmm) cc_final: 0.7824 (pmm) REVERT: G 110 PHE cc_start: 0.7867 (m-80) cc_final: 0.7185 (m-10) REVERT: G 131 LEU cc_start: 0.9310 (mt) cc_final: 0.9076 (mt) REVERT: G 157 HIS cc_start: 0.8951 (p-80) cc_final: 0.8488 (p90) REVERT: G 161 LYS cc_start: 0.9277 (tptt) cc_final: 0.8961 (mmmt) REVERT: G 168 ILE cc_start: 0.7802 (mt) cc_final: 0.7480 (pt) REVERT: G 171 PHE cc_start: 0.7046 (m-80) cc_final: 0.6612 (m-80) REVERT: G 183 ILE cc_start: 0.7365 (mt) cc_final: 0.7155 (mt) REVERT: G 197 PRO cc_start: 0.8505 (Cg_exo) cc_final: 0.8222 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8910 (m-30) cc_final: 0.8371 (m-30) REVERT: G 209 ARG cc_start: 0.8876 (ttp80) cc_final: 0.8264 (ttp80) REVERT: G 210 ILE cc_start: 0.8676 (pt) cc_final: 0.8000 (pt) REVERT: H 78 TRP cc_start: 0.7231 (m-10) cc_final: 0.6876 (m-10) REVERT: H 85 LEU cc_start: 0.8752 (tp) cc_final: 0.8523 (tp) REVERT: H 87 TYR cc_start: 0.8492 (t80) cc_final: 0.7969 (t80) REVERT: H 101 VAL cc_start: 0.8824 (p) cc_final: 0.8607 (p) REVERT: H 104 MET cc_start: 0.9091 (mmp) cc_final: 0.8474 (mmp) REVERT: H 106 TRP cc_start: 0.8436 (t60) cc_final: 0.7895 (t60) REVERT: H 207 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7887 (mm-40) REVERT: H 238 GLN cc_start: 0.7063 (mm110) cc_final: 0.6824 (mm-40) REVERT: I 48 MET cc_start: 0.6040 (mmp) cc_final: 0.5818 (mmm) REVERT: I 60 ILE cc_start: 0.8880 (mp) cc_final: 0.8325 (mm) REVERT: I 66 ASP cc_start: 0.7918 (t70) cc_final: 0.7405 (t70) REVERT: I 79 VAL cc_start: 0.8223 (t) cc_final: 0.7484 (p) REVERT: I 80 GLU cc_start: 0.6705 (tm-30) cc_final: 0.6356 (tm-30) REVERT: I 81 THR cc_start: 0.8791 (p) cc_final: 0.8514 (t) REVERT: I 86 ILE cc_start: 0.8546 (pt) cc_final: 0.8077 (mp) REVERT: I 92 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8537 (mtpp) REVERT: I 98 GLU cc_start: 0.8234 (mp0) cc_final: 0.7955 (mp0) REVERT: I 113 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7662 (mmmm) REVERT: I 116 GLN cc_start: 0.7238 (tm-30) cc_final: 0.6875 (tm-30) REVERT: I 152 LEU cc_start: 0.7516 (pt) cc_final: 0.6588 (mp) REVERT: I 155 ARG cc_start: 0.8349 (tpt90) cc_final: 0.7538 (mmm160) REVERT: I 158 GLN cc_start: 0.8984 (tt0) cc_final: 0.8578 (tt0) REVERT: I 159 THR cc_start: 0.8614 (p) cc_final: 0.8361 (m) REVERT: I 160 LEU cc_start: 0.8775 (tt) cc_final: 0.8479 (tt) REVERT: I 161 LYS cc_start: 0.8888 (tptt) cc_final: 0.8660 (tptt) REVERT: I 164 LEU cc_start: 0.8736 (mt) cc_final: 0.8382 (mt) REVERT: I 198 MET cc_start: 0.8708 (ttm) cc_final: 0.8408 (tpp) REVERT: I 203 PHE cc_start: 0.8403 (t80) cc_final: 0.7970 (t80) REVERT: I 264 ILE cc_start: 0.7959 (mm) cc_final: 0.7672 (mm) REVERT: J 13 ASN cc_start: 0.7272 (m-40) cc_final: 0.7032 (m110) REVERT: J 40 CYS cc_start: 0.7373 (t) cc_final: 0.6883 (m) REVERT: J 64 GLN cc_start: 0.7182 (tp40) cc_final: 0.5713 (mm-40) REVERT: J 70 TYR cc_start: 0.8385 (t80) cc_final: 0.7710 (t80) REVERT: J 86 ILE cc_start: 0.8950 (pt) cc_final: 0.8391 (mm) REVERT: J 92 LYS cc_start: 0.8896 (tptp) cc_final: 0.8489 (tptp) REVERT: J 104 MET cc_start: 0.8325 (tpp) cc_final: 0.7821 (tpp) REVERT: J 106 TRP cc_start: 0.8582 (t60) cc_final: 0.8321 (t60) REVERT: J 116 GLN cc_start: 0.7570 (tm-30) cc_final: 0.6602 (tm-30) REVERT: J 131 LEU cc_start: 0.8780 (tt) cc_final: 0.8406 (tt) REVERT: J 137 ILE cc_start: 0.8574 (tt) cc_final: 0.8374 (tt) REVERT: J 139 HIS cc_start: 0.8592 (t70) cc_final: 0.8178 (t70) REVERT: J 162 ASN cc_start: 0.8866 (m110) cc_final: 0.8595 (m110) REVERT: J 178 LEU cc_start: 0.9143 (mm) cc_final: 0.8909 (mm) REVERT: J 204 ASN cc_start: 0.8457 (m110) cc_final: 0.7785 (p0) REVERT: J 205 LYS cc_start: 0.8528 (tptp) cc_final: 0.7937 (tptp) REVERT: J 207 GLN cc_start: 0.7746 (mp10) cc_final: 0.7357 (mp10) REVERT: J 208 GLN cc_start: 0.8153 (pt0) cc_final: 0.7745 (pt0) REVERT: K 34 GLU cc_start: 0.8743 (pt0) cc_final: 0.8358 (pp20) REVERT: K 35 ASP cc_start: 0.8705 (m-30) cc_final: 0.8257 (m-30) REVERT: K 39 GLN cc_start: 0.8468 (tp40) cc_final: 0.8013 (tp40) REVERT: K 132 MET cc_start: 0.7425 (ppp) cc_final: 0.6855 (ppp) REVERT: K 190 LYS cc_start: 0.6706 (mttm) cc_final: 0.6352 (mmmt) REVERT: K 199 ASP cc_start: 0.9061 (m-30) cc_final: 0.8854 (m-30) REVERT: L 254 LYS cc_start: 0.8384 (tmtt) cc_final: 0.7755 (tppt) REVERT: L 262 LEU cc_start: 0.8277 (mm) cc_final: 0.7919 (mm) REVERT: L 266 ASN cc_start: 0.8391 (m110) cc_final: 0.8029 (m110) REVERT: L 269 VAL cc_start: 0.7786 (m) cc_final: 0.7555 (m) REVERT: M 7 LEU cc_start: 0.8629 (tt) cc_final: 0.7892 (tt) REVERT: M 11 GLU cc_start: 0.8618 (mp0) cc_final: 0.7905 (mp0) REVERT: M 18 ASP cc_start: 0.7844 (t70) cc_final: 0.7634 (t70) REVERT: M 22 LEU cc_start: 0.8070 (pp) cc_final: 0.7791 (pp) REVERT: M 63 TRP cc_start: 0.7408 (m100) cc_final: 0.7058 (m100) REVERT: M 133 LYS cc_start: 0.8799 (ptpp) cc_final: 0.8523 (pttp) REVERT: M 154 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8689 (mm-30) REVERT: M 155 ARG cc_start: 0.8655 (ttt180) cc_final: 0.8420 (mtt90) REVERT: M 158 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7705 (tm-30) REVERT: M 159 THR cc_start: 0.8673 (m) cc_final: 0.8077 (p) REVERT: M 178 LEU cc_start: 0.8851 (mt) cc_final: 0.8598 (mt) REVERT: M 195 THR cc_start: 0.8371 (m) cc_final: 0.8079 (p) REVERT: M 202 ILE cc_start: 0.8820 (mm) cc_final: 0.8340 (mm) REVERT: M 205 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8561 (mtmm) REVERT: M 206 GLU cc_start: 0.8633 (pt0) cc_final: 0.8163 (pt0) REVERT: M 207 GLN cc_start: 0.8680 (mm110) cc_final: 0.8431 (mm110) REVERT: M 209 ARG cc_start: 0.8812 (tmt170) cc_final: 0.8444 (ttp80) REVERT: N 23 HIS cc_start: 0.7743 (t70) cc_final: 0.7438 (t70) REVERT: N 104 MET cc_start: 0.8333 (ptm) cc_final: 0.7848 (ppp) REVERT: N 105 LYS cc_start: 0.9349 (mtmm) cc_final: 0.8841 (mttt) REVERT: N 157 HIS cc_start: 0.8158 (m90) cc_final: 0.7883 (m90) REVERT: N 203 PHE cc_start: 0.8083 (t80) cc_final: 0.7831 (t80) REVERT: N 207 GLN cc_start: 0.8295 (mp10) cc_final: 0.7891 (mp10) REVERT: N 210 ILE cc_start: 0.8465 (pt) cc_final: 0.8143 (pt) REVERT: N 213 GLN cc_start: 0.8800 (mt0) cc_final: 0.8211 (mt0) REVERT: N 233 HIS cc_start: 0.7814 (m90) cc_final: 0.7407 (m90) REVERT: N 242 GLN cc_start: 0.7776 (tt0) cc_final: 0.7254 (pp30) REVERT: N 243 VAL cc_start: 0.8567 (t) cc_final: 0.8023 (p) REVERT: N 244 LEU cc_start: 0.8395 (tt) cc_final: 0.8093 (tt) REVERT: N 256 ARG cc_start: 0.8400 (ttm110) cc_final: 0.7815 (ttm110) REVERT: N 270 LYS cc_start: 0.7912 (mptt) cc_final: 0.7233 (mmtp) REVERT: O 48 MET cc_start: -0.1515 (ppp) cc_final: -0.1912 (ppp) REVERT: O 62 HIS cc_start: 0.6532 (p-80) cc_final: 0.6268 (p90) REVERT: O 85 LEU cc_start: 0.7769 (tp) cc_final: 0.7565 (tp) REVERT: O 110 PHE cc_start: 0.8158 (m-80) cc_final: 0.7806 (m-10) REVERT: O 132 MET cc_start: 0.8103 (tmm) cc_final: 0.7617 (tmm) REVERT: O 193 LEU cc_start: 0.8755 (mm) cc_final: 0.8475 (mm) REVERT: O 199 ASP cc_start: 0.8847 (m-30) cc_final: 0.8394 (m-30) REVERT: O 209 ARG cc_start: 0.8886 (ptm-80) cc_final: 0.8528 (ptm-80) REVERT: O 211 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8248 (tp40) REVERT: P 87 TYR cc_start: 0.8692 (t80) cc_final: 0.8341 (t80) REVERT: P 104 MET cc_start: 0.9137 (mmp) cc_final: 0.8628 (mmp) REVERT: P 105 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8555 (mtmm) REVERT: P 106 TRP cc_start: 0.8490 (t60) cc_final: 0.8018 (t60) REVERT: P 109 MET cc_start: 0.7500 (mmp) cc_final: 0.6965 (mmm) REVERT: P 110 PHE cc_start: 0.7970 (m-10) cc_final: 0.7620 (m-10) REVERT: P 115 LEU cc_start: 0.4839 (tp) cc_final: 0.4586 (tp) REVERT: P 132 MET cc_start: 0.6685 (tmm) cc_final: 0.6198 (tmm) REVERT: P 137 ILE cc_start: 0.8343 (mm) cc_final: 0.8139 (mm) REVERT: P 170 MET cc_start: 0.7729 (mtt) cc_final: 0.7288 (mpp) REVERT: P 201 PHE cc_start: 0.7694 (t80) cc_final: 0.7481 (t80) REVERT: P 205 LYS cc_start: 0.7979 (ptpp) cc_final: 0.7371 (ptpp) REVERT: P 207 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8087 (mm-40) REVERT: P 222 ARG cc_start: 0.6554 (mmm-85) cc_final: 0.5836 (mmm160) REVERT: P 223 PHE cc_start: 0.6484 (m-80) cc_final: 0.5230 (m-80) REVERT: P 230 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7579 (mmtm) REVERT: P 233 HIS cc_start: 0.6729 (m-70) cc_final: 0.6497 (m-70) REVERT: P 272 ILE cc_start: 0.7982 (mp) cc_final: 0.7714 (mp) outliers start: 0 outliers final: 0 residues processed: 1165 average time/residue: 0.2302 time to fit residues: 424.1315 Evaluate side-chains 1080 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1080 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 251 optimal weight: 0.0000 chunk 32 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 329 optimal weight: 0.8980 chunk 274 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN C 186 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** J 62 HIS J 97 GLN J 102 GLN J 158 GLN J 242 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.196988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.150362 restraints weight = 70954.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.156082 restraints weight = 44224.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160113 restraints weight = 30890.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.162949 restraints weight = 23280.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.165005 restraints weight = 18698.602| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34119 Z= 0.168 Angle : 0.765 14.506 46515 Z= 0.412 Chirality : 0.051 0.276 5006 Planarity : 0.005 0.091 5714 Dihedral : 14.932 171.496 5007 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.39 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -0.55 (0.13), residues: 3851 helix: 0.62 (0.12), residues: 1875 sheet: -0.61 (0.18), residues: 815 loop : -1.69 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 256 TYR 0.045 0.002 TYR N 134 PHE 0.052 0.002 PHE N 201 TRP 0.068 0.002 TRP F 78 HIS 0.015 0.001 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (34119) covalent geometry : angle 0.76504 / 0.41 (46515) hydrogen bonds : bond 0.04401 / 3.01 ( 1746) hydrogen bonds : angle 5.61078 / 4.05 ( 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 1150 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1150 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8698 (mm) cc_final: 0.8251 (mm) REVERT: A 64 GLN cc_start: 0.6396 (pm20) cc_final: 0.5963 (pm20) REVERT: A 66 ASP cc_start: 0.7806 (t70) cc_final: 0.7304 (t70) REVERT: A 81 THR cc_start: 0.8673 (p) cc_final: 0.8373 (t) REVERT: A 90 ARG cc_start: 0.8062 (tmm-80) cc_final: 0.7571 (tmm-80) REVERT: A 92 LYS cc_start: 0.8778 (mtmm) cc_final: 0.8297 (mtpp) REVERT: A 97 GLN cc_start: 0.8005 (pm20) cc_final: 0.7757 (pm20) REVERT: A 104 MET cc_start: 0.8429 (ttm) cc_final: 0.7861 (ttm) REVERT: A 107 TYR cc_start: 0.8336 (t80) cc_final: 0.8093 (t80) REVERT: A 113 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7760 (mmmm) REVERT: A 118 ASP cc_start: 0.7545 (p0) cc_final: 0.7297 (p0) REVERT: A 129 GLN cc_start: 0.8139 (tt0) cc_final: 0.7837 (tt0) REVERT: A 131 LEU cc_start: 0.8869 (pp) cc_final: 0.8620 (pp) REVERT: A 132 MET cc_start: 0.7995 (mmm) cc_final: 0.7562 (mmm) REVERT: A 135 LEU cc_start: 0.8884 (mt) cc_final: 0.8626 (mt) REVERT: A 164 LEU cc_start: 0.8485 (mt) cc_final: 0.8199 (mt) REVERT: A 174 PHE cc_start: 0.6422 (p90) cc_final: 0.5839 (p90) REVERT: A 175 GLU cc_start: 0.8438 (pm20) cc_final: 0.8113 (pm20) REVERT: A 190 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7212 (mtpp) REVERT: A 203 PHE cc_start: 0.8439 (t80) cc_final: 0.8008 (t80) REVERT: A 211 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7786 (tp-100) REVERT: A 226 TYR cc_start: 0.6477 (p90) cc_final: 0.6252 (p90) REVERT: A 254 LYS cc_start: 0.8423 (tmmt) cc_final: 0.8029 (ttpp) REVERT: B 15 TRP cc_start: 0.7712 (m100) cc_final: 0.7214 (m100) REVERT: B 40 CYS cc_start: 0.7542 (t) cc_final: 0.6978 (p) REVERT: B 63 TRP cc_start: 0.7824 (m100) cc_final: 0.6322 (m100) REVERT: B 64 GLN cc_start: 0.7136 (tp40) cc_final: 0.6460 (mm110) REVERT: B 65 VAL cc_start: 0.8640 (t) cc_final: 0.8347 (t) REVERT: B 70 TYR cc_start: 0.8428 (t80) cc_final: 0.7859 (t80) REVERT: B 82 ASN cc_start: 0.8019 (p0) cc_final: 0.7754 (p0) REVERT: B 86 ILE cc_start: 0.8915 (pt) cc_final: 0.7988 (mm) REVERT: B 89 GLU cc_start: 0.7833 (tt0) cc_final: 0.7295 (tt0) REVERT: B 90 ARG cc_start: 0.8759 (tpt-90) cc_final: 0.8137 (tpp80) REVERT: B 92 LYS cc_start: 0.8866 (tppt) cc_final: 0.8314 (tptp) REVERT: B 104 MET cc_start: 0.8656 (mmp) cc_final: 0.8117 (mmp) REVERT: B 129 GLN cc_start: 0.8444 (pt0) cc_final: 0.8079 (pt0) REVERT: B 132 MET cc_start: 0.8698 (mmp) cc_final: 0.8457 (mmt) REVERT: B 137 ILE cc_start: 0.8618 (tt) cc_final: 0.7719 (tt) REVERT: B 138 GLU cc_start: 0.7848 (tp30) cc_final: 0.7587 (tp30) REVERT: B 139 HIS cc_start: 0.8501 (t70) cc_final: 0.7927 (t70) REVERT: B 165 GLU cc_start: 0.8016 (tp30) cc_final: 0.7673 (tp30) REVERT: B 174 PHE cc_start: 0.7674 (t80) cc_final: 0.7431 (t80) REVERT: B 178 LEU cc_start: 0.9203 (mm) cc_final: 0.8789 (mm) REVERT: B 183 ILE cc_start: 0.8789 (mt) cc_final: 0.8479 (mt) REVERT: B 188 LYS cc_start: 0.7045 (mmtp) cc_final: 0.6580 (mmtp) REVERT: B 189 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6805 (ttp-110) REVERT: B 198 MET cc_start: 0.8069 (tpt) cc_final: 0.7628 (tpp) REVERT: C 11 GLU cc_start: 0.8328 (tp30) cc_final: 0.7500 (tp30) REVERT: C 15 TRP cc_start: 0.8233 (m100) cc_final: 0.7797 (m100) REVERT: C 34 GLU cc_start: 0.8303 (pp20) cc_final: 0.8015 (pp20) REVERT: C 39 GLN cc_start: 0.8443 (tp40) cc_final: 0.7785 (tp40) REVERT: C 106 TRP cc_start: 0.6583 (t60) cc_final: 0.6314 (t60) REVERT: C 110 PHE cc_start: 0.7784 (m-80) cc_final: 0.7215 (m-80) REVERT: C 164 LEU cc_start: 0.8966 (mt) cc_final: 0.8406 (tp) REVERT: C 190 LYS cc_start: 0.6443 (mttm) cc_final: 0.6153 (mmmt) REVERT: C 199 ASP cc_start: 0.8888 (m-30) cc_final: 0.8672 (m-30) REVERT: C 244 LEU cc_start: 0.8326 (mm) cc_final: 0.7872 (mm) REVERT: D 218 GLN cc_start: 0.8438 (mm110) cc_final: 0.7880 (mm110) REVERT: D 226 TYR cc_start: 0.6924 (p90) cc_final: 0.6001 (p90) REVERT: D 254 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7873 (ttmt) REVERT: E 12 HIS cc_start: 0.8412 (t70) cc_final: 0.7162 (t70) REVERT: E 14 LYS cc_start: 0.8304 (tttt) cc_final: 0.8015 (mtpp) REVERT: E 15 TRP cc_start: 0.8635 (m-10) cc_final: 0.8164 (m-10) REVERT: E 16 HIS cc_start: 0.7728 (m-70) cc_final: 0.6827 (m170) REVERT: E 97 GLN cc_start: 0.7978 (pm20) cc_final: 0.7753 (pm20) REVERT: E 100 ARG cc_start: 0.8738 (ptp90) cc_final: 0.8204 (ptp-170) REVERT: E 130 LEU cc_start: 0.8464 (pp) cc_final: 0.8187 (pp) REVERT: E 133 LYS cc_start: 0.9215 (ptpp) cc_final: 0.8473 (pttm) REVERT: E 150 GLN cc_start: 0.8171 (mm110) cc_final: 0.7519 (mm-40) REVERT: E 158 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7496 (tm-30) REVERT: E 159 THR cc_start: 0.8500 (m) cc_final: 0.7838 (p) REVERT: E 178 LEU cc_start: 0.8892 (mt) cc_final: 0.8623 (mt) REVERT: E 201 PHE cc_start: 0.8527 (t80) cc_final: 0.8063 (t80) REVERT: E 204 ASN cc_start: 0.8574 (t0) cc_final: 0.8353 (t0) REVERT: E 224 CYS cc_start: 0.6351 (p) cc_final: 0.5748 (p) REVERT: E 242 GLN cc_start: 0.5020 (pp30) cc_final: 0.4728 (pp30) REVERT: F 23 HIS cc_start: 0.7593 (t70) cc_final: 0.7259 (t70) REVERT: F 65 VAL cc_start: 0.6819 (t) cc_final: 0.6565 (p) REVERT: F 89 GLU cc_start: 0.6447 (tp30) cc_final: 0.6186 (tp30) REVERT: F 104 MET cc_start: 0.8182 (ptm) cc_final: 0.7501 (ppp) REVERT: F 131 LEU cc_start: 0.8556 (tp) cc_final: 0.8336 (mm) REVERT: F 154 GLU cc_start: 0.8595 (tp30) cc_final: 0.8329 (mm-30) REVERT: F 162 ASN cc_start: 0.8960 (m-40) cc_final: 0.8716 (m-40) REVERT: F 164 LEU cc_start: 0.8462 (mt) cc_final: 0.8256 (mt) REVERT: F 230 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8046 (mmmm) REVERT: F 233 HIS cc_start: 0.7740 (m-70) cc_final: 0.7528 (m-70) REVERT: F 237 TRP cc_start: 0.8369 (m100) cc_final: 0.8109 (m100) REVERT: F 242 GLN cc_start: 0.7411 (tt0) cc_final: 0.6875 (pp30) REVERT: F 243 VAL cc_start: 0.8494 (t) cc_final: 0.7440 (m) REVERT: F 244 LEU cc_start: 0.8292 (tt) cc_final: 0.7771 (tt) REVERT: F 256 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8003 (ttm110) REVERT: G 48 MET cc_start: -0.0473 (ppp) cc_final: -0.1315 (ppp) REVERT: G 62 HIS cc_start: 0.7433 (t70) cc_final: 0.6491 (t70) REVERT: G 71 GLU cc_start: 0.7381 (tp30) cc_final: 0.7023 (tp30) REVERT: G 85 LEU cc_start: 0.7185 (tp) cc_final: 0.6940 (tp) REVERT: G 104 MET cc_start: 0.8087 (pmm) cc_final: 0.7820 (pmm) REVERT: G 110 PHE cc_start: 0.7808 (m-80) cc_final: 0.7036 (m-10) REVERT: G 131 LEU cc_start: 0.9319 (mt) cc_final: 0.9050 (mt) REVERT: G 155 ARG cc_start: 0.9108 (ttm110) cc_final: 0.8907 (mtp-110) REVERT: G 157 HIS cc_start: 0.8947 (p-80) cc_final: 0.8467 (p90) REVERT: G 161 LYS cc_start: 0.9279 (tptt) cc_final: 0.8886 (mmmt) REVERT: G 168 ILE cc_start: 0.7853 (mt) cc_final: 0.7520 (pt) REVERT: G 171 PHE cc_start: 0.7105 (m-80) cc_final: 0.6633 (m-80) REVERT: G 175 GLU cc_start: 0.8728 (pm20) cc_final: 0.8078 (mm-30) REVERT: G 183 ILE cc_start: 0.7339 (mt) cc_final: 0.7127 (mt) REVERT: G 197 PRO cc_start: 0.8431 (Cg_exo) cc_final: 0.8143 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8888 (m-30) cc_final: 0.8348 (m-30) REVERT: G 205 LYS cc_start: 0.9323 (mmtm) cc_final: 0.9009 (mmtm) REVERT: G 209 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8182 (ttp80) REVERT: G 210 ILE cc_start: 0.8614 (pt) cc_final: 0.7915 (pt) REVERT: H 78 TRP cc_start: 0.7148 (m-10) cc_final: 0.6604 (m-10) REVERT: H 85 LEU cc_start: 0.8699 (tp) cc_final: 0.8459 (tp) REVERT: H 87 TYR cc_start: 0.8492 (t80) cc_final: 0.7995 (t80) REVERT: H 101 VAL cc_start: 0.8820 (p) cc_final: 0.8596 (p) REVERT: H 104 MET cc_start: 0.9095 (mmp) cc_final: 0.8447 (mmp) REVERT: H 106 TRP cc_start: 0.8405 (t60) cc_final: 0.7620 (t60) REVERT: H 109 MET cc_start: 0.7473 (mmp) cc_final: 0.6946 (mmm) REVERT: H 110 PHE cc_start: 0.7855 (m-10) cc_final: 0.7492 (m-10) REVERT: H 202 ILE cc_start: 0.9143 (mt) cc_final: 0.8851 (mt) REVERT: H 207 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7593 (mm-40) REVERT: H 223 PHE cc_start: 0.6865 (m-80) cc_final: 0.6533 (m-80) REVERT: H 238 GLN cc_start: 0.7209 (mm110) cc_final: 0.6523 (mm-40) REVERT: I 48 MET cc_start: 0.5971 (mmp) cc_final: 0.5742 (mmm) REVERT: I 60 ILE cc_start: 0.8863 (mp) cc_final: 0.8315 (mm) REVERT: I 66 ASP cc_start: 0.7770 (t70) cc_final: 0.7370 (t70) REVERT: I 79 VAL cc_start: 0.8194 (t) cc_final: 0.7504 (p) REVERT: I 86 ILE cc_start: 0.8510 (pt) cc_final: 0.7992 (mp) REVERT: I 92 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8574 (mtpp) REVERT: I 98 GLU cc_start: 0.8280 (mp0) cc_final: 0.7912 (mp0) REVERT: I 113 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7649 (mmmm) REVERT: I 116 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6468 (tm-30) REVERT: I 152 LEU cc_start: 0.7416 (pt) cc_final: 0.6507 (mp) REVERT: I 155 ARG cc_start: 0.8366 (tpt90) cc_final: 0.7553 (mmm160) REVERT: I 158 GLN cc_start: 0.9073 (tt0) cc_final: 0.8527 (tt0) REVERT: I 159 THR cc_start: 0.8548 (p) cc_final: 0.8317 (m) REVERT: I 160 LEU cc_start: 0.8697 (tt) cc_final: 0.8412 (tt) REVERT: I 164 LEU cc_start: 0.8675 (mt) cc_final: 0.8442 (mt) REVERT: I 198 MET cc_start: 0.8581 (ttm) cc_final: 0.8324 (tpp) REVERT: I 201 PHE cc_start: 0.8562 (t80) cc_final: 0.8342 (t80) REVERT: I 203 PHE cc_start: 0.8378 (t80) cc_final: 0.7897 (t80) REVERT: I 211 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7825 (tp-100) REVERT: I 253 VAL cc_start: 0.7899 (t) cc_final: 0.7655 (m) REVERT: I 264 ILE cc_start: 0.7670 (mm) cc_final: 0.7426 (mm) REVERT: J 13 ASN cc_start: 0.7275 (m-40) cc_final: 0.7020 (m110) REVERT: J 62 HIS cc_start: 0.7481 (t70) cc_final: 0.7024 (t-170) REVERT: J 63 TRP cc_start: 0.7654 (m100) cc_final: 0.6102 (m100) REVERT: J 64 GLN cc_start: 0.7166 (tp40) cc_final: 0.5536 (mm-40) REVERT: J 86 ILE cc_start: 0.8935 (pt) cc_final: 0.8284 (mm) REVERT: J 92 LYS cc_start: 0.8926 (tptp) cc_final: 0.8521 (tptp) REVERT: J 100 ARG cc_start: 0.8706 (mpp80) cc_final: 0.8098 (mtt180) REVERT: J 104 MET cc_start: 0.8254 (tpp) cc_final: 0.7791 (tpp) REVERT: J 106 TRP cc_start: 0.8505 (t60) cc_final: 0.8303 (t60) REVERT: J 116 GLN cc_start: 0.7672 (tm-30) cc_final: 0.6676 (tm-30) REVERT: J 131 LEU cc_start: 0.8754 (tt) cc_final: 0.8367 (tt) REVERT: J 139 HIS cc_start: 0.8600 (t70) cc_final: 0.8133 (t70) REVERT: J 162 ASN cc_start: 0.8835 (m110) cc_final: 0.8564 (m110) REVERT: J 170 MET cc_start: 0.8293 (tmm) cc_final: 0.7996 (tmm) REVERT: J 189 ARG cc_start: 0.7265 (ttp-110) cc_final: 0.6599 (mtm110) REVERT: J 204 ASN cc_start: 0.8413 (m110) cc_final: 0.7322 (p0) REVERT: J 205 LYS cc_start: 0.8450 (tptp) cc_final: 0.7896 (tptp) REVERT: J 208 GLN cc_start: 0.8199 (pt0) cc_final: 0.7864 (pt0) REVERT: K 7 LEU cc_start: 0.8632 (tt) cc_final: 0.8378 (tt) REVERT: K 34 GLU cc_start: 0.8762 (pt0) cc_final: 0.8374 (pp20) REVERT: K 35 ASP cc_start: 0.8696 (m-30) cc_final: 0.8227 (m-30) REVERT: K 132 MET cc_start: 0.7434 (ppp) cc_final: 0.6877 (ppp) REVERT: L 209 ARG cc_start: 0.8642 (mmp-170) cc_final: 0.8350 (mmp-170) REVERT: L 226 TYR cc_start: 0.6719 (p90) cc_final: 0.5757 (p90) REVERT: L 254 LYS cc_start: 0.8396 (tmtt) cc_final: 0.7790 (tppt) REVERT: L 266 ASN cc_start: 0.8372 (m110) cc_final: 0.8002 (m110) REVERT: L 269 VAL cc_start: 0.7783 (m) cc_final: 0.7527 (m) REVERT: M 7 LEU cc_start: 0.8510 (tt) cc_final: 0.7872 (tt) REVERT: M 11 GLU cc_start: 0.8582 (mp0) cc_final: 0.7964 (mp0) REVERT: M 16 HIS cc_start: 0.8156 (m170) cc_final: 0.7599 (m90) REVERT: M 18 ASP cc_start: 0.7797 (t70) cc_final: 0.7472 (t70) REVERT: M 25 GLU cc_start: 0.8497 (tt0) cc_final: 0.8172 (tt0) REVERT: M 63 TRP cc_start: 0.7283 (m100) cc_final: 0.7073 (m100) REVERT: M 89 GLU cc_start: 0.6842 (pm20) cc_final: 0.6148 (mp0) REVERT: M 109 MET cc_start: 0.8704 (tmm) cc_final: 0.8151 (ttt) REVERT: M 154 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8791 (mm-30) REVERT: M 155 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8364 (mtt90) REVERT: M 158 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7643 (tm-30) REVERT: M 159 THR cc_start: 0.8613 (m) cc_final: 0.8033 (p) REVERT: M 178 LEU cc_start: 0.8867 (mt) cc_final: 0.8648 (mt) REVERT: M 195 THR cc_start: 0.8334 (m) cc_final: 0.8059 (p) REVERT: M 202 ILE cc_start: 0.8685 (mm) cc_final: 0.8252 (mm) REVERT: M 205 LYS cc_start: 0.9028 (mtmm) cc_final: 0.8395 (mtmm) REVERT: M 206 GLU cc_start: 0.8613 (pt0) cc_final: 0.7944 (pt0) REVERT: M 207 GLN cc_start: 0.8499 (mm110) cc_final: 0.8279 (mm110) REVERT: M 209 ARG cc_start: 0.8768 (tmt170) cc_final: 0.8391 (ttp80) REVERT: N 23 HIS cc_start: 0.7784 (t70) cc_final: 0.7485 (t70) REVERT: N 104 MET cc_start: 0.8117 (ptm) cc_final: 0.7498 (ppp) REVERT: N 150 GLN cc_start: 0.7855 (mt0) cc_final: 0.7634 (mt0) REVERT: N 157 HIS cc_start: 0.8100 (m90) cc_final: 0.7747 (m90) REVERT: N 164 LEU cc_start: 0.8539 (mt) cc_final: 0.8322 (mt) REVERT: N 165 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8064 (mm-30) REVERT: N 183 ILE cc_start: 0.7267 (mt) cc_final: 0.7057 (mt) REVERT: N 202 ILE cc_start: 0.8250 (mt) cc_final: 0.7941 (mt) REVERT: N 203 PHE cc_start: 0.7926 (t80) cc_final: 0.7186 (t80) REVERT: N 206 GLU cc_start: 0.8077 (pp20) cc_final: 0.6808 (pp20) REVERT: N 213 GLN cc_start: 0.8763 (mt0) cc_final: 0.8415 (mt0) REVERT: N 233 HIS cc_start: 0.7824 (m90) cc_final: 0.7427 (m-70) REVERT: N 242 GLN cc_start: 0.7738 (tt0) cc_final: 0.7213 (pp30) REVERT: N 243 VAL cc_start: 0.8561 (t) cc_final: 0.8008 (p) REVERT: N 244 LEU cc_start: 0.8419 (tt) cc_final: 0.8098 (tt) REVERT: N 256 ARG cc_start: 0.8409 (ttm110) cc_final: 0.7776 (ttm110) REVERT: N 270 LYS cc_start: 0.7917 (mptt) cc_final: 0.7290 (mmtp) REVERT: O 48 MET cc_start: -0.1496 (ppp) cc_final: -0.1910 (ppp) REVERT: O 62 HIS cc_start: 0.6951 (p-80) cc_final: 0.6499 (p90) REVERT: O 70 TYR cc_start: 0.6079 (t80) cc_final: 0.5312 (t80) REVERT: O 115 LEU cc_start: 0.8781 (tp) cc_final: 0.8453 (tp) REVERT: O 152 LEU cc_start: 0.8637 (tp) cc_final: 0.8317 (tp) REVERT: O 157 HIS cc_start: 0.8987 (p90) cc_final: 0.8730 (p-80) REVERT: O 158 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8779 (tp-100) REVERT: O 168 ILE cc_start: 0.7386 (mt) cc_final: 0.7130 (mt) REVERT: O 193 LEU cc_start: 0.8756 (mm) cc_final: 0.8455 (mm) REVERT: O 208 GLN cc_start: 0.8741 (tm130) cc_final: 0.8495 (tm-30) REVERT: O 209 ARG cc_start: 0.8813 (ptm-80) cc_final: 0.8530 (ptm-80) REVERT: O 211 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8204 (tp40) REVERT: P 87 TYR cc_start: 0.8682 (t80) cc_final: 0.8356 (t80) REVERT: P 104 MET cc_start: 0.9120 (mmp) cc_final: 0.8574 (mmp) REVERT: P 106 TRP cc_start: 0.8457 (t60) cc_final: 0.7912 (t60) REVERT: P 109 MET cc_start: 0.7444 (mmp) cc_final: 0.7166 (mmm) REVERT: P 110 PHE cc_start: 0.7926 (m-10) cc_final: 0.7566 (m-10) REVERT: P 115 LEU cc_start: 0.5013 (tp) cc_final: 0.4712 (tp) REVERT: P 132 MET cc_start: 0.6766 (tmm) cc_final: 0.6272 (tmm) REVERT: P 170 MET cc_start: 0.7623 (mtt) cc_final: 0.7149 (mpp) REVERT: P 172 ASN cc_start: 0.8838 (m-40) cc_final: 0.8534 (p0) REVERT: P 201 PHE cc_start: 0.7751 (t80) cc_final: 0.7379 (t80) REVERT: P 205 LYS cc_start: 0.8089 (ptpp) cc_final: 0.7423 (ptpp) REVERT: P 207 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8003 (mm-40) REVERT: P 222 ARG cc_start: 0.6744 (mmm-85) cc_final: 0.6035 (mmm160) REVERT: P 223 PHE cc_start: 0.6612 (m-80) cc_final: 0.5400 (m-80) REVERT: P 233 HIS cc_start: 0.6617 (m-70) cc_final: 0.6391 (m-70) REVERT: P 238 GLN cc_start: 0.6794 (mm110) cc_final: 0.6446 (mp10) REVERT: P 272 ILE cc_start: 0.8039 (mp) cc_final: 0.7809 (mp) outliers start: 0 outliers final: 0 residues processed: 1150 average time/residue: 0.2282 time to fit residues: 415.5434 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 : 1.204 ------------------------------------------------------------------------------- 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: 1.9990 chunk 300 optimal weight: 0.9990 chunk 280 optimal weight: 0.7980 chunk 380 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 273 optimal weight: 0.9990 chunk 356 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 HIS A 16 HIS ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 HIS H 162 ASN I 16 HIS ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 HIS ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.196128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.149352 restraints weight = 70975.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155012 restraints weight = 43933.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159000 restraints weight = 30654.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161826 restraints weight = 23117.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.163844 restraints weight = 18551.671| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34119 Z= 0.166 Angle : 0.781 14.026 46515 Z= 0.418 Chirality : 0.052 0.524 5006 Planarity : 0.005 0.089 5714 Dihedral : 14.936 171.674 5007 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.65 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 3851 helix: 0.62 (0.12), residues: 1877 sheet: -0.60 (0.18), residues: 802 loop : -1.79 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG N 209 TYR 0.023 0.001 TYR G 70 PHE 0.046 0.002 PHE N 201 TRP 0.050 0.002 TRP F 78 HIS 0.018 0.001 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (34119) covalent geometry : angle 0.78144 / 0.42 (46515) hydrogen bonds : bond 0.04389 / 2.99 ( 1746) hydrogen bonds : angle 5.65361 / 4.08 ( 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 1147 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1147 time to evaluate : 1.191 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: A 60 ILE cc_start: 0.8687 (mm) cc_final: 0.8160 (mm) REVERT: A 64 GLN cc_start: 0.6359 (pm20) cc_final: 0.5935 (pm20) REVERT: A 66 ASP cc_start: 0.7769 (t70) cc_final: 0.7178 (t70) REVERT: A 81 THR cc_start: 0.8692 (p) cc_final: 0.8398 (t) REVERT: A 90 ARG cc_start: 0.8092 (tmm-80) cc_final: 0.7474 (tmm-80) REVERT: A 92 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8303 (mtpp) REVERT: A 97 GLN cc_start: 0.8074 (pm20) cc_final: 0.7801 (pm20) REVERT: A 104 MET cc_start: 0.8454 (ttm) cc_final: 0.7839 (ttm) REVERT: A 105 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8804 (mtpp) REVERT: A 107 TYR cc_start: 0.8321 (t80) cc_final: 0.8065 (t80) REVERT: A 113 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7742 (mmmm) REVERT: A 118 ASP cc_start: 0.7575 (p0) cc_final: 0.7332 (p0) REVERT: A 129 GLN cc_start: 0.8167 (tt0) cc_final: 0.7878 (tt0) REVERT: A 131 LEU cc_start: 0.8853 (pp) cc_final: 0.8614 (pp) REVERT: A 132 MET cc_start: 0.8003 (mmm) cc_final: 0.7561 (mmm) REVERT: A 135 LEU cc_start: 0.8928 (mt) cc_final: 0.8681 (mt) REVERT: A 158 GLN cc_start: 0.8916 (tt0) cc_final: 0.8617 (tt0) REVERT: A 164 LEU cc_start: 0.8460 (mt) cc_final: 0.8204 (mt) REVERT: A 174 PHE cc_start: 0.6433 (p90) cc_final: 0.5932 (p90) REVERT: A 175 GLU cc_start: 0.8461 (pm20) cc_final: 0.8134 (pm20) REVERT: A 178 LEU cc_start: 0.8050 (tp) cc_final: 0.7686 (tp) REVERT: A 190 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7202 (mtpt) REVERT: A 203 PHE cc_start: 0.8450 (t80) cc_final: 0.8023 (t80) REVERT: A 211 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7778 (tp-100) REVERT: A 226 TYR cc_start: 0.6548 (p90) cc_final: 0.6312 (p90) REVERT: A 243 VAL cc_start: 0.8718 (p) cc_final: 0.8267 (p) REVERT: A 254 LYS cc_start: 0.8370 (tmmt) cc_final: 0.7972 (ttpp) REVERT: B 15 TRP cc_start: 0.7606 (m100) cc_final: 0.7098 (m100) REVERT: B 40 CYS cc_start: 0.7582 (t) cc_final: 0.6995 (p) REVERT: B 63 TRP cc_start: 0.7829 (m100) cc_final: 0.6307 (m100) REVERT: B 64 GLN cc_start: 0.7112 (tp40) cc_final: 0.5445 (mm-40) REVERT: B 70 TYR cc_start: 0.8351 (t80) cc_final: 0.7818 (t80) REVERT: B 82 ASN cc_start: 0.8015 (p0) cc_final: 0.7755 (p0) REVERT: B 86 ILE cc_start: 0.8924 (pt) cc_final: 0.7952 (mm) REVERT: B 87 TYR cc_start: 0.7949 (t80) cc_final: 0.7672 (t80) REVERT: B 89 GLU cc_start: 0.7919 (tt0) cc_final: 0.7051 (tt0) REVERT: B 90 ARG cc_start: 0.8749 (tpt-90) cc_final: 0.8188 (tpp80) REVERT: B 92 LYS cc_start: 0.8957 (tppt) cc_final: 0.8366 (tptp) REVERT: B 100 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8352 (mtt180) REVERT: B 104 MET cc_start: 0.8596 (mmp) cc_final: 0.8024 (mmp) REVERT: B 116 GLN cc_start: 0.7627 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 129 GLN cc_start: 0.8436 (pt0) cc_final: 0.8057 (pt0) REVERT: B 132 MET cc_start: 0.8705 (mmp) cc_final: 0.8456 (mmt) REVERT: B 137 ILE cc_start: 0.8567 (tt) cc_final: 0.7712 (tt) REVERT: B 138 GLU cc_start: 0.7855 (tp30) cc_final: 0.7623 (tp30) REVERT: B 139 HIS cc_start: 0.8524 (t70) cc_final: 0.7972 (t70) REVERT: B 165 GLU cc_start: 0.7993 (tp30) cc_final: 0.7664 (tp30) REVERT: B 174 PHE cc_start: 0.7786 (t80) cc_final: 0.7486 (t80) REVERT: B 178 LEU cc_start: 0.9211 (mm) cc_final: 0.8798 (mm) REVERT: B 183 ILE cc_start: 0.8784 (mt) cc_final: 0.8549 (mt) REVERT: B 186 ASN cc_start: 0.8346 (m-40) cc_final: 0.8041 (m-40) REVERT: B 188 LYS cc_start: 0.6997 (mmtp) cc_final: 0.6584 (mmtp) REVERT: B 189 ARG cc_start: 0.7082 (mtm-85) cc_final: 0.6799 (ttp-110) REVERT: B 198 MET cc_start: 0.8058 (tpt) cc_final: 0.7504 (tpp) REVERT: C 11 GLU cc_start: 0.8364 (tp30) cc_final: 0.7541 (tp30) REVERT: C 15 TRP cc_start: 0.8251 (m100) cc_final: 0.7827 (m100) REVERT: C 34 GLU cc_start: 0.8447 (pp20) cc_final: 0.8194 (pp20) REVERT: C 39 GLN cc_start: 0.8533 (tp40) cc_final: 0.7868 (tp40) REVERT: C 106 TRP cc_start: 0.6575 (t60) cc_final: 0.6074 (t60) REVERT: C 110 PHE cc_start: 0.7782 (m-80) cc_final: 0.7141 (m-80) REVERT: C 132 MET cc_start: 0.7248 (ppp) cc_final: 0.6853 (ppp) REVERT: C 190 LYS cc_start: 0.6371 (mttm) cc_final: 0.6155 (mmmt) REVERT: C 209 ARG cc_start: 0.8678 (ptt90) cc_final: 0.8310 (ptt90) REVERT: C 245 TRP cc_start: 0.8282 (m-90) cc_final: 0.8026 (m-90) REVERT: D 218 GLN cc_start: 0.8426 (mm110) cc_final: 0.7850 (mm110) REVERT: D 223 PHE cc_start: 0.5891 (p90) cc_final: 0.5476 (p90) REVERT: D 226 TYR cc_start: 0.6914 (p90) cc_final: 0.5851 (p90) REVERT: D 254 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7848 (ttmt) REVERT: E 12 HIS cc_start: 0.8427 (t70) cc_final: 0.7112 (t70) REVERT: E 14 LYS cc_start: 0.8374 (tttt) cc_final: 0.7857 (tttp) REVERT: E 15 TRP cc_start: 0.8683 (m-10) cc_final: 0.8175 (m-10) REVERT: E 16 HIS cc_start: 0.7741 (m-70) cc_final: 0.7020 (m170) REVERT: E 89 GLU cc_start: 0.6782 (mp0) cc_final: 0.6368 (mp0) REVERT: E 97 GLN cc_start: 0.8001 (pm20) cc_final: 0.7701 (pm20) REVERT: E 100 ARG cc_start: 0.8739 (ptp90) cc_final: 0.8186 (ptp-170) REVERT: E 101 VAL cc_start: 0.8835 (t) cc_final: 0.8623 (t) REVERT: E 130 LEU cc_start: 0.8502 (pp) cc_final: 0.8228 (pp) REVERT: E 133 LYS cc_start: 0.9194 (ptpp) cc_final: 0.8432 (pttm) REVERT: E 150 GLN cc_start: 0.8221 (mm110) cc_final: 0.7599 (mm-40) REVERT: E 158 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 159 THR cc_start: 0.8481 (m) cc_final: 0.7839 (p) REVERT: E 174 PHE cc_start: 0.7418 (t80) cc_final: 0.7188 (t80) REVERT: E 178 LEU cc_start: 0.8889 (mt) cc_final: 0.8406 (mt) REVERT: E 204 ASN cc_start: 0.8642 (t0) cc_final: 0.8395 (t0) REVERT: E 224 CYS cc_start: 0.6540 (p) cc_final: 0.5948 (p) REVERT: E 242 GLN cc_start: 0.5319 (pp30) cc_final: 0.5039 (pp30) REVERT: F 23 HIS cc_start: 0.7612 (t70) cc_final: 0.7273 (t70) REVERT: F 65 VAL cc_start: 0.7576 (t) cc_final: 0.7234 (p) REVERT: F 89 GLU cc_start: 0.6450 (tp30) cc_final: 0.6129 (tp30) REVERT: F 104 MET cc_start: 0.8257 (ptm) cc_final: 0.7600 (ppp) REVERT: F 131 LEU cc_start: 0.8565 (tp) cc_final: 0.8364 (mm) REVERT: F 158 GLN cc_start: 0.9097 (mt0) cc_final: 0.8769 (mm-40) REVERT: F 162 ASN cc_start: 0.8989 (m-40) cc_final: 0.8785 (m-40) REVERT: F 164 LEU cc_start: 0.8467 (mt) cc_final: 0.8248 (mt) REVERT: F 230 LYS cc_start: 0.8467 (mmmt) cc_final: 0.7870 (mmmm) REVERT: F 233 HIS cc_start: 0.7740 (m-70) cc_final: 0.7502 (m90) REVERT: F 242 GLN cc_start: 0.7479 (tt0) cc_final: 0.6912 (pp30) REVERT: F 243 VAL cc_start: 0.8483 (t) cc_final: 0.7459 (m) REVERT: F 244 LEU cc_start: 0.8313 (tt) cc_final: 0.7843 (tt) REVERT: F 260 ARG cc_start: 0.6895 (mtm110) cc_final: 0.6503 (ptp-110) REVERT: F 270 LYS cc_start: 0.8183 (mttt) cc_final: 0.7643 (mptt) REVERT: G 7 LEU cc_start: 0.3141 (mp) cc_final: 0.2920 (tp) REVERT: G 22 LEU cc_start: 0.7908 (mm) cc_final: 0.7624 (mm) REVERT: G 48 MET cc_start: -0.0451 (ppp) cc_final: -0.1319 (ppp) REVERT: G 62 HIS cc_start: 0.7666 (t70) cc_final: 0.6599 (t70) REVERT: G 71 GLU cc_start: 0.7323 (tp30) cc_final: 0.6957 (tp30) REVERT: G 85 LEU cc_start: 0.7205 (tp) cc_final: 0.6907 (tp) REVERT: G 104 MET cc_start: 0.8072 (pmm) cc_final: 0.7774 (pmm) REVERT: G 110 PHE cc_start: 0.7939 (m-80) cc_final: 0.7179 (m-10) REVERT: G 131 LEU cc_start: 0.9330 (mt) cc_final: 0.9067 (mt) REVERT: G 157 HIS cc_start: 0.8953 (p-80) cc_final: 0.8460 (p90) REVERT: G 158 GLN cc_start: 0.8976 (tp40) cc_final: 0.8735 (tp40) REVERT: G 161 LYS cc_start: 0.9182 (tptt) cc_final: 0.8974 (mmmt) REVERT: G 162 ASN cc_start: 0.8757 (m110) cc_final: 0.8494 (m110) REVERT: G 168 ILE cc_start: 0.7829 (mt) cc_final: 0.7495 (pt) REVERT: G 171 PHE cc_start: 0.7068 (m-80) cc_final: 0.6596 (m-80) REVERT: G 175 GLU cc_start: 0.8736 (pm20) cc_final: 0.8034 (mm-30) REVERT: G 197 PRO cc_start: 0.8379 (Cg_exo) cc_final: 0.8109 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8856 (m-30) cc_final: 0.8342 (m-30) REVERT: G 205 LYS cc_start: 0.9336 (mmtm) cc_final: 0.9038 (mmtm) REVERT: G 209 ARG cc_start: 0.8836 (ttp80) cc_final: 0.8221 (ttp80) REVERT: G 210 ILE cc_start: 0.8646 (pt) cc_final: 0.7920 (pt) REVERT: H 78 TRP cc_start: 0.7227 (m-10) cc_final: 0.5870 (m-10) REVERT: H 87 TYR cc_start: 0.8522 (t80) cc_final: 0.8026 (t80) REVERT: H 101 VAL cc_start: 0.8787 (p) cc_final: 0.8546 (p) REVERT: H 104 MET cc_start: 0.9083 (mmp) cc_final: 0.8405 (mmp) REVERT: H 106 TRP cc_start: 0.8392 (t60) cc_final: 0.7239 (t60) REVERT: H 110 PHE cc_start: 0.7884 (m-10) cc_final: 0.7362 (m-10) REVERT: H 170 MET cc_start: 0.7881 (mtt) cc_final: 0.7215 (mpp) REVERT: H 207 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7634 (mm-40) REVERT: H 223 PHE cc_start: 0.6870 (m-80) cc_final: 0.6504 (m-80) REVERT: H 256 ARG cc_start: 0.8207 (ppt170) cc_final: 0.7793 (ppt170) REVERT: I 60 ILE cc_start: 0.8869 (mp) cc_final: 0.8333 (mm) REVERT: I 66 ASP cc_start: 0.7884 (t70) cc_final: 0.7450 (t70) REVERT: I 79 VAL cc_start: 0.8179 (t) cc_final: 0.7646 (p) REVERT: I 80 GLU cc_start: 0.6555 (tm-30) cc_final: 0.6330 (tm-30) REVERT: I 85 LEU cc_start: 0.7958 (tp) cc_final: 0.7580 (tp) REVERT: I 86 ILE cc_start: 0.8537 (pt) cc_final: 0.8062 (mp) REVERT: I 92 LYS cc_start: 0.9068 (mtmm) cc_final: 0.8551 (mtpp) REVERT: I 98 GLU cc_start: 0.8221 (mp0) cc_final: 0.7869 (mp0) REVERT: I 102 GLN cc_start: 0.9149 (mm110) cc_final: 0.8762 (mm-40) REVERT: I 104 MET cc_start: 0.8486 (ttm) cc_final: 0.7459 (ttm) REVERT: I 105 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8155 (mtmm) REVERT: I 113 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7619 (mmmm) REVERT: I 116 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6776 (tm-30) REVERT: I 143 ILE cc_start: 0.8896 (tp) cc_final: 0.8414 (tp) REVERT: I 145 TRP cc_start: 0.8604 (m-90) cc_final: 0.7828 (m-90) REVERT: I 152 LEU cc_start: 0.7279 (pt) cc_final: 0.6223 (mp) REVERT: I 153 VAL cc_start: 0.8908 (m) cc_final: 0.8692 (p) REVERT: I 155 ARG cc_start: 0.8332 (tpt90) cc_final: 0.7583 (mmm160) REVERT: I 158 GLN cc_start: 0.9054 (tt0) cc_final: 0.8538 (tt0) REVERT: I 160 LEU cc_start: 0.8711 (tt) cc_final: 0.8495 (tt) REVERT: I 174 PHE cc_start: 0.7222 (t80) cc_final: 0.6849 (t80) REVERT: I 183 ILE cc_start: 0.9131 (mt) cc_final: 0.8677 (mm) REVERT: I 198 MET cc_start: 0.8615 (ttm) cc_final: 0.8271 (tpp) REVERT: I 203 PHE cc_start: 0.8360 (t80) cc_final: 0.7847 (t80) REVERT: I 211 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7842 (tp-100) REVERT: J 7 LEU cc_start: 0.7815 (mt) cc_final: 0.7564 (mt) REVERT: J 13 ASN cc_start: 0.7496 (m-40) cc_final: 0.7110 (m110) REVERT: J 62 HIS cc_start: 0.7490 (t-90) cc_final: 0.6912 (t-170) REVERT: J 63 TRP cc_start: 0.7663 (m100) cc_final: 0.6076 (m100) REVERT: J 64 GLN cc_start: 0.7115 (tp40) cc_final: 0.6373 (mm110) REVERT: J 70 TYR cc_start: 0.7832 (t80) cc_final: 0.7040 (t80) REVERT: J 86 ILE cc_start: 0.8931 (pt) cc_final: 0.8272 (mm) REVERT: J 92 LYS cc_start: 0.8928 (tptp) cc_final: 0.8511 (tptp) REVERT: J 102 GLN cc_start: 0.8511 (mp10) cc_final: 0.8015 (mp10) REVERT: J 104 MET cc_start: 0.8209 (tpp) cc_final: 0.7950 (tpp) REVERT: J 106 TRP cc_start: 0.8553 (t60) cc_final: 0.8320 (t60) REVERT: J 116 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7265 (tm-30) REVERT: J 131 LEU cc_start: 0.8739 (tt) cc_final: 0.8400 (tt) REVERT: J 139 HIS cc_start: 0.8228 (t70) cc_final: 0.7811 (t70) REVERT: J 154 GLU cc_start: 0.8205 (mp0) cc_final: 0.7781 (pm20) REVERT: J 158 GLN cc_start: 0.8513 (mp-120) cc_final: 0.8259 (mp10) REVERT: J 165 GLU cc_start: 0.8270 (tp30) cc_final: 0.7942 (tp30) REVERT: J 178 LEU cc_start: 0.9259 (mm) cc_final: 0.8980 (mm) REVERT: J 182 LEU cc_start: 0.8437 (mt) cc_final: 0.8235 (mt) REVERT: J 189 ARG cc_start: 0.7297 (ttp-110) cc_final: 0.6382 (mtm180) REVERT: J 204 ASN cc_start: 0.8538 (m110) cc_final: 0.7498 (p0) REVERT: J 205 LYS cc_start: 0.8534 (tptp) cc_final: 0.7974 (tptp) REVERT: J 208 GLN cc_start: 0.8191 (pt0) cc_final: 0.7813 (pt0) REVERT: K 11 GLU cc_start: 0.8217 (tp30) cc_final: 0.8010 (tp30) REVERT: K 34 GLU cc_start: 0.8683 (pt0) cc_final: 0.8292 (pp20) REVERT: K 35 ASP cc_start: 0.8704 (m-30) cc_final: 0.8236 (m-30) REVERT: K 132 MET cc_start: 0.7479 (ppp) cc_final: 0.6913 (ppp) REVERT: L 209 ARG cc_start: 0.8716 (mmp-170) cc_final: 0.8493 (mmp-170) REVERT: L 226 TYR cc_start: 0.6636 (p90) cc_final: 0.5640 (p90) REVERT: L 254 LYS cc_start: 0.8332 (tmtt) cc_final: 0.7824 (tppt) REVERT: L 261 TYR cc_start: 0.7839 (m-80) cc_final: 0.7622 (m-80) REVERT: M 7 LEU cc_start: 0.8523 (tt) cc_final: 0.8303 (tt) REVERT: M 10 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7488 (tm-30) REVERT: M 16 HIS cc_start: 0.8153 (m170) cc_final: 0.6730 (m90) REVERT: M 18 ASP cc_start: 0.7834 (t70) cc_final: 0.7486 (t70) REVERT: M 25 GLU cc_start: 0.8447 (tt0) cc_final: 0.8119 (tt0) REVERT: M 89 GLU cc_start: 0.6805 (pm20) cc_final: 0.6178 (mp0) REVERT: M 109 MET cc_start: 0.8626 (tmm) cc_final: 0.8048 (ttt) REVERT: M 154 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8783 (mm-30) REVERT: M 155 ARG cc_start: 0.8655 (ttt180) cc_final: 0.8426 (mtt90) REVERT: M 158 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7611 (tm-30) REVERT: M 159 THR cc_start: 0.8658 (m) cc_final: 0.8046 (p) REVERT: M 178 LEU cc_start: 0.8877 (mt) cc_final: 0.8665 (mt) REVERT: M 195 THR cc_start: 0.8343 (m) cc_final: 0.8085 (p) REVERT: M 205 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8423 (mtmm) REVERT: M 207 GLN cc_start: 0.8497 (mm110) cc_final: 0.8212 (mm110) REVERT: M 209 ARG cc_start: 0.8800 (tmt170) cc_final: 0.8423 (ttp80) REVERT: M 224 CYS cc_start: 0.5860 (p) cc_final: 0.5541 (p) REVERT: N 23 HIS cc_start: 0.7778 (t70) cc_final: 0.7493 (t70) REVERT: N 102 GLN cc_start: 0.8829 (mp10) cc_final: 0.8523 (mp10) REVERT: N 104 MET cc_start: 0.8128 (ptm) cc_final: 0.7520 (ppp) REVERT: N 105 LYS cc_start: 0.9270 (mtmm) cc_final: 0.9029 (mtmm) REVERT: N 150 GLN cc_start: 0.7851 (mt0) cc_final: 0.7649 (mt0) REVERT: N 157 HIS cc_start: 0.8023 (m90) cc_final: 0.7678 (m90) REVERT: N 164 LEU cc_start: 0.8553 (mt) cc_final: 0.8340 (mt) REVERT: N 165 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8062 (mm-30) REVERT: N 183 ILE cc_start: 0.7315 (mt) cc_final: 0.7098 (mt) REVERT: N 203 PHE cc_start: 0.7799 (t80) cc_final: 0.7145 (t80) REVERT: N 206 GLU cc_start: 0.7948 (pp20) cc_final: 0.7709 (pp20) REVERT: N 210 ILE cc_start: 0.8241 (pt) cc_final: 0.7991 (pt) REVERT: N 213 GLN cc_start: 0.8870 (mt0) cc_final: 0.7958 (mt0) REVERT: N 233 HIS cc_start: 0.7789 (m90) cc_final: 0.7404 (m90) REVERT: N 243 VAL cc_start: 0.8558 (t) cc_final: 0.7564 (p) REVERT: N 256 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7797 (ttm110) REVERT: N 266 ASN cc_start: 0.8287 (p0) cc_final: 0.8071 (m-40) REVERT: N 270 LYS cc_start: 0.7835 (mptt) cc_final: 0.7277 (mmtp) REVERT: O 48 MET cc_start: -0.1498 (ppp) cc_final: -0.1911 (ppp) REVERT: O 62 HIS cc_start: 0.6990 (p-80) cc_final: 0.6744 (p90) REVERT: O 70 TYR cc_start: 0.6553 (t80) cc_final: 0.5394 (t80) REVERT: O 115 LEU cc_start: 0.8667 (tp) cc_final: 0.8384 (tp) REVERT: O 132 MET cc_start: 0.8157 (tmm) cc_final: 0.7616 (tmm) REVERT: O 152 LEU cc_start: 0.8726 (tp) cc_final: 0.8365 (tp) REVERT: O 158 GLN cc_start: 0.9260 (tp-100) cc_final: 0.8835 (tp-100) REVERT: O 161 LYS cc_start: 0.9050 (tppt) cc_final: 0.8422 (tppt) REVERT: O 162 ASN cc_start: 0.8744 (m110) cc_final: 0.8509 (m-40) REVERT: O 168 ILE cc_start: 0.7368 (mt) cc_final: 0.7138 (mt) REVERT: O 193 LEU cc_start: 0.8744 (mm) cc_final: 0.8483 (mm) REVERT: O 208 GLN cc_start: 0.8745 (tm130) cc_final: 0.8506 (tm-30) REVERT: O 209 ARG cc_start: 0.8812 (ptm-80) cc_final: 0.8589 (ptm-80) REVERT: O 211 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8171 (tp40) REVERT: P 87 TYR cc_start: 0.8700 (t80) cc_final: 0.8331 (t80) REVERT: P 104 MET cc_start: 0.9108 (mmp) cc_final: 0.8562 (mmp) REVERT: P 106 TRP cc_start: 0.8444 (t60) cc_final: 0.7972 (t60) REVERT: P 109 MET cc_start: 0.7317 (mmp) cc_final: 0.6963 (mmm) REVERT: P 110 PHE cc_start: 0.7939 (m-10) cc_final: 0.7612 (m-10) REVERT: P 115 LEU cc_start: 0.5187 (tp) cc_final: 0.4918 (tp) REVERT: P 170 MET cc_start: 0.7749 (mtt) cc_final: 0.7211 (mpp) REVERT: P 172 ASN cc_start: 0.8834 (m-40) cc_final: 0.8534 (p0) REVERT: P 207 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8007 (mm-40) REVERT: P 222 ARG cc_start: 0.6736 (mmm-85) cc_final: 0.6040 (mmm160) REVERT: P 223 PHE cc_start: 0.6698 (m-80) cc_final: 0.5554 (m-80) REVERT: P 233 HIS cc_start: 0.6701 (m-70) cc_final: 0.6477 (m-70) REVERT: P 238 GLN cc_start: 0.6732 (mm110) cc_final: 0.6372 (mp10) REVERT: P 272 ILE cc_start: 0.8090 (mp) cc_final: 0.7856 (mp) outliers start: 0 outliers final: 0 residues processed: 1147 average time/residue: 0.2216 time to fit residues: 400.5801 Evaluate side-chains 1083 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1083 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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: 0.4980 chunk 8 optimal weight: 0.9980 chunk 262 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 300 optimal weight: 10.0000 chunk 248 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 236 optimal weight: 0.5980 chunk 201 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 HIS ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 GLN O 208 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.196251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149587 restraints weight = 70321.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155323 restraints weight = 43486.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.159330 restraints weight = 30279.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162128 restraints weight = 22820.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.164123 restraints weight = 18309.066| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 34119 Z= 0.162 Angle : 0.776 13.664 46515 Z= 0.414 Chirality : 0.051 0.461 5006 Planarity : 0.005 0.091 5714 Dihedral : 14.927 171.778 5007 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 0.03 % Allowed : 0.44 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.61 (0.13), residues: 3851 helix: 0.58 (0.12), residues: 1877 sheet: -0.55 (0.18), residues: 796 loop : -1.78 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 256 TYR 0.034 0.001 TYR I 70 PHE 0.046 0.002 PHE E 201 TRP 0.052 0.002 TRP B 106 HIS 0.060 0.002 HIS M 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (34119) covalent geometry : angle 0.77572 / 0.41 (46515) hydrogen bonds : bond 0.04317 / 2.97 ( 1746) hydrogen bonds : angle 5.64022 / 4.08 ( 5114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9053.96 seconds wall clock time: 156 minutes 25.20 seconds (9385.20 seconds total)