Starting phenix.real_space_refine on Sat Jun 28 15:30:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpp_14860/06_2025/7zpp_14860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpp_14860/06_2025/7zpp_14860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpp_14860/06_2025/7zpp_14860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpp_14860/06_2025/7zpp_14860.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpp_14860/06_2025/7zpp_14860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpp_14860/06_2025/7zpp_14860.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.81, per 1000 atoms: 0.60 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: 8.55 Conformation dependent library (CDL) restraints added in 4.1 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: 12.70 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: 13.24 Time building geometry restraints manager: 10.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9808 1.34 - 1.46: 5962 1.46 - 1.57: 17989 1.57 - 1.69: 154 1.69 - 1.81: 206 Bond restraints: 34119 Sorted by residual: bond pdb=" CA PRO L 273 " pdb=" C PRO L 273 " ideal model delta sigma weight residual 1.514 1.525 -0.011 5.50e-03 3.31e+04 3.87e+00 bond pdb=" CA PRO D 273 " pdb=" C PRO D 273 " ideal model delta sigma weight residual 1.514 1.525 -0.011 5.50e-03 3.31e+04 3.81e+00 bond pdb=" N GLU E 219 " pdb=" CA GLU E 219 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.44e-02 4.82e+03 3.51e+00 bond pdb=" N GLU M 219 " pdb=" CA GLU M 219 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.44e-02 4.82e+03 3.41e+00 bond pdb=" CA PRO F 273 " pdb=" C PRO F 273 " ideal model delta sigma weight residual 1.514 1.506 0.009 5.50e-03 3.31e+04 2.46e+00 ... (remaining 34114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 46061 2.61 - 5.22: 374 5.22 - 7.84: 64 7.84 - 10.45: 8 10.45 - 13.06: 8 Bond angle restraints: 46515 Sorted by residual: angle pdb=" C GLN E 218 " pdb=" N GLU E 219 " pdb=" CA GLU E 219 " ideal model delta sigma weight residual 122.55 110.04 12.51 2.03e+00 2.43e-01 3.80e+01 angle pdb=" C GLN M 218 " pdb=" N GLU M 219 " pdb=" CA GLU M 219 " ideal model delta sigma weight residual 122.55 110.09 12.46 2.03e+00 2.43e-01 3.77e+01 angle pdb=" CB ARG O 189 " pdb=" CG ARG O 189 " pdb=" CD ARG O 189 " ideal model delta sigma weight residual 111.30 121.95 -10.65 2.30e+00 1.89e-01 2.14e+01 angle pdb=" CB ARG G 189 " pdb=" CG ARG G 189 " pdb=" CD ARG G 189 " ideal model delta sigma weight residual 111.30 121.93 -10.63 2.30e+00 1.89e-01 2.13e+01 angle pdb=" C THR O 103 " pdb=" N MET O 104 " pdb=" CA MET O 104 " ideal model delta sigma weight residual 121.14 113.07 8.07 1.75e+00 3.27e-01 2.13e+01 ... (remaining 46510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 19552 34.44 - 68.88: 495 68.88 - 103.31: 62 103.31 - 137.75: 0 137.75 - 172.19: 4 Dihedral angle restraints: 20113 sinusoidal: 8860 harmonic: 11253 Sorted by residual: dihedral pdb=" CA ILE D 187 " pdb=" C ILE D 187 " pdb=" N LYS D 188 " pdb=" CA LYS D 188 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ILE L 187 " pdb=" C ILE L 187 " pdb=" N LYS L 188 " pdb=" CA LYS L 188 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA TYR B 70 " pdb=" C TYR B 70 " pdb=" N GLU B 71 " pdb=" CA GLU B 71 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 20110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3513 0.038 - 0.075: 960 0.075 - 0.113: 415 0.113 - 0.151: 105 0.151 - 0.188: 13 Chirality restraints: 5006 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CB VAL F 153 " pdb=" CA VAL F 153 " pdb=" CG1 VAL F 153 " pdb=" CG2 VAL F 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CB ILE J 221 " pdb=" CA ILE J 221 " pdb=" CG1 ILE J 221 " pdb=" CG2 ILE J 221 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 5003 not shown) Planarity restraints: 5714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 28 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 29 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 28 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO I 29 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO I 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 29 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 272 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO D 273 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " -0.026 5.00e-02 4.00e+02 ... (remaining 5711 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1270 2.71 - 3.26: 33763 3.26 - 3.81: 56135 3.81 - 4.35: 67169 4.35 - 4.90: 108427 Nonbonded interactions: 266764 Sorted by model distance: nonbonded pdb=" OG1 THR I 95 " pdb=" OE1 GLU I 98 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR A 95 " pdb=" OE1 GLU A 98 " model vdw 2.167 3.040 nonbonded pdb=" O ASP G 18 " pdb=" OG SER G 21 " model vdw 2.170 3.040 nonbonded pdb=" O ASP O 18 " pdb=" OG SER O 21 " model vdw 2.170 3.040 nonbonded pdb=" ND1 HIS M 23 " pdb=" O ILE M 28 " model vdw 2.195 3.120 ... (remaining 266759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'B' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'C' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'E' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'F' and (resid 4 through 44 or resid 60 through 216 or (resid 217 and (na \ me N or name CA or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'I' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'J' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'K' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'M' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'N' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 through 272)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 60 through 227 or (resid 228 through 231 and (name N or na \ me CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N o \ r name CA or name C or name O or name CB )) or resid 234 through 275)) selection = chain 'L' selection = (chain 'P' and (resid 60 through 227 or (resid 228 through 231 and (name N or na \ me CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N o \ r name CA or name C or name O or name CB )) or resid 234 through 275)) } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.310 Process input model: 84.340 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.180 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34119 Z= 0.135 Angle : 0.640 13.062 46515 Z= 0.346 Chirality : 0.044 0.188 5006 Planarity : 0.004 0.056 5714 Dihedral : 15.322 172.189 12859 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.025 0.002 TRP I 78 HIS 0.004 0.001 HIS G 62 PHE 0.030 0.002 PHE M 110 TYR 0.025 0.001 TYR F 134 ARG 0.018 0.001 ARG O 189 Details of bonding type rmsd hydrogen bonds : bond 0.14599 ( 1746) hydrogen bonds : angle 6.49516 ( 5114) covalent geometry : bond 0.00261 (34119) covalent geometry : angle 0.63975 (46515) *********************** 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 : 3.796 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: 0.8105 (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: 0.8095 (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: 0.6324 (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: 0.4924 time to fit residues: 933.7235 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 : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.9990 chunk 294 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 chunk 304 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 352 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 HIS B 139 HIS B 158 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS C 116 GLN C 129 GLN 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 186 ASN D 266 ASN E 23 HIS E 204 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS G 148 GLN G 208 GLN G 211 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 GLN I 139 HIS J 16 HIS J 158 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 242 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN K 102 GLN K 116 GLN K 129 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 HIS N 186 ASN N 213 GLN O 69 HIS O 102 GLN O 208 GLN ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 GLN P 242 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.193704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147512 restraints weight = 72602.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.152953 restraints weight = 45668.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.156749 restraints weight = 32071.634| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 34119 Z= 0.298 Angle : 0.813 14.826 46515 Z= 0.438 Chirality : 0.051 0.232 5006 Planarity : 0.006 0.143 5714 Dihedral : 14.666 174.282 5007 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 0.33 % Allowed : 5.68 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 3851 helix: 0.91 (0.12), residues: 1864 sheet: -0.72 (0.17), residues: 856 loop : -1.63 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 245 HIS 0.017 0.002 HIS K 157 PHE 0.042 0.003 PHE F 26 TYR 0.034 0.002 TYR E 70 ARG 0.018 0.001 ARG O 155 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 1746) hydrogen bonds : angle 5.84026 ( 5114) covalent geometry : bond 0.00606 (34119) covalent geometry : angle 0.81291 (46515) *********************** 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 1220 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1209 time to evaluate : 3.539 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: A 15 TRP cc_start: 0.6868 (m-90) cc_final: 0.5956 (m-90) REVERT: A 66 ASP cc_start: 0.7937 (t0) cc_final: 0.7651 (t70) REVERT: A 79 VAL cc_start: 0.8079 (t) cc_final: 0.7580 (p) REVERT: A 92 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8545 (mtpp) REVERT: A 104 MET cc_start: 0.8416 (ttm) cc_final: 0.8003 (ttm) REVERT: A 107 TYR cc_start: 0.8588 (t80) cc_final: 0.8277 (t80) REVERT: A 118 ASP cc_start: 0.7720 (p0) cc_final: 0.7368 (p0) REVERT: A 132 MET cc_start: 0.8112 (mmm) cc_final: 0.7809 (mmm) REVERT: A 158 GLN cc_start: 0.8924 (tt0) cc_final: 0.8144 (pt0) REVERT: A 161 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8414 (tppt) REVERT: A 164 LEU cc_start: 0.8463 (mt) cc_final: 0.8173 (mt) REVERT: A 203 PHE cc_start: 0.8464 (t80) cc_final: 0.8039 (t80) REVERT: A 208 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 226 TYR cc_start: 0.6583 (p90) cc_final: 0.6338 (p90) REVERT: A 251 ILE cc_start: 0.7987 (pt) cc_final: 0.7343 (mm) REVERT: A 254 LYS cc_start: 0.8212 (pptt) cc_final: 0.7550 (pptt) REVERT: A 260 ARG cc_start: 0.7539 (ptm160) cc_final: 0.7224 (ptm160) REVERT: B 15 TRP cc_start: 0.8056 (m100) cc_final: 0.7488 (m100) REVERT: B 42 VAL cc_start: 0.4008 (t) cc_final: 0.3635 (t) REVERT: B 75 ILE cc_start: 0.7982 (pt) cc_final: 0.7736 (mp) REVERT: B 80 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 86 ILE cc_start: 0.8708 (pt) cc_final: 0.8339 (mm) REVERT: B 89 GLU cc_start: 0.7879 (tt0) cc_final: 0.7633 (tt0) REVERT: B 92 LYS cc_start: 0.8788 (tppt) cc_final: 0.8229 (tptp) REVERT: B 100 ARG cc_start: 0.8573 (mtt180) cc_final: 0.8000 (mtt-85) REVERT: B 104 MET cc_start: 0.8664 (mmp) cc_final: 0.8411 (mmp) REVERT: B 105 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8836 (mtpp) REVERT: B 129 GLN cc_start: 0.8624 (pt0) cc_final: 0.8221 (pt0) REVERT: B 131 LEU cc_start: 0.9077 (tt) cc_final: 0.8853 (tt) REVERT: B 132 MET cc_start: 0.8647 (mmp) cc_final: 0.8435 (mmt) REVERT: B 137 ILE cc_start: 0.8576 (tt) cc_final: 0.8115 (tt) REVERT: B 138 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6018 (tm-30) REVERT: B 186 ASN cc_start: 0.8341 (m-40) cc_final: 0.7965 (m-40) REVERT: B 198 MET cc_start: 0.8213 (tpt) cc_final: 0.7804 (tpp) REVERT: B 205 LYS cc_start: 0.8524 (tptp) cc_final: 0.8281 (tppp) REVERT: B 208 GLN cc_start: 0.8292 (pt0) cc_final: 0.8050 (pt0) REVERT: C 7 LEU cc_start: 0.8819 (tt) cc_final: 0.8605 (tt) REVERT: C 34 GLU cc_start: 0.8865 (pt0) cc_final: 0.8219 (pp20) REVERT: C 35 ASP cc_start: 0.8786 (m-30) cc_final: 0.8214 (m-30) REVERT: C 38 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7911 (tp-100) REVERT: C 106 TRP cc_start: 0.6828 (t60) cc_final: 0.6620 (t60) REVERT: C 110 PHE cc_start: 0.7785 (m-80) cc_final: 0.7205 (m-80) REVERT: C 132 MET cc_start: 0.8284 (ppp) cc_final: 0.7838 (ppp) REVERT: C 186 ASN cc_start: 0.8073 (m-40) cc_final: 0.7802 (m110) REVERT: C 206 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: C 209 ARG cc_start: 0.8431 (ptt90) cc_final: 0.7987 (ptt90) REVERT: C 245 TRP cc_start: 0.8239 (m100) cc_final: 0.7983 (m100) REVERT: D 63 TRP cc_start: 0.5720 (m100) cc_final: 0.5488 (m100) REVERT: D 86 ILE cc_start: 0.7856 (pt) cc_final: 0.7551 (mm) REVERT: D 209 ARG cc_start: 0.8551 (mmp80) cc_final: 0.8247 (mmp80) REVERT: D 218 GLN cc_start: 0.8437 (mm110) cc_final: 0.7958 (mm110) REVERT: D 223 PHE cc_start: 0.6712 (p90) cc_final: 0.6185 (p90) REVERT: D 226 TYR cc_start: 0.7193 (p90) cc_final: 0.6315 (p90) REVERT: D 227 ARG cc_start: 0.5913 (mpt-90) cc_final: 0.5691 (mmt90) REVERT: D 244 LEU cc_start: 0.8551 (mt) cc_final: 0.8316 (mt) REVERT: D 254 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7993 (tptt) REVERT: D 262 LEU cc_start: 0.7989 (mp) cc_final: 0.7735 (mp) REVERT: D 263 VAL cc_start: 0.8377 (m) cc_final: 0.8140 (t) REVERT: D 266 ASN cc_start: 0.8358 (m110) cc_final: 0.8060 (m-40) REVERT: E 9 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8050 (mm-30) REVERT: E 10 GLU cc_start: 0.8136 (tp30) cc_final: 0.7680 (tp30) REVERT: E 12 HIS cc_start: 0.8192 (t70) cc_final: 0.7445 (t70) REVERT: E 15 TRP cc_start: 0.8808 (m-10) cc_final: 0.8115 (m-10) REVERT: E 16 HIS cc_start: 0.8186 (m-70) cc_final: 0.7312 (m170) REVERT: E 22 LEU cc_start: 0.8202 (pp) cc_final: 0.7998 (pp) REVERT: E 87 TYR cc_start: 0.7259 (t80) cc_final: 0.6700 (t80) REVERT: E 101 VAL cc_start: 0.8761 (t) cc_final: 0.8443 (t) REVERT: E 150 GLN cc_start: 0.7859 (mm110) cc_final: 0.7017 (mm-40) REVERT: E 159 THR cc_start: 0.8663 (m) cc_final: 0.8053 (p) REVERT: E 165 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7706 (mm-30) REVERT: E 178 LEU cc_start: 0.8691 (mt) cc_final: 0.8411 (mt) REVERT: E 199 ASP cc_start: 0.8438 (m-30) cc_final: 0.7443 (m-30) REVERT: E 206 GLU cc_start: 0.8701 (pt0) cc_final: 0.7535 (pp20) REVERT: E 209 ARG cc_start: 0.8732 (tmt170) cc_final: 0.8332 (ttp80) REVERT: E 210 ILE cc_start: 0.9069 (mt) cc_final: 0.8627 (mt) REVERT: E 220 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8112 (mmtt) REVERT: F 23 HIS cc_start: 0.7831 (t70) cc_final: 0.7513 (t70) REVERT: F 65 VAL cc_start: 0.7161 (t) cc_final: 0.6680 (p) REVERT: F 154 GLU cc_start: 0.8363 (tp30) cc_final: 0.8096 (tp30) REVERT: F 183 ILE cc_start: 0.6145 (mt) cc_final: 0.5824 (mt) REVERT: F 198 MET cc_start: 0.8306 (ppp) cc_final: 0.7953 (ppp) REVERT: F 202 ILE cc_start: 0.8494 (mt) cc_final: 0.8049 (mt) REVERT: F 203 PHE cc_start: 0.8031 (t80) cc_final: 0.7669 (t80) REVERT: F 242 GLN cc_start: 0.7802 (tt0) cc_final: 0.7006 (pp30) REVERT: F 243 VAL cc_start: 0.8558 (t) cc_final: 0.7486 (m) REVERT: F 256 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7962 (ttm110) REVERT: G 22 LEU cc_start: 0.8718 (mm) cc_final: 0.7650 (mm) REVERT: G 25 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6259 (tp30) REVERT: G 48 MET cc_start: -0.0503 (ppp) cc_final: -0.1269 (ppp) REVERT: G 85 LEU cc_start: 0.7209 (tp) cc_final: 0.6911 (tp) REVERT: G 131 LEU cc_start: 0.9296 (mt) cc_final: 0.9092 (mt) REVERT: G 157 HIS cc_start: 0.8662 (m90) cc_final: 0.8400 (m90) REVERT: G 164 LEU cc_start: 0.8742 (mt) cc_final: 0.8464 (mt) REVERT: G 197 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8376 (Cg_endo) REVERT: G 210 ILE cc_start: 0.8724 (pt) cc_final: 0.8517 (pt) REVERT: H 62 HIS cc_start: 0.7729 (t-90) cc_final: 0.7102 (t-170) REVERT: H 87 TYR cc_start: 0.8294 (t80) cc_final: 0.7777 (t80) REVERT: H 101 VAL cc_start: 0.8800 (p) cc_final: 0.8581 (p) REVERT: H 104 MET cc_start: 0.9089 (mmp) cc_final: 0.8424 (mmp) REVERT: H 109 MET cc_start: 0.8209 (tpt) cc_final: 0.7480 (tpt) REVERT: H 110 PHE cc_start: 0.8354 (m-10) cc_final: 0.7808 (m-10) REVERT: H 164 LEU cc_start: 0.9175 (mm) cc_final: 0.8909 (pp) REVERT: H 222 ARG cc_start: 0.6235 (mmm-85) cc_final: 0.5815 (mmm160) REVERT: H 223 PHE cc_start: 0.6405 (m-10) cc_final: 0.5792 (m-80) REVERT: I 60 ILE cc_start: 0.8850 (mt) cc_final: 0.8273 (mm) REVERT: I 66 ASP cc_start: 0.8081 (t0) cc_final: 0.7680 (t70) REVERT: I 79 VAL cc_start: 0.8086 (t) cc_final: 0.7668 (p) REVERT: I 86 ILE cc_start: 0.8573 (pt) cc_final: 0.7878 (mm) REVERT: I 92 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8443 (mtpp) REVERT: I 100 ARG cc_start: 0.8420 (mtt90) cc_final: 0.7882 (mtm180) REVERT: I 102 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8764 (mm-40) REVERT: I 118 ASP cc_start: 0.7850 (p0) cc_final: 0.7469 (p0) REVERT: I 129 GLN cc_start: 0.7861 (tt0) cc_final: 0.7615 (tt0) REVERT: I 132 MET cc_start: 0.8275 (mmm) cc_final: 0.7850 (mmm) REVERT: I 158 GLN cc_start: 0.8974 (tt0) cc_final: 0.8158 (pt0) REVERT: I 164 LEU cc_start: 0.8651 (mt) cc_final: 0.8347 (mt) REVERT: I 172 ASN cc_start: 0.7391 (m-40) cc_final: 0.7154 (p0) REVERT: I 178 LEU cc_start: 0.8346 (tp) cc_final: 0.7884 (tp) REVERT: I 203 PHE cc_start: 0.8464 (t80) cc_final: 0.8138 (t80) REVERT: I 208 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8059 (tm-30) REVERT: I 251 ILE cc_start: 0.7672 (pt) cc_final: 0.6918 (mm) REVERT: I 260 ARG cc_start: 0.7233 (ptm160) cc_final: 0.7007 (ptm160) REVERT: J 15 TRP cc_start: 0.8105 (m100) cc_final: 0.7569 (m100) REVERT: J 42 VAL cc_start: 0.4897 (t) cc_final: 0.4615 (t) REVERT: J 64 GLN cc_start: 0.6922 (tp40) cc_final: 0.6477 (mm110) REVERT: J 65 VAL cc_start: 0.8803 (t) cc_final: 0.8404 (t) REVERT: J 73 LYS cc_start: 0.8297 (mttt) cc_final: 0.7190 (mttt) REVERT: J 86 ILE cc_start: 0.8901 (pt) cc_final: 0.8433 (mm) REVERT: J 92 LYS cc_start: 0.8792 (tptp) cc_final: 0.8447 (tptp) REVERT: J 116 GLN cc_start: 0.6988 (tm-30) cc_final: 0.6341 (tm-30) REVERT: J 127 SER cc_start: 0.8651 (m) cc_final: 0.8354 (t) REVERT: J 131 LEU cc_start: 0.8810 (tt) cc_final: 0.8404 (tt) REVERT: J 132 MET cc_start: 0.8770 (mmp) cc_final: 0.7961 (mmp) REVERT: J 160 LEU cc_start: 0.8827 (tt) cc_final: 0.8582 (tt) REVERT: J 161 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8681 (pttm) REVERT: J 162 ASN cc_start: 0.8999 (m110) cc_final: 0.8710 (m-40) REVERT: J 174 PHE cc_start: 0.7723 (t80) cc_final: 0.7520 (t80) REVERT: J 178 LEU cc_start: 0.9162 (mm) cc_final: 0.8950 (mm) REVERT: J 201 PHE cc_start: 0.9149 (t80) cc_final: 0.8729 (t80) REVERT: J 204 ASN cc_start: 0.8327 (m110) cc_final: 0.7457 (p0) REVERT: J 205 LYS cc_start: 0.8447 (tptp) cc_final: 0.7795 (tptp) REVERT: J 208 GLN cc_start: 0.8229 (pt0) cc_final: 0.7955 (pt0) REVERT: K 15 TRP cc_start: 0.8180 (m100) cc_final: 0.7787 (m100) REVERT: K 25 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8089 (tm-30) REVERT: K 34 GLU cc_start: 0.8820 (pt0) cc_final: 0.8355 (pp20) REVERT: K 35 ASP cc_start: 0.8810 (m-30) cc_final: 0.8468 (m-30) REVERT: K 106 TRP cc_start: 0.6979 (t60) cc_final: 0.6712 (t60) REVERT: K 110 PHE cc_start: 0.7687 (m-80) cc_final: 0.7468 (m-80) REVERT: K 132 MET cc_start: 0.7431 (ppp) cc_final: 0.7150 (ppp) REVERT: K 190 LYS cc_start: 0.6477 (mttp) cc_final: 0.6133 (mttm) REVERT: K 205 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8334 (mmtm) REVERT: K 206 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: K 245 TRP cc_start: 0.8136 (m100) cc_final: 0.7753 (m100) REVERT: L 63 TRP cc_start: 0.6419 (m100) cc_final: 0.5901 (m100) REVERT: L 86 ILE cc_start: 0.7123 (pt) cc_final: 0.6877 (mm) REVERT: L 226 TYR cc_start: 0.7259 (p90) cc_final: 0.6330 (p90) REVERT: L 244 LEU cc_start: 0.8638 (mt) cc_final: 0.8338 (mt) REVERT: L 259 ASP cc_start: 0.8698 (m-30) cc_final: 0.8241 (m-30) REVERT: L 263 VAL cc_start: 0.8117 (m) cc_final: 0.7915 (t) REVERT: M 7 LEU cc_start: 0.8295 (tt) cc_final: 0.8088 (tt) REVERT: M 14 LYS cc_start: 0.8427 (mttp) cc_final: 0.8110 (mtmt) REVERT: M 15 TRP cc_start: 0.8684 (m-10) cc_final: 0.8190 (m-10) REVERT: M 16 HIS cc_start: 0.7755 (m-70) cc_final: 0.7248 (m170) REVERT: M 18 ASP cc_start: 0.7639 (t70) cc_final: 0.7395 (t70) REVERT: M 36 ILE cc_start: 0.8701 (mt) cc_final: 0.8437 (mt) REVERT: M 76 LEU cc_start: 0.7627 (tp) cc_final: 0.6688 (tp) REVERT: M 87 TYR cc_start: 0.7233 (t80) cc_final: 0.6721 (t80) REVERT: M 158 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7459 (tm-30) REVERT: M 159 THR cc_start: 0.8704 (m) cc_final: 0.7930 (p) REVERT: M 199 ASP cc_start: 0.8519 (m-30) cc_final: 0.7422 (m-30) REVERT: M 209 ARG cc_start: 0.8883 (tmt170) cc_final: 0.8571 (ttp80) REVERT: N 23 HIS cc_start: 0.7696 (t70) cc_final: 0.7374 (t70) REVERT: N 61 ASP cc_start: 0.6512 (t0) cc_final: 0.6119 (t0) REVERT: N 63 TRP cc_start: 0.7539 (t-100) cc_final: 0.7130 (t-100) REVERT: N 65 VAL cc_start: 0.7505 (t) cc_final: 0.7262 (p) REVERT: N 89 GLU cc_start: 0.7158 (tp30) cc_final: 0.6916 (tp30) REVERT: N 104 MET cc_start: 0.8559 (ptm) cc_final: 0.8277 (ptm) REVERT: N 110 PHE cc_start: 0.8222 (m-80) cc_final: 0.7808 (m-80) REVERT: N 127 SER cc_start: 0.8530 (t) cc_final: 0.8282 (t) REVERT: N 183 ILE cc_start: 0.7104 (mt) cc_final: 0.6864 (mt) REVERT: N 198 MET cc_start: 0.8058 (ppp) cc_final: 0.7740 (ppp) REVERT: N 199 ASP cc_start: 0.8419 (m-30) cc_final: 0.8201 (m-30) REVERT: N 202 ILE cc_start: 0.8272 (mt) cc_final: 0.7983 (mt) REVERT: N 203 PHE cc_start: 0.7887 (t80) cc_final: 0.7452 (t80) REVERT: N 208 GLN cc_start: 0.8513 (tt0) cc_final: 0.8269 (tm-30) REVERT: N 210 ILE cc_start: 0.8479 (pt) cc_final: 0.8264 (pt) REVERT: N 213 GLN cc_start: 0.8940 (mt0) cc_final: 0.8609 (mt0) REVERT: N 230 LYS cc_start: 0.8352 (mttt) cc_final: 0.7461 (ttpp) REVERT: N 233 HIS cc_start: 0.7720 (m90) cc_final: 0.7476 (m-70) REVERT: N 236 GLU cc_start: 0.8106 (pm20) cc_final: 0.7667 (pm20) REVERT: N 242 GLN cc_start: 0.7998 (tt0) cc_final: 0.7378 (pp30) REVERT: N 243 VAL cc_start: 0.8660 (t) cc_final: 0.7797 (m) REVERT: N 244 LEU cc_start: 0.8452 (tt) cc_final: 0.8073 (tt) REVERT: N 256 ARG cc_start: 0.8422 (ttm110) cc_final: 0.7775 (ttm110) REVERT: O 22 LEU cc_start: 0.8944 (mm) cc_final: 0.7917 (mm) REVERT: O 25 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6649 (tp30) REVERT: O 48 MET cc_start: -0.1106 (ppp) cc_final: -0.1969 (ppp) REVERT: O 85 LEU cc_start: 0.7663 (tp) cc_final: 0.7418 (tp) REVERT: O 104 MET cc_start: 0.8317 (pmm) cc_final: 0.8087 (pmm) REVERT: O 110 PHE cc_start: 0.7927 (m-80) cc_final: 0.7548 (m-80) REVERT: O 115 LEU cc_start: 0.8784 (tp) cc_final: 0.8561 (tp) REVERT: O 132 MET cc_start: 0.8260 (tmm) cc_final: 0.7889 (tmm) REVERT: O 157 HIS cc_start: 0.8761 (m90) cc_final: 0.8555 (m90) REVERT: O 208 GLN cc_start: 0.8652 (tm130) cc_final: 0.8418 (tm-30) REVERT: O 209 ARG cc_start: 0.8888 (ptm-80) cc_final: 0.8515 (ptm-80) REVERT: O 211 GLN cc_start: 0.8790 (mm110) cc_final: 0.8290 (tp40) REVERT: P 62 HIS cc_start: 0.7810 (t-90) cc_final: 0.7240 (t-170) REVERT: P 101 VAL cc_start: 0.9176 (p) cc_final: 0.8943 (p) REVERT: P 104 MET cc_start: 0.9150 (mmp) cc_final: 0.8673 (mmp) REVERT: P 132 MET cc_start: 0.6198 (tmm) cc_final: 0.5967 (tmm) REVERT: P 170 MET cc_start: 0.7684 (mtt) cc_final: 0.7236 (mpp) REVERT: P 199 ASP cc_start: 0.8138 (m-30) cc_final: 0.7614 (m-30) REVERT: P 205 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8160 (mttt) REVERT: P 230 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7199 (mmtm) REVERT: P 254 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8483 (mmmt) outliers start: 11 outliers final: 3 residues processed: 1214 average time/residue: 0.4863 time to fit residues: 919.4041 Evaluate side-chains 1120 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1113 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 239 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 chunk 355 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 384 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 ASN B 102 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN C 129 GLN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN E 23 HIS E 102 GLN G 207 GLN G 208 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 157 HIS H 207 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN L 212 GLN M 102 GLN N 158 GLN O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.195944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149886 restraints weight = 71416.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155566 restraints weight = 44154.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159500 restraints weight = 30618.149| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34119 Z= 0.190 Angle : 0.688 13.806 46515 Z= 0.367 Chirality : 0.048 0.242 5006 Planarity : 0.005 0.060 5714 Dihedral : 14.687 173.146 5007 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 0.27 % Allowed : 3.87 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3851 helix: 0.92 (0.12), residues: 1861 sheet: -0.80 (0.17), residues: 892 loop : -1.72 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 78 HIS 0.014 0.001 HIS F 62 PHE 0.024 0.002 PHE D 203 TYR 0.021 0.002 TYR E 70 ARG 0.007 0.001 ARG L 227 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 1746) hydrogen bonds : angle 5.47178 ( 5114) covalent geometry : bond 0.00399 (34119) covalent geometry : angle 0.68779 (46515) *********************** 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 1219 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1210 time to evaluate : 3.396 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: A 15 TRP cc_start: 0.6922 (m-90) cc_final: 0.5657 (m-90) REVERT: A 66 ASP cc_start: 0.7955 (t0) cc_final: 0.7689 (t70) REVERT: A 79 VAL cc_start: 0.8073 (t) cc_final: 0.7590 (p) REVERT: A 92 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8526 (mtpp) REVERT: A 97 GLN cc_start: 0.7961 (pm20) cc_final: 0.7401 (pm20) REVERT: A 104 MET cc_start: 0.8466 (ttm) cc_final: 0.7905 (ttm) REVERT: A 107 TYR cc_start: 0.8513 (t80) cc_final: 0.8216 (t80) REVERT: A 113 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7757 (mmmm) REVERT: A 118 ASP cc_start: 0.7551 (p0) cc_final: 0.7323 (p0) REVERT: A 129 GLN cc_start: 0.8100 (tt0) cc_final: 0.7842 (tt0) REVERT: A 155 ARG cc_start: 0.8534 (tpt90) cc_final: 0.7636 (mmm160) REVERT: A 161 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8475 (tptt) REVERT: A 190 LYS cc_start: 0.7470 (mtmm) cc_final: 0.6679 (mtpt) REVERT: A 203 PHE cc_start: 0.8514 (t80) cc_final: 0.8026 (t80) REVERT: A 208 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 226 TYR cc_start: 0.6627 (p90) cc_final: 0.6300 (p90) REVERT: A 254 LYS cc_start: 0.8235 (pptt) cc_final: 0.7796 (pptt) REVERT: A 260 ARG cc_start: 0.7490 (ptm160) cc_final: 0.7219 (ptm160) REVERT: B 15 TRP cc_start: 0.8016 (m100) cc_final: 0.7420 (m100) REVERT: B 40 CYS cc_start: 0.7764 (t) cc_final: 0.7347 (t) REVERT: B 63 TRP cc_start: 0.7772 (m100) cc_final: 0.6437 (m100) REVERT: B 64 GLN cc_start: 0.6991 (tp40) cc_final: 0.6646 (mp10) REVERT: B 65 VAL cc_start: 0.8719 (t) cc_final: 0.8497 (t) REVERT: B 75 ILE cc_start: 0.8067 (pt) cc_final: 0.7829 (mp) REVERT: B 86 ILE cc_start: 0.8659 (pt) cc_final: 0.8121 (mm) REVERT: B 104 MET cc_start: 0.8708 (mmp) cc_final: 0.8404 (mmp) REVERT: B 105 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8737 (mtpp) REVERT: B 106 TRP cc_start: 0.8713 (t60) cc_final: 0.8293 (t60) REVERT: B 129 GLN cc_start: 0.8573 (pt0) cc_final: 0.8190 (pt0) REVERT: B 131 LEU cc_start: 0.9097 (tt) cc_final: 0.8558 (tt) REVERT: B 132 MET cc_start: 0.8772 (mmp) cc_final: 0.7972 (mmp) REVERT: B 137 ILE cc_start: 0.8669 (tt) cc_final: 0.8467 (tt) REVERT: B 186 ASN cc_start: 0.8299 (m-40) cc_final: 0.7911 (m-40) REVERT: B 198 MET cc_start: 0.8113 (tpt) cc_final: 0.7713 (tpp) REVERT: B 204 ASN cc_start: 0.7720 (p0) cc_final: 0.7261 (p0) REVERT: B 207 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8020 (mm-40) REVERT: B 208 GLN cc_start: 0.8208 (pt0) cc_final: 0.7974 (pt0) REVERT: C 7 LEU cc_start: 0.8858 (tt) cc_final: 0.8621 (tt) REVERT: C 11 GLU cc_start: 0.8199 (tp30) cc_final: 0.6937 (tp30) REVERT: C 34 GLU cc_start: 0.8826 (pt0) cc_final: 0.8247 (pp20) REVERT: C 35 ASP cc_start: 0.8787 (m-30) cc_final: 0.8175 (m-30) REVERT: C 106 TRP cc_start: 0.6981 (t60) cc_final: 0.6768 (t60) REVERT: C 110 PHE cc_start: 0.7791 (m-80) cc_final: 0.7296 (m-80) REVERT: C 132 MET cc_start: 0.8305 (ppp) cc_final: 0.7859 (ppp) REVERT: C 165 GLU cc_start: 0.7956 (tp30) cc_final: 0.7597 (tp30) REVERT: C 186 ASN cc_start: 0.7992 (m-40) cc_final: 0.7763 (m110) REVERT: C 199 ASP cc_start: 0.8932 (m-30) cc_final: 0.8692 (m-30) REVERT: C 209 ARG cc_start: 0.8576 (ptt90) cc_final: 0.8038 (ptt90) REVERT: C 270 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8492 (mmtm) REVERT: D 63 TRP cc_start: 0.6591 (m100) cc_final: 0.6080 (m100) REVERT: D 203 PHE cc_start: 0.7966 (t80) cc_final: 0.7729 (t80) REVERT: D 218 GLN cc_start: 0.8445 (mm110) cc_final: 0.7934 (mm110) REVERT: D 226 TYR cc_start: 0.7390 (p90) cc_final: 0.6404 (p90) REVERT: D 227 ARG cc_start: 0.5971 (mpt-90) cc_final: 0.5660 (mmt90) REVERT: D 244 LEU cc_start: 0.8426 (mt) cc_final: 0.8156 (mt) REVERT: D 248 ASP cc_start: 0.8175 (p0) cc_final: 0.7956 (p0) REVERT: D 254 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8067 (ttmm) REVERT: D 266 ASN cc_start: 0.8458 (m110) cc_final: 0.7923 (m-40) REVERT: D 268 ASP cc_start: 0.7153 (t70) cc_final: 0.6863 (t70) REVERT: E 7 LEU cc_start: 0.8488 (tt) cc_final: 0.8071 (tt) REVERT: E 16 HIS cc_start: 0.7908 (m-70) cc_final: 0.7015 (m170) REVERT: E 138 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7185 (tm-30) REVERT: E 150 GLN cc_start: 0.7811 (mm110) cc_final: 0.7501 (mm-40) REVERT: E 154 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8610 (mm-30) REVERT: E 158 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7657 (tm-30) REVERT: E 159 THR cc_start: 0.8400 (m) cc_final: 0.7744 (p) REVERT: E 201 PHE cc_start: 0.8297 (t80) cc_final: 0.7975 (t80) REVERT: E 207 GLN cc_start: 0.8516 (mm110) cc_final: 0.8147 (mm-40) REVERT: E 208 GLN cc_start: 0.8930 (pp30) cc_final: 0.8698 (pp30) REVERT: E 224 CYS cc_start: 0.5961 (p) cc_final: 0.5705 (p) REVERT: E 270 LYS cc_start: 0.8095 (mttm) cc_final: 0.7865 (mttm) REVERT: F 23 HIS cc_start: 0.7830 (t70) cc_final: 0.7562 (t70) REVERT: F 82 ASN cc_start: 0.8578 (m110) cc_final: 0.8147 (m110) REVERT: F 131 LEU cc_start: 0.8619 (tp) cc_final: 0.8408 (mm) REVERT: F 154 GLU cc_start: 0.8397 (tp30) cc_final: 0.8089 (mm-30) REVERT: F 157 HIS cc_start: 0.7581 (m90) cc_final: 0.7326 (m90) REVERT: F 161 LYS cc_start: 0.9237 (ptpp) cc_final: 0.8806 (ptpp) REVERT: F 162 ASN cc_start: 0.8957 (m-40) cc_final: 0.8547 (m110) REVERT: F 164 LEU cc_start: 0.8509 (mt) cc_final: 0.8300 (mt) REVERT: F 183 ILE cc_start: 0.6468 (mt) cc_final: 0.6154 (mt) REVERT: F 198 MET cc_start: 0.8229 (ppp) cc_final: 0.7947 (ppp) REVERT: F 199 ASP cc_start: 0.8440 (m-30) cc_final: 0.8032 (m-30) REVERT: F 204 ASN cc_start: 0.8730 (p0) cc_final: 0.8183 (p0) REVERT: F 207 GLN cc_start: 0.8502 (mp10) cc_final: 0.8256 (mp10) REVERT: F 230 LYS cc_start: 0.8398 (mmmt) cc_final: 0.7803 (mmmm) REVERT: F 231 ARG cc_start: 0.7945 (mpp-170) cc_final: 0.7449 (mpp-170) REVERT: F 233 HIS cc_start: 0.7769 (m-70) cc_final: 0.7540 (m-70) REVERT: F 236 GLU cc_start: 0.7826 (pm20) cc_final: 0.7566 (pm20) REVERT: F 242 GLN cc_start: 0.7474 (tt0) cc_final: 0.6804 (pp30) REVERT: F 243 VAL cc_start: 0.8531 (t) cc_final: 0.7808 (p) REVERT: F 244 LEU cc_start: 0.8212 (tt) cc_final: 0.7855 (tt) REVERT: G 22 LEU cc_start: 0.8496 (mm) cc_final: 0.7447 (mm) REVERT: G 25 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6808 (tp30) REVERT: G 48 MET cc_start: -0.0393 (ppp) cc_final: -0.1285 (ppp) REVERT: G 62 HIS cc_start: 0.7368 (t70) cc_final: 0.6650 (t70) REVERT: G 85 LEU cc_start: 0.7329 (tp) cc_final: 0.7064 (tp) REVERT: G 104 MET cc_start: 0.7906 (pmm) cc_final: 0.7520 (pmm) REVERT: G 110 PHE cc_start: 0.7995 (m-10) cc_final: 0.7771 (m-10) REVERT: G 131 LEU cc_start: 0.9304 (mt) cc_final: 0.9074 (mt) REVERT: G 155 ARG cc_start: 0.9056 (mtp-110) cc_final: 0.8483 (ptp-110) REVERT: G 157 HIS cc_start: 0.8546 (m90) cc_final: 0.8338 (m90) REVERT: G 161 LYS cc_start: 0.9082 (tppt) cc_final: 0.8752 (tppt) REVERT: G 171 PHE cc_start: 0.7136 (m-80) cc_final: 0.6646 (m-80) REVERT: G 183 ILE cc_start: 0.7599 (mt) cc_final: 0.7393 (mt) REVERT: G 197 PRO cc_start: 0.8471 (Cg_exo) cc_final: 0.8195 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8845 (m-30) cc_final: 0.8545 (m-30) REVERT: G 202 ILE cc_start: 0.8946 (mt) cc_final: 0.8283 (mt) REVERT: H 62 HIS cc_start: 0.7815 (t-90) cc_final: 0.7179 (t-170) REVERT: H 78 TRP cc_start: 0.6676 (m-10) cc_final: 0.5980 (m-10) REVERT: H 87 TYR cc_start: 0.8370 (t80) cc_final: 0.7666 (t80) REVERT: H 101 VAL cc_start: 0.8852 (p) cc_final: 0.8617 (p) REVERT: H 104 MET cc_start: 0.9034 (mmp) cc_final: 0.8374 (mmp) REVERT: H 110 PHE cc_start: 0.7791 (m-10) cc_final: 0.7464 (m-10) REVERT: H 164 LEU cc_start: 0.9276 (mm) cc_final: 0.8854 (pp) REVERT: H 207 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7904 (mm-40) REVERT: H 222 ARG cc_start: 0.6693 (mmm-85) cc_final: 0.6339 (mmm160) REVERT: H 223 PHE cc_start: 0.6856 (m-10) cc_final: 0.6648 (m-80) REVERT: I 48 MET cc_start: 0.5951 (mmp) cc_final: 0.5536 (mmm) REVERT: I 60 ILE cc_start: 0.8785 (mt) cc_final: 0.8354 (mm) REVERT: I 66 ASP cc_start: 0.8140 (t0) cc_final: 0.7830 (t0) REVERT: I 79 VAL cc_start: 0.8193 (t) cc_final: 0.7623 (p) REVERT: I 85 LEU cc_start: 0.7885 (tp) cc_final: 0.7589 (tp) REVERT: I 86 ILE cc_start: 0.8535 (pt) cc_final: 0.8060 (mp) REVERT: I 92 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8422 (mtpp) REVERT: I 98 GLU cc_start: 0.8212 (mp0) cc_final: 0.7891 (mp0) REVERT: I 100 ARG cc_start: 0.8450 (mtt90) cc_final: 0.7876 (mtm-85) REVERT: I 102 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8355 (mm-40) REVERT: I 105 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8151 (mtmm) REVERT: I 155 ARG cc_start: 0.8381 (tpt90) cc_final: 0.7410 (mmm160) REVERT: I 158 GLN cc_start: 0.8995 (tt0) cc_final: 0.8563 (tt0) REVERT: I 161 LYS cc_start: 0.8937 (tptt) cc_final: 0.8724 (tptt) REVERT: I 178 LEU cc_start: 0.8264 (tp) cc_final: 0.8020 (tp) REVERT: I 203 PHE cc_start: 0.8376 (t80) cc_final: 0.8120 (t80) REVERT: I 207 GLN cc_start: 0.8267 (mm110) cc_final: 0.7920 (tp40) REVERT: I 208 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8264 (tm-30) REVERT: I 211 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7801 (tp40) REVERT: I 264 ILE cc_start: 0.7667 (mm) cc_final: 0.7378 (mm) REVERT: J 15 TRP cc_start: 0.8162 (m100) cc_final: 0.7637 (m100) REVERT: J 40 CYS cc_start: 0.7545 (t) cc_final: 0.6986 (p) REVERT: J 63 TRP cc_start: 0.7668 (m100) cc_final: 0.5834 (m100) REVERT: J 64 GLN cc_start: 0.6962 (tp40) cc_final: 0.6192 (mm110) REVERT: J 65 VAL cc_start: 0.8808 (t) cc_final: 0.8467 (t) REVERT: J 70 TYR cc_start: 0.7775 (t80) cc_final: 0.7373 (t80) REVERT: J 86 ILE cc_start: 0.8842 (pt) cc_final: 0.8191 (mm) REVERT: J 92 LYS cc_start: 0.8787 (tptp) cc_final: 0.8452 (tptp) REVERT: J 101 VAL cc_start: 0.9030 (t) cc_final: 0.8805 (t) REVERT: J 104 MET cc_start: 0.8588 (mmt) cc_final: 0.8270 (mmt) REVERT: J 113 LYS cc_start: 0.7629 (mmmt) cc_final: 0.7382 (mmmt) REVERT: J 116 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6528 (tm-30) REVERT: J 131 LEU cc_start: 0.8856 (tt) cc_final: 0.8342 (tt) REVERT: J 132 MET cc_start: 0.8762 (mmp) cc_final: 0.7939 (mmp) REVERT: J 137 ILE cc_start: 0.8552 (tt) cc_final: 0.8346 (tt) REVERT: J 139 HIS cc_start: 0.8567 (t70) cc_final: 0.8288 (t70) REVERT: J 162 ASN cc_start: 0.8960 (m110) cc_final: 0.8710 (m-40) REVERT: J 178 LEU cc_start: 0.9114 (mm) cc_final: 0.8814 (mm) REVERT: J 204 ASN cc_start: 0.8248 (m110) cc_final: 0.7877 (m110) REVERT: J 205 LYS cc_start: 0.8551 (tptp) cc_final: 0.8125 (tptp) REVERT: J 208 GLN cc_start: 0.8313 (pt0) cc_final: 0.7987 (pt0) REVERT: K 7 LEU cc_start: 0.8804 (tt) cc_final: 0.8576 (tt) REVERT: K 15 TRP cc_start: 0.8169 (m100) cc_final: 0.7628 (m100) REVERT: K 25 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8404 (tm-30) REVERT: K 34 GLU cc_start: 0.8808 (pt0) cc_final: 0.8342 (pp20) REVERT: K 35 ASP cc_start: 0.8766 (m-30) cc_final: 0.8417 (m-30) REVERT: K 132 MET cc_start: 0.7548 (ppp) cc_final: 0.7253 (ppp) REVERT: K 245 TRP cc_start: 0.8025 (m100) cc_final: 0.7658 (m100) REVERT: K 270 LYS cc_start: 0.8003 (mmtm) cc_final: 0.6972 (tmtt) REVERT: L 63 TRP cc_start: 0.6447 (m100) cc_final: 0.6106 (m100) REVERT: L 86 ILE cc_start: 0.7454 (pt) cc_final: 0.6955 (mm) REVERT: L 226 TYR cc_start: 0.7431 (p90) cc_final: 0.6384 (p90) REVERT: L 244 LEU cc_start: 0.8591 (mt) cc_final: 0.8347 (mt) REVERT: L 263 VAL cc_start: 0.8371 (m) cc_final: 0.8134 (t) REVERT: L 266 ASN cc_start: 0.8616 (m-40) cc_final: 0.8093 (m-40) REVERT: L 269 VAL cc_start: 0.7898 (m) cc_final: 0.7649 (m) REVERT: M 7 LEU cc_start: 0.8432 (tt) cc_final: 0.7891 (tt) REVERT: M 15 TRP cc_start: 0.8625 (m-10) cc_final: 0.8088 (m-10) REVERT: M 16 HIS cc_start: 0.7877 (m-70) cc_final: 0.6390 (m-70) REVERT: M 18 ASP cc_start: 0.7671 (t70) cc_final: 0.7273 (t70) REVERT: M 36 ILE cc_start: 0.8682 (mt) cc_final: 0.8420 (mt) REVERT: M 86 ILE cc_start: 0.8355 (pt) cc_final: 0.8126 (mm) REVERT: M 154 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8693 (mm-30) REVERT: M 158 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7739 (tm-30) REVERT: M 159 THR cc_start: 0.8674 (m) cc_final: 0.8087 (p) REVERT: M 166 LYS cc_start: 0.8320 (mttt) cc_final: 0.8025 (ttmm) REVERT: M 178 LEU cc_start: 0.8861 (mt) cc_final: 0.8597 (mt) REVERT: M 207 GLN cc_start: 0.8515 (mm110) cc_final: 0.8200 (mm110) REVERT: M 209 ARG cc_start: 0.8847 (tmt170) cc_final: 0.8476 (ttp80) REVERT: N 23 HIS cc_start: 0.7649 (t70) cc_final: 0.7298 (t70) REVERT: N 65 VAL cc_start: 0.7593 (t) cc_final: 0.7153 (p) REVERT: N 102 GLN cc_start: 0.8965 (mp-120) cc_final: 0.8527 (mp10) REVERT: N 104 MET cc_start: 0.8421 (ptm) cc_final: 0.7882 (ppp) REVERT: N 105 LYS cc_start: 0.9328 (mtmm) cc_final: 0.9103 (mttt) REVERT: N 109 MET cc_start: 0.7869 (ptm) cc_final: 0.7543 (ptp) REVERT: N 154 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7569 (mp0) REVERT: N 183 ILE cc_start: 0.7097 (mt) cc_final: 0.6864 (mt) REVERT: N 203 PHE cc_start: 0.7917 (t80) cc_final: 0.7587 (t80) REVERT: N 210 ILE cc_start: 0.8399 (pt) cc_final: 0.8031 (pt) REVERT: N 213 GLN cc_start: 0.8791 (mt0) cc_final: 0.8089 (mt0) REVERT: N 224 CYS cc_start: 0.8157 (p) cc_final: 0.7858 (p) REVERT: N 230 LYS cc_start: 0.8343 (mttt) cc_final: 0.7816 (tptp) REVERT: N 233 HIS cc_start: 0.7702 (m90) cc_final: 0.7368 (m-70) REVERT: N 242 GLN cc_start: 0.7729 (tt0) cc_final: 0.7296 (pp30) REVERT: N 243 VAL cc_start: 0.8542 (t) cc_final: 0.8184 (p) REVERT: N 244 LEU cc_start: 0.8367 (tt) cc_final: 0.8072 (tt) REVERT: N 253 VAL cc_start: 0.7843 (p) cc_final: 0.7614 (m) REVERT: N 256 ARG cc_start: 0.8472 (ttm110) cc_final: 0.7820 (ttm110) REVERT: N 270 LYS cc_start: 0.7939 (mptt) cc_final: 0.7193 (mmtm) REVERT: O 22 LEU cc_start: 0.8797 (mm) cc_final: 0.7862 (mm) REVERT: O 23 HIS cc_start: 0.7725 (t70) cc_final: 0.7056 (t70) REVERT: O 25 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6739 (tp30) REVERT: O 48 MET cc_start: -0.1540 (ppp) cc_final: -0.1923 (ppp) REVERT: O 104 MET cc_start: 0.8144 (pmm) cc_final: 0.7866 (pmm) REVERT: O 110 PHE cc_start: 0.8133 (m-80) cc_final: 0.7658 (m-80) REVERT: O 132 MET cc_start: 0.8218 (tmm) cc_final: 0.7758 (tmm) REVERT: O 155 ARG cc_start: 0.9014 (mtm110) cc_final: 0.8698 (ptp-110) REVERT: O 157 HIS cc_start: 0.8823 (m90) cc_final: 0.8545 (m90) REVERT: O 193 LEU cc_start: 0.8777 (mm) cc_final: 0.8539 (mm) REVERT: O 199 ASP cc_start: 0.8796 (m-30) cc_final: 0.8548 (m-30) REVERT: O 209 ARG cc_start: 0.8842 (ptm-80) cc_final: 0.8441 (ptm-80) REVERT: P 62 HIS cc_start: 0.7859 (t-90) cc_final: 0.7260 (t-170) REVERT: P 87 TYR cc_start: 0.8529 (t80) cc_final: 0.8281 (t80) REVERT: P 101 VAL cc_start: 0.9164 (p) cc_final: 0.8930 (p) REVERT: P 104 MET cc_start: 0.9151 (mmp) cc_final: 0.8663 (mmp) REVERT: P 106 TRP cc_start: 0.8567 (t60) cc_final: 0.8149 (t60) REVERT: P 170 MET cc_start: 0.7796 (mtt) cc_final: 0.7286 (mpp) REVERT: P 172 ASN cc_start: 0.8824 (m-40) cc_final: 0.8496 (p0) REVERT: P 207 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7976 (mm-40) REVERT: P 222 ARG cc_start: 0.6658 (mmm-85) cc_final: 0.5952 (mmm160) REVERT: P 223 PHE cc_start: 0.6816 (m-80) cc_final: 0.6613 (m-80) REVERT: P 272 ILE cc_start: 0.8071 (mm) cc_final: 0.7856 (mm) outliers start: 9 outliers final: 1 residues processed: 1211 average time/residue: 0.4642 time to fit residues: 872.8453 Evaluate side-chains 1126 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1123 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 147 optimal weight: 0.7980 chunk 212 optimal weight: 0.2980 chunk 382 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 120 optimal weight: 0.0170 chunk 239 optimal weight: 7.9990 chunk 34 optimal weight: 0.0870 chunk 229 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 340 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 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 102 GLN B 158 GLN B 211 GLN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN F 158 GLN G 102 GLN G 208 GLN H 62 HIS H 157 HIS ** I 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 HIS I 146 ASN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN L 158 GLN M 69 HIS N 158 GLN ** O 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN P 62 HIS ** 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 = 0.4528 r_free = 0.4528 target = 0.198445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152227 restraints weight = 70652.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.158024 restraints weight = 43732.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.161957 restraints weight = 30372.583| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34119 Z= 0.137 Angle : 0.651 12.675 46515 Z= 0.345 Chirality : 0.047 0.208 5006 Planarity : 0.004 0.060 5714 Dihedral : 14.661 173.502 5007 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.05 % Rotamer: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 3851 helix: 1.10 (0.12), residues: 1875 sheet: -0.81 (0.17), residues: 848 loop : -1.71 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 63 HIS 0.012 0.001 HIS C 233 PHE 0.030 0.002 PHE J 174 TYR 0.023 0.001 TYR F 134 ARG 0.012 0.001 ARG F 155 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 1746) hydrogen bonds : angle 5.22387 ( 5114) covalent geometry : bond 0.00288 (34119) covalent geometry : angle 0.65140 (46515) *********************** 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 1199 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1198 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TRP cc_start: 0.6694 (m-90) cc_final: 0.5902 (m-10) REVERT: A 66 ASP cc_start: 0.7811 (t0) cc_final: 0.7490 (t70) REVERT: A 79 VAL cc_start: 0.8089 (t) cc_final: 0.7484 (p) REVERT: A 80 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6589 (tm-30) REVERT: A 92 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8466 (mtpp) REVERT: A 98 GLU cc_start: 0.8168 (mp0) cc_final: 0.7902 (mp0) REVERT: A 104 MET cc_start: 0.8514 (ttm) cc_final: 0.7931 (ttm) REVERT: A 113 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7685 (mmmm) REVERT: A 116 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7184 (tm-30) REVERT: A 129 GLN cc_start: 0.8140 (tt0) cc_final: 0.7913 (tt0) REVERT: A 132 MET cc_start: 0.8355 (mmm) cc_final: 0.7929 (mmm) REVERT: A 152 LEU cc_start: 0.7600 (pt) cc_final: 0.6773 (mp) REVERT: A 153 VAL cc_start: 0.8956 (m) cc_final: 0.8741 (m) REVERT: A 158 GLN cc_start: 0.8662 (tt0) cc_final: 0.7878 (pt0) REVERT: A 160 LEU cc_start: 0.8559 (tt) cc_final: 0.8332 (tt) REVERT: A 161 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8323 (tppt) REVERT: A 164 LEU cc_start: 0.8340 (mt) cc_final: 0.8005 (mt) REVERT: A 184 THR cc_start: 0.8577 (m) cc_final: 0.8258 (p) REVERT: A 190 LYS cc_start: 0.7355 (mtmm) cc_final: 0.6824 (mtpp) REVERT: A 203 PHE cc_start: 0.8495 (t80) cc_final: 0.7960 (t80) REVERT: A 226 TYR cc_start: 0.6672 (p90) cc_final: 0.4643 (p90) REVERT: A 254 LYS cc_start: 0.8088 (pptt) cc_final: 0.7519 (pptt) REVERT: A 260 ARG cc_start: 0.7499 (ptm160) cc_final: 0.7290 (ptm160) REVERT: B 15 TRP cc_start: 0.7877 (m100) cc_final: 0.7293 (m100) REVERT: B 40 CYS cc_start: 0.7647 (t) cc_final: 0.7025 (p) REVERT: B 63 TRP cc_start: 0.7715 (m100) cc_final: 0.6112 (m100) REVERT: B 64 GLN cc_start: 0.6982 (tp40) cc_final: 0.6762 (mm-40) REVERT: B 86 ILE cc_start: 0.8540 (pt) cc_final: 0.8064 (mm) REVERT: B 87 TYR cc_start: 0.7978 (t80) cc_final: 0.7740 (t80) REVERT: B 89 GLU cc_start: 0.7816 (tt0) cc_final: 0.7192 (tt0) REVERT: B 104 MET cc_start: 0.8762 (mmp) cc_final: 0.8450 (mmp) REVERT: B 106 TRP cc_start: 0.8622 (t60) cc_final: 0.8366 (t60) REVERT: B 129 GLN cc_start: 0.8502 (pt0) cc_final: 0.8095 (pt0) REVERT: B 131 LEU cc_start: 0.9092 (tt) cc_final: 0.8614 (tt) REVERT: B 132 MET cc_start: 0.8812 (mmp) cc_final: 0.8000 (mmp) REVERT: B 137 ILE cc_start: 0.8555 (tt) cc_final: 0.8291 (tt) REVERT: B 138 GLU cc_start: 0.7870 (tp30) cc_final: 0.7618 (tp30) REVERT: B 139 HIS cc_start: 0.8536 (t70) cc_final: 0.8108 (t70) REVERT: B 175 GLU cc_start: 0.8795 (pm20) cc_final: 0.8563 (mp0) REVERT: B 178 LEU cc_start: 0.9120 (mm) cc_final: 0.8893 (mm) REVERT: B 186 ASN cc_start: 0.8279 (m-40) cc_final: 0.7964 (m-40) REVERT: B 198 MET cc_start: 0.8142 (tpt) cc_final: 0.7676 (tpp) REVERT: B 204 ASN cc_start: 0.7710 (p0) cc_final: 0.7317 (p0) REVERT: B 208 GLN cc_start: 0.8189 (pt0) cc_final: 0.7781 (pt0) REVERT: C 7 LEU cc_start: 0.8795 (tt) cc_final: 0.8445 (tt) REVERT: C 11 GLU cc_start: 0.8179 (tp30) cc_final: 0.6810 (tp30) REVERT: C 35 ASP cc_start: 0.8792 (m-30) cc_final: 0.8558 (m-30) REVERT: C 110 PHE cc_start: 0.7713 (m-80) cc_final: 0.7257 (m-80) REVERT: C 162 ASN cc_start: 0.8805 (m-40) cc_final: 0.8389 (m-40) REVERT: C 209 ARG cc_start: 0.8613 (ptt90) cc_final: 0.8163 (ptt90) REVERT: C 270 LYS cc_start: 0.8377 (mmtm) cc_final: 0.8052 (tmtt) REVERT: D 63 TRP cc_start: 0.6634 (m100) cc_final: 0.6139 (m100) REVERT: D 209 ARG cc_start: 0.8747 (mmp-170) cc_final: 0.8370 (mmp80) REVERT: D 218 GLN cc_start: 0.8487 (mm110) cc_final: 0.7967 (mm110) REVERT: D 223 PHE cc_start: 0.6277 (p90) cc_final: 0.5884 (p90) REVERT: D 224 CYS cc_start: 0.7227 (p) cc_final: 0.6954 (p) REVERT: D 226 TYR cc_start: 0.7446 (p90) cc_final: 0.6280 (p90) REVERT: D 227 ARG cc_start: 0.5522 (mpt-90) cc_final: 0.5283 (mmt90) REVERT: D 244 LEU cc_start: 0.8347 (mt) cc_final: 0.8011 (mt) REVERT: D 254 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8014 (ttmm) REVERT: D 268 ASP cc_start: 0.7269 (t70) cc_final: 0.6961 (t70) REVERT: E 7 LEU cc_start: 0.8616 (tt) cc_final: 0.8197 (tt) REVERT: E 12 HIS cc_start: 0.8434 (t70) cc_final: 0.7617 (t70) REVERT: E 15 TRP cc_start: 0.8482 (m-10) cc_final: 0.8215 (m-10) REVERT: E 16 HIS cc_start: 0.8127 (m-70) cc_final: 0.7225 (m170) REVERT: E 101 VAL cc_start: 0.8676 (t) cc_final: 0.8432 (t) REVERT: E 133 LYS cc_start: 0.9235 (ptpp) cc_final: 0.8792 (pttm) REVERT: E 138 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7093 (tm-30) REVERT: E 150 GLN cc_start: 0.7865 (mm110) cc_final: 0.7399 (mm-40) REVERT: E 154 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8595 (mm-30) REVERT: E 201 PHE cc_start: 0.8320 (t80) cc_final: 0.8048 (t80) REVERT: E 204 ASN cc_start: 0.8673 (t0) cc_final: 0.8410 (t0) REVERT: E 205 LYS cc_start: 0.8980 (mttt) cc_final: 0.8493 (mmtp) REVERT: E 206 GLU cc_start: 0.8712 (pt0) cc_final: 0.8321 (pt0) REVERT: E 207 GLN cc_start: 0.8577 (mm110) cc_final: 0.8322 (mm110) REVERT: E 224 CYS cc_start: 0.5828 (p) cc_final: 0.5525 (p) REVERT: F 23 HIS cc_start: 0.7867 (t70) cc_final: 0.7456 (t70) REVERT: F 86 ILE cc_start: 0.7508 (pt) cc_final: 0.6951 (tp) REVERT: F 89 GLU cc_start: 0.6693 (tp30) cc_final: 0.6378 (tp30) REVERT: F 104 MET cc_start: 0.8339 (ptm) cc_final: 0.7855 (ppp) REVERT: F 105 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8939 (mttt) REVERT: F 131 LEU cc_start: 0.8606 (tp) cc_final: 0.8384 (mm) REVERT: F 164 LEU cc_start: 0.8381 (mt) cc_final: 0.8073 (mt) REVERT: F 183 ILE cc_start: 0.6598 (mt) cc_final: 0.6328 (mt) REVERT: F 198 MET cc_start: 0.8319 (ppp) cc_final: 0.8023 (ppp) REVERT: F 209 ARG cc_start: 0.7943 (ppt170) cc_final: 0.7720 (ttp80) REVERT: F 210 ILE cc_start: 0.8376 (pt) cc_final: 0.8126 (pt) REVERT: F 230 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7843 (mmmm) REVERT: F 231 ARG cc_start: 0.7919 (mpp-170) cc_final: 0.7396 (mpp-170) REVERT: F 233 HIS cc_start: 0.7783 (m-70) cc_final: 0.7482 (m-70) REVERT: F 237 TRP cc_start: 0.8008 (m100) cc_final: 0.7751 (m-10) REVERT: F 242 GLN cc_start: 0.7517 (tt0) cc_final: 0.6841 (pp30) REVERT: F 243 VAL cc_start: 0.8516 (t) cc_final: 0.7534 (m) REVERT: F 244 LEU cc_start: 0.8311 (tt) cc_final: 0.7873 (tt) REVERT: G 48 MET cc_start: -0.0560 (ppp) cc_final: -0.1356 (ppp) REVERT: G 62 HIS cc_start: 0.7546 (t70) cc_final: 0.6844 (t70) REVERT: G 97 GLN cc_start: 0.9012 (tt0) cc_final: 0.8765 (tp-100) REVERT: G 104 MET cc_start: 0.7959 (pmm) cc_final: 0.7623 (pmm) REVERT: G 130 LEU cc_start: 0.9060 (pp) cc_final: 0.8858 (pp) REVERT: G 131 LEU cc_start: 0.9284 (mt) cc_final: 0.9049 (mt) REVERT: G 155 ARG cc_start: 0.9112 (mtp-110) cc_final: 0.8586 (ptp-110) REVERT: G 158 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8886 (tp-100) REVERT: G 161 LYS cc_start: 0.9289 (tppt) cc_final: 0.9063 (tppt) REVERT: G 165 GLU cc_start: 0.8524 (tp30) cc_final: 0.8310 (tp30) REVERT: G 171 PHE cc_start: 0.7142 (m-80) cc_final: 0.6591 (m-80) REVERT: G 197 PRO cc_start: 0.8338 (Cg_exo) cc_final: 0.8106 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8858 (m-30) cc_final: 0.8523 (m-30) REVERT: G 201 PHE cc_start: 0.8544 (t80) cc_final: 0.8278 (t80) REVERT: G 206 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7748 (tm-30) REVERT: G 209 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8289 (ttp80) REVERT: G 210 ILE cc_start: 0.8465 (pt) cc_final: 0.7709 (pt) REVERT: H 62 HIS cc_start: 0.7811 (t70) cc_final: 0.7157 (t70) REVERT: H 78 TRP cc_start: 0.7223 (m-10) cc_final: 0.6753 (m-10) REVERT: H 85 LEU cc_start: 0.8462 (tp) cc_final: 0.8129 (tp) REVERT: H 87 TYR cc_start: 0.8420 (t80) cc_final: 0.7815 (t80) REVERT: H 101 VAL cc_start: 0.8800 (p) cc_final: 0.8575 (p) REVERT: H 104 MET cc_start: 0.9070 (mmp) cc_final: 0.8409 (mmp) REVERT: H 106 TRP cc_start: 0.8406 (t60) cc_final: 0.7847 (t60) REVERT: H 110 PHE cc_start: 0.7926 (m-10) cc_final: 0.7687 (m-10) REVERT: H 205 LYS cc_start: 0.8382 (mttp) cc_final: 0.7897 (mttp) REVERT: H 207 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7839 (mm-40) REVERT: H 222 ARG cc_start: 0.6956 (mmm-85) cc_final: 0.6319 (mmm160) REVERT: H 223 PHE cc_start: 0.7049 (m-10) cc_final: 0.6650 (m-80) REVERT: H 272 ILE cc_start: 0.8331 (mp) cc_final: 0.8095 (mp) REVERT: I 48 MET cc_start: 0.5861 (mmp) cc_final: 0.5575 (mmm) REVERT: I 60 ILE cc_start: 0.8686 (mt) cc_final: 0.8236 (mm) REVERT: I 66 ASP cc_start: 0.8014 (t0) cc_final: 0.7685 (t0) REVERT: I 79 VAL cc_start: 0.8159 (t) cc_final: 0.7656 (p) REVERT: I 86 ILE cc_start: 0.8453 (pt) cc_final: 0.8107 (mp) REVERT: I 92 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8545 (mtpp) REVERT: I 98 GLU cc_start: 0.8174 (mp0) cc_final: 0.7862 (mp0) REVERT: I 100 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7822 (mtm-85) REVERT: I 102 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8535 (mm-40) REVERT: I 105 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8164 (mtmm) REVERT: I 113 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7523 (mmmm) REVERT: I 117 SER cc_start: 0.5573 (p) cc_final: 0.5359 (p) REVERT: I 134 TYR cc_start: 0.8842 (t80) cc_final: 0.8313 (t80) REVERT: I 146 ASN cc_start: 0.8275 (m110) cc_final: 0.7892 (t0) REVERT: I 155 ARG cc_start: 0.8319 (tpt90) cc_final: 0.7462 (mmm160) REVERT: I 158 GLN cc_start: 0.9096 (tt0) cc_final: 0.8568 (tt0) REVERT: I 160 LEU cc_start: 0.8587 (tt) cc_final: 0.8080 (tt) REVERT: I 163 THR cc_start: 0.8458 (m) cc_final: 0.8165 (p) REVERT: I 164 LEU cc_start: 0.8545 (mt) cc_final: 0.8183 (mt) REVERT: I 190 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7285 (mtpp) REVERT: I 203 PHE cc_start: 0.8368 (t80) cc_final: 0.8064 (t80) REVERT: I 207 GLN cc_start: 0.8159 (mm110) cc_final: 0.7787 (tt0) REVERT: I 208 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8060 (tm-30) REVERT: I 211 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7816 (tp-100) REVERT: I 238 GLN cc_start: 0.6194 (mt0) cc_final: 0.5820 (mt0) REVERT: I 251 ILE cc_start: 0.7844 (pt) cc_final: 0.7357 (mp) REVERT: I 260 ARG cc_start: 0.7175 (mtp180) cc_final: 0.6717 (mtp180) REVERT: I 261 TYR cc_start: 0.7602 (m-10) cc_final: 0.7370 (m-10) REVERT: J 15 TRP cc_start: 0.8240 (m100) cc_final: 0.7647 (m100) REVERT: J 40 CYS cc_start: 0.7440 (t) cc_final: 0.6940 (p) REVERT: J 63 TRP cc_start: 0.7635 (m100) cc_final: 0.5821 (m100) REVERT: J 75 ILE cc_start: 0.7859 (mp) cc_final: 0.7653 (mm) REVERT: J 86 ILE cc_start: 0.8815 (pt) cc_final: 0.8124 (mm) REVERT: J 87 TYR cc_start: 0.8204 (t80) cc_final: 0.7741 (t80) REVERT: J 92 LYS cc_start: 0.8841 (tptp) cc_final: 0.8514 (tptp) REVERT: J 100 ARG cc_start: 0.8645 (mtt180) cc_final: 0.7814 (mtm-85) REVERT: J 104 MET cc_start: 0.8552 (mmt) cc_final: 0.8090 (mmt) REVERT: J 106 TRP cc_start: 0.8508 (t60) cc_final: 0.8300 (t60) REVERT: J 131 LEU cc_start: 0.8770 (tt) cc_final: 0.8373 (tt) REVERT: J 132 MET cc_start: 0.8778 (mmp) cc_final: 0.8546 (mmt) REVERT: J 137 ILE cc_start: 0.8578 (tt) cc_final: 0.7776 (tt) REVERT: J 138 GLU cc_start: 0.7794 (tp30) cc_final: 0.7592 (tp30) REVERT: J 139 HIS cc_start: 0.8624 (t70) cc_final: 0.8265 (t70) REVERT: J 162 ASN cc_start: 0.8993 (m110) cc_final: 0.8740 (m-40) REVERT: J 164 LEU cc_start: 0.8724 (tp) cc_final: 0.8522 (tp) REVERT: J 204 ASN cc_start: 0.8208 (m110) cc_final: 0.7654 (m110) REVERT: J 205 LYS cc_start: 0.8488 (tptp) cc_final: 0.8082 (tptp) REVERT: J 207 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8180 (mm-40) REVERT: J 208 GLN cc_start: 0.8271 (pt0) cc_final: 0.7866 (pt0) REVERT: K 7 LEU cc_start: 0.8552 (tt) cc_final: 0.8351 (tt) REVERT: K 34 GLU cc_start: 0.8829 (pt0) cc_final: 0.8403 (pp20) REVERT: K 35 ASP cc_start: 0.8757 (m-30) cc_final: 0.8426 (m-30) REVERT: K 245 TRP cc_start: 0.7988 (m100) cc_final: 0.7502 (m100) REVERT: K 270 LYS cc_start: 0.7521 (mmtm) cc_final: 0.7147 (tmtt) REVERT: L 63 TRP cc_start: 0.6199 (m100) cc_final: 0.5791 (m100) REVERT: L 209 ARG cc_start: 0.8634 (mmp-170) cc_final: 0.8290 (mmp80) REVERT: L 226 TYR cc_start: 0.7307 (p90) cc_final: 0.6322 (p90) REVERT: L 244 LEU cc_start: 0.8516 (mt) cc_final: 0.8275 (mt) REVERT: L 254 LYS cc_start: 0.8416 (tmtt) cc_final: 0.7681 (tmtt) REVERT: L 266 ASN cc_start: 0.8470 (m-40) cc_final: 0.7959 (m-40) REVERT: L 268 ASP cc_start: 0.7048 (t0) cc_final: 0.6748 (t70) REVERT: L 269 VAL cc_start: 0.7845 (m) cc_final: 0.7572 (m) REVERT: M 7 LEU cc_start: 0.8308 (tt) cc_final: 0.7568 (tt) REVERT: M 15 TRP cc_start: 0.8538 (m-10) cc_final: 0.8005 (m-10) REVERT: M 16 HIS cc_start: 0.7887 (m-70) cc_final: 0.7254 (m-70) REVERT: M 18 ASP cc_start: 0.7689 (t70) cc_final: 0.7213 (t70) REVERT: M 36 ILE cc_start: 0.8582 (mt) cc_final: 0.8270 (mt) REVERT: M 39 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7879 (tm-30) REVERT: M 86 ILE cc_start: 0.8333 (pt) cc_final: 0.8074 (mm) REVERT: M 154 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8735 (mm-30) REVERT: M 155 ARG cc_start: 0.8692 (ttt180) cc_final: 0.8376 (mtt90) REVERT: M 158 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7815 (tm-30) REVERT: M 159 THR cc_start: 0.8656 (m) cc_final: 0.8122 (p) REVERT: M 174 PHE cc_start: 0.7235 (t80) cc_final: 0.7028 (t80) REVERT: M 178 LEU cc_start: 0.8883 (mt) cc_final: 0.8358 (mt) REVERT: M 205 LYS cc_start: 0.9104 (mttm) cc_final: 0.8871 (mtpp) REVERT: M 207 GLN cc_start: 0.8543 (mm110) cc_final: 0.8284 (mm110) REVERT: M 217 LYS cc_start: 0.8052 (ptpp) cc_final: 0.7776 (ptpp) REVERT: N 23 HIS cc_start: 0.7760 (t70) cc_final: 0.7452 (t70) REVERT: N 104 MET cc_start: 0.8416 (ptm) cc_final: 0.7857 (ppp) REVERT: N 154 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7769 (mm-30) REVERT: N 157 HIS cc_start: 0.7817 (m90) cc_final: 0.7615 (m90) REVERT: N 170 MET cc_start: 0.7085 (mpp) cc_final: 0.6846 (mpp) REVERT: N 183 ILE cc_start: 0.7125 (mt) cc_final: 0.6921 (mt) REVERT: N 203 PHE cc_start: 0.7927 (t80) cc_final: 0.7487 (t80) REVERT: N 210 ILE cc_start: 0.8426 (pt) cc_final: 0.8101 (pt) REVERT: N 213 GLN cc_start: 0.8810 (mt0) cc_final: 0.8152 (mt0) REVERT: N 224 CYS cc_start: 0.8055 (p) cc_final: 0.7827 (p) REVERT: N 230 LYS cc_start: 0.8253 (mttt) cc_final: 0.7726 (tptp) REVERT: N 233 HIS cc_start: 0.7679 (m90) cc_final: 0.7291 (m-70) REVERT: N 242 GLN cc_start: 0.7882 (tt0) cc_final: 0.7308 (pp30) REVERT: N 243 VAL cc_start: 0.8519 (t) cc_final: 0.8222 (p) REVERT: N 244 LEU cc_start: 0.8396 (tt) cc_final: 0.8066 (tt) REVERT: N 256 ARG cc_start: 0.8581 (ttm110) cc_final: 0.7909 (ttm110) REVERT: N 267 LYS cc_start: 0.8972 (ptmt) cc_final: 0.8242 (mmtm) REVERT: N 270 LYS cc_start: 0.7786 (mptt) cc_final: 0.7076 (mmtm) REVERT: O 48 MET cc_start: -0.1477 (ppp) cc_final: -0.1859 (ppp) REVERT: O 104 MET cc_start: 0.8138 (pmm) cc_final: 0.7885 (pmm) REVERT: O 110 PHE cc_start: 0.8149 (m-80) cc_final: 0.7896 (m-80) REVERT: O 115 LEU cc_start: 0.8708 (tp) cc_final: 0.8507 (tp) REVERT: O 132 MET cc_start: 0.8169 (tmm) cc_final: 0.7797 (tmm) REVERT: O 155 ARG cc_start: 0.9099 (mtm110) cc_final: 0.8745 (ptp-110) REVERT: O 199 ASP cc_start: 0.8773 (m-30) cc_final: 0.8469 (m-30) REVERT: O 209 ARG cc_start: 0.8825 (ptm-80) cc_final: 0.8469 (ptm-80) REVERT: P 62 HIS cc_start: 0.7675 (t70) cc_final: 0.7153 (t70) REVERT: P 87 TYR cc_start: 0.8692 (t80) cc_final: 0.8310 (t80) REVERT: P 101 VAL cc_start: 0.9076 (p) cc_final: 0.8852 (p) REVERT: P 104 MET cc_start: 0.9186 (mmp) cc_final: 0.8669 (mmp) REVERT: P 106 TRP cc_start: 0.8557 (t60) cc_final: 0.8038 (t60) REVERT: P 170 MET cc_start: 0.7677 (mtt) cc_final: 0.7208 (mpp) REVERT: P 172 ASN cc_start: 0.8851 (m-40) cc_final: 0.8514 (p0) REVERT: P 207 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7904 (mm-40) REVERT: P 222 ARG cc_start: 0.6654 (mmm-85) cc_final: 0.5990 (mmm160) REVERT: P 233 HIS cc_start: 0.6758 (m-70) cc_final: 0.6528 (m-70) REVERT: P 254 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8329 (mmmt) REVERT: P 272 ILE cc_start: 0.8137 (mm) cc_final: 0.7879 (mm) outliers start: 1 outliers final: 0 residues processed: 1198 average time/residue: 0.4835 time to fit residues: 908.9379 Evaluate side-chains 1110 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1110 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 225 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 201 optimal weight: 0.6980 chunk 357 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 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 158 GLN ** C 102 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** D 158 GLN E 238 GLN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN F 150 GLN F 158 GLN G 208 GLN H 157 HIS J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 208 GLN P 157 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.195632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.149570 restraints weight = 70649.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155290 restraints weight = 43448.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.159214 restraints weight = 29995.093| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34119 Z= 0.163 Angle : 0.686 12.878 46515 Z= 0.365 Chirality : 0.048 0.305 5006 Planarity : 0.005 0.086 5714 Dihedral : 14.738 173.308 5007 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 3851 helix: 1.02 (0.12), residues: 1876 sheet: -0.82 (0.18), residues: 814 loop : -1.68 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP P 78 HIS 0.010 0.001 HIS P 157 PHE 0.037 0.002 PHE H 201 TYR 0.031 0.002 TYR N 134 ARG 0.007 0.001 ARG L 256 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 1746) hydrogen bonds : angle 5.31279 ( 5114) covalent geometry : bond 0.00340 (34119) covalent geometry : angle 0.68605 (46515) *********************** 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 1200 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1199 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TRP cc_start: 0.7109 (m-90) cc_final: 0.6371 (m100) REVERT: A 60 ILE cc_start: 0.8629 (mm) cc_final: 0.8234 (mm) REVERT: A 66 ASP cc_start: 0.7944 (t0) cc_final: 0.7701 (t0) REVERT: A 79 VAL cc_start: 0.8150 (t) cc_final: 0.7517 (p) REVERT: A 92 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8545 (mtpp) REVERT: A 97 GLN cc_start: 0.7636 (pm20) cc_final: 0.7194 (pm20) REVERT: A 98 GLU cc_start: 0.8173 (mp0) cc_final: 0.7882 (mp0) REVERT: A 104 MET cc_start: 0.8469 (ttm) cc_final: 0.7845 (ttm) REVERT: A 113 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7785 (mmmm) REVERT: A 116 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 118 ASP cc_start: 0.7631 (p0) cc_final: 0.7269 (p0) REVERT: A 129 GLN cc_start: 0.8163 (tt0) cc_final: 0.7926 (tt0) REVERT: A 132 MET cc_start: 0.7855 (mmm) cc_final: 0.7500 (mmm) REVERT: A 152 LEU cc_start: 0.7410 (pt) cc_final: 0.6131 (mp) REVERT: A 153 VAL cc_start: 0.8993 (m) cc_final: 0.8754 (m) REVERT: A 155 ARG cc_start: 0.8435 (tpt90) cc_final: 0.7641 (mmm160) REVERT: A 158 GLN cc_start: 0.8644 (tt0) cc_final: 0.8164 (tt0) REVERT: A 161 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8306 (tppt) REVERT: A 164 LEU cc_start: 0.8425 (mt) cc_final: 0.8106 (mt) REVERT: A 190 LYS cc_start: 0.7623 (mtmm) cc_final: 0.7039 (mtpt) REVERT: A 203 PHE cc_start: 0.8384 (t80) cc_final: 0.7882 (t80) REVERT: A 211 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7812 (tp-100) REVERT: A 226 TYR cc_start: 0.6726 (p90) cc_final: 0.4812 (p90) REVERT: A 254 LYS cc_start: 0.8122 (pptt) cc_final: 0.7452 (pptt) REVERT: A 260 ARG cc_start: 0.7443 (ptm160) cc_final: 0.7230 (ptm160) REVERT: B 15 TRP cc_start: 0.7864 (m100) cc_final: 0.7288 (m100) REVERT: B 40 CYS cc_start: 0.7695 (t) cc_final: 0.7019 (p) REVERT: B 63 TRP cc_start: 0.7894 (m100) cc_final: 0.6192 (m100) REVERT: B 64 GLN cc_start: 0.7015 (tp40) cc_final: 0.6421 (mp10) REVERT: B 86 ILE cc_start: 0.8735 (pt) cc_final: 0.8113 (mm) REVERT: B 87 TYR cc_start: 0.8135 (t80) cc_final: 0.7458 (t80) REVERT: B 89 GLU cc_start: 0.7805 (tt0) cc_final: 0.6926 (tt0) REVERT: B 92 LYS cc_start: 0.8802 (tppp) cc_final: 0.8547 (tppp) REVERT: B 104 MET cc_start: 0.8757 (mmp) cc_final: 0.8290 (mmp) REVERT: B 106 TRP cc_start: 0.8659 (t60) cc_final: 0.8405 (t60) REVERT: B 129 GLN cc_start: 0.8623 (pt0) cc_final: 0.8216 (pt0) REVERT: B 131 LEU cc_start: 0.9057 (tt) cc_final: 0.8591 (tt) REVERT: B 132 MET cc_start: 0.8826 (mmp) cc_final: 0.7993 (mmp) REVERT: B 137 ILE cc_start: 0.8569 (tt) cc_final: 0.8265 (tt) REVERT: B 138 GLU cc_start: 0.7944 (tp30) cc_final: 0.7697 (tp30) REVERT: B 139 HIS cc_start: 0.8583 (t70) cc_final: 0.8147 (t70) REVERT: B 175 GLU cc_start: 0.8800 (pm20) cc_final: 0.8598 (mp0) REVERT: B 178 LEU cc_start: 0.9117 (mm) cc_final: 0.8897 (mm) REVERT: B 186 ASN cc_start: 0.8290 (m-40) cc_final: 0.8004 (m-40) REVERT: B 198 MET cc_start: 0.8102 (tpt) cc_final: 0.7647 (tpp) REVERT: B 204 ASN cc_start: 0.7867 (p0) cc_final: 0.7561 (p0) REVERT: B 208 GLN cc_start: 0.8156 (pt0) cc_final: 0.7756 (pt0) REVERT: C 7 LEU cc_start: 0.8736 (tt) cc_final: 0.8174 (tt) REVERT: C 11 GLU cc_start: 0.8055 (tp30) cc_final: 0.7543 (tp30) REVERT: C 110 PHE cc_start: 0.7808 (m-80) cc_final: 0.7472 (m-80) REVERT: C 132 MET cc_start: 0.8332 (ppp) cc_final: 0.7881 (ppp) REVERT: C 190 LYS cc_start: 0.6656 (mttm) cc_final: 0.6262 (mmmt) REVERT: C 198 MET cc_start: 0.8250 (tpt) cc_final: 0.7834 (tpt) REVERT: C 199 ASP cc_start: 0.8845 (m-30) cc_final: 0.8559 (m-30) REVERT: C 202 ILE cc_start: 0.8391 (mt) cc_final: 0.8152 (mt) REVERT: C 244 LEU cc_start: 0.8189 (mm) cc_final: 0.7719 (mm) REVERT: C 270 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8109 (tmtt) REVERT: D 63 TRP cc_start: 0.6521 (m100) cc_final: 0.5782 (m100) REVERT: D 209 ARG cc_start: 0.8678 (mmp-170) cc_final: 0.8369 (mmp-170) REVERT: D 218 GLN cc_start: 0.8450 (mm110) cc_final: 0.7857 (mm110) REVERT: D 226 TYR cc_start: 0.7084 (p90) cc_final: 0.6169 (p90) REVERT: D 254 LYS cc_start: 0.8391 (ttmm) cc_final: 0.7981 (ttmm) REVERT: D 262 LEU cc_start: 0.8173 (mm) cc_final: 0.7956 (mm) REVERT: D 266 ASN cc_start: 0.8391 (m110) cc_final: 0.7942 (m110) REVERT: D 268 ASP cc_start: 0.7055 (t70) cc_final: 0.6785 (t70) REVERT: E 7 LEU cc_start: 0.8319 (tt) cc_final: 0.7838 (tt) REVERT: E 12 HIS cc_start: 0.8521 (t70) cc_final: 0.7326 (t70) REVERT: E 15 TRP cc_start: 0.8401 (m-10) cc_final: 0.8164 (m-10) REVERT: E 16 HIS cc_start: 0.8019 (m-70) cc_final: 0.7429 (m170) REVERT: E 101 VAL cc_start: 0.8764 (t) cc_final: 0.8534 (t) REVERT: E 103 THR cc_start: 0.8973 (t) cc_final: 0.8705 (p) REVERT: E 132 MET cc_start: 0.7148 (mmm) cc_final: 0.6712 (mmm) REVERT: E 150 GLN cc_start: 0.7889 (mm110) cc_final: 0.7494 (mm110) REVERT: E 154 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8671 (mm-30) REVERT: E 158 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7615 (tm-30) REVERT: E 159 THR cc_start: 0.8366 (m) cc_final: 0.7754 (p) REVERT: E 178 LEU cc_start: 0.8870 (mt) cc_final: 0.8513 (mt) REVERT: E 206 GLU cc_start: 0.8666 (pt0) cc_final: 0.7427 (pp20) REVERT: E 224 CYS cc_start: 0.6296 (p) cc_final: 0.5995 (p) REVERT: E 236 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8495 (mm-30) REVERT: E 260 ARG cc_start: 0.7822 (pmt-80) cc_final: 0.7551 (pmt-80) REVERT: E 270 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8041 (mtmt) REVERT: F 23 HIS cc_start: 0.7833 (t70) cc_final: 0.7431 (t70) REVERT: F 82 ASN cc_start: 0.8521 (m-40) cc_final: 0.8077 (m-40) REVERT: F 86 ILE cc_start: 0.7690 (pt) cc_final: 0.7230 (tp) REVERT: F 89 GLU cc_start: 0.6728 (tp30) cc_final: 0.6405 (tp30) REVERT: F 131 LEU cc_start: 0.8598 (tp) cc_final: 0.8372 (mm) REVERT: F 154 GLU cc_start: 0.8613 (mm-30) cc_final: 0.7844 (mm-30) REVERT: F 157 HIS cc_start: 0.7711 (m90) cc_final: 0.7388 (m90) REVERT: F 162 ASN cc_start: 0.8999 (m110) cc_final: 0.8781 (m110) REVERT: F 164 LEU cc_start: 0.8424 (mt) cc_final: 0.8221 (mt) REVERT: F 183 ILE cc_start: 0.6368 (mt) cc_final: 0.6117 (mt) REVERT: F 199 ASP cc_start: 0.8411 (m-30) cc_final: 0.8187 (m-30) REVERT: F 202 ILE cc_start: 0.8559 (mt) cc_final: 0.8113 (mt) REVERT: F 205 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8482 (mtmt) REVERT: F 230 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8035 (mmmm) REVERT: F 233 HIS cc_start: 0.7712 (m-70) cc_final: 0.7510 (m-70) REVERT: F 237 TRP cc_start: 0.8016 (m100) cc_final: 0.7604 (m100) REVERT: F 242 GLN cc_start: 0.7592 (tt0) cc_final: 0.6942 (pp30) REVERT: F 243 VAL cc_start: 0.8547 (t) cc_final: 0.7543 (m) REVERT: F 244 LEU cc_start: 0.8279 (tt) cc_final: 0.7840 (tt) REVERT: F 256 ARG cc_start: 0.8326 (ttm110) cc_final: 0.7925 (ttm110) REVERT: G 48 MET cc_start: -0.0556 (ppp) cc_final: -0.1339 (ppp) REVERT: G 62 HIS cc_start: 0.7549 (t70) cc_final: 0.7072 (t70) REVERT: G 97 GLN cc_start: 0.8993 (tt0) cc_final: 0.8705 (tp-100) REVERT: G 104 MET cc_start: 0.7949 (pmm) cc_final: 0.7681 (pmm) REVERT: G 109 MET cc_start: 0.7421 (tpp) cc_final: 0.6981 (tpt) REVERT: G 130 LEU cc_start: 0.9005 (pp) cc_final: 0.8789 (pp) REVERT: G 131 LEU cc_start: 0.9327 (mt) cc_final: 0.9084 (mt) REVERT: G 155 ARG cc_start: 0.9059 (mtp-110) cc_final: 0.8607 (ptp-110) REVERT: G 158 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8786 (tp-100) REVERT: G 171 PHE cc_start: 0.7113 (m-80) cc_final: 0.6628 (m-80) REVERT: G 175 GLU cc_start: 0.8686 (pm20) cc_final: 0.8279 (mp0) REVERT: G 197 PRO cc_start: 0.8335 (Cg_exo) cc_final: 0.8085 (Cg_endo) REVERT: G 199 ASP cc_start: 0.8721 (m-30) cc_final: 0.8256 (m-30) REVERT: G 201 PHE cc_start: 0.8466 (t80) cc_final: 0.8060 (t80) REVERT: G 209 ARG cc_start: 0.8848 (ttp80) cc_final: 0.8291 (ttp80) REVERT: G 210 ILE cc_start: 0.8562 (pt) cc_final: 0.7968 (pt) REVERT: H 62 HIS cc_start: 0.7900 (t70) cc_final: 0.7194 (t70) REVERT: H 78 TRP cc_start: 0.7210 (m-10) cc_final: 0.6894 (m-10) REVERT: H 85 LEU cc_start: 0.8515 (tp) cc_final: 0.8181 (tp) REVERT: H 87 TYR cc_start: 0.8438 (t80) cc_final: 0.7849 (t80) REVERT: H 101 VAL cc_start: 0.8825 (p) cc_final: 0.8522 (p) REVERT: H 104 MET cc_start: 0.9070 (mmp) cc_final: 0.8364 (mmp) REVERT: H 106 TRP cc_start: 0.8401 (t60) cc_final: 0.7830 (t60) REVERT: H 199 ASP cc_start: 0.7870 (m-30) cc_final: 0.7413 (m-30) REVERT: H 201 PHE cc_start: 0.7964 (t80) cc_final: 0.7675 (t80) REVERT: H 207 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7795 (mm-40) REVERT: H 222 ARG cc_start: 0.6840 (mmm-85) cc_final: 0.6352 (mmm160) REVERT: H 223 PHE cc_start: 0.6954 (m-10) cc_final: 0.6438 (m-80) REVERT: H 256 ARG cc_start: 0.8273 (ppt170) cc_final: 0.7683 (ppt170) REVERT: H 272 ILE cc_start: 0.8387 (mp) cc_final: 0.8142 (mp) REVERT: I 30 ARG cc_start: 0.7409 (ptm160) cc_final: 0.6953 (mtm-85) REVERT: I 48 MET cc_start: 0.5948 (mmp) cc_final: 0.5697 (mmm) REVERT: I 60 ILE cc_start: 0.8791 (mt) cc_final: 0.8407 (mm) REVERT: I 66 ASP cc_start: 0.8093 (t0) cc_final: 0.7808 (t0) REVERT: I 79 VAL cc_start: 0.8232 (t) cc_final: 0.7725 (p) REVERT: I 86 ILE cc_start: 0.8592 (pt) cc_final: 0.7938 (mm) REVERT: I 92 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8491 (mtpp) REVERT: I 100 ARG cc_start: 0.8401 (mtt90) cc_final: 0.7925 (mtm-85) REVERT: I 109 MET cc_start: 0.8242 (tpp) cc_final: 0.8039 (tpp) REVERT: I 113 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7605 (mmmm) REVERT: I 152 LEU cc_start: 0.7518 (pt) cc_final: 0.6536 (mp) REVERT: I 155 ARG cc_start: 0.8321 (tpt90) cc_final: 0.7488 (tpp-160) REVERT: I 163 THR cc_start: 0.8522 (m) cc_final: 0.8166 (p) REVERT: I 164 LEU cc_start: 0.8596 (mt) cc_final: 0.8238 (mt) REVERT: I 190 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7623 (mtpp) REVERT: I 203 PHE cc_start: 0.8349 (t80) cc_final: 0.8091 (t80) REVERT: I 207 GLN cc_start: 0.8281 (mm110) cc_final: 0.7792 (tp40) REVERT: I 211 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7686 (tp40) REVERT: I 238 GLN cc_start: 0.6391 (mt0) cc_final: 0.6070 (mt0) REVERT: I 244 LEU cc_start: 0.8617 (mt) cc_final: 0.8402 (mt) REVERT: I 251 ILE cc_start: 0.7906 (pt) cc_final: 0.7473 (mp) REVERT: J 13 ASN cc_start: 0.7648 (m-40) cc_final: 0.7397 (m110) REVERT: J 15 TRP cc_start: 0.8050 (m100) cc_final: 0.7510 (m100) REVERT: J 40 CYS cc_start: 0.7478 (t) cc_final: 0.6920 (p) REVERT: J 63 TRP cc_start: 0.7718 (m100) cc_final: 0.6220 (m100) REVERT: J 86 ILE cc_start: 0.8897 (pt) cc_final: 0.8217 (mm) REVERT: J 92 LYS cc_start: 0.8854 (tptp) cc_final: 0.8514 (tptp) REVERT: J 104 MET cc_start: 0.8617 (mmt) cc_final: 0.8079 (mmt) REVERT: J 131 LEU cc_start: 0.8800 (tt) cc_final: 0.8359 (tt) REVERT: J 132 MET cc_start: 0.8741 (mmp) cc_final: 0.8524 (mmt) REVERT: J 137 ILE cc_start: 0.8512 (tt) cc_final: 0.7703 (tt) REVERT: J 139 HIS cc_start: 0.8601 (t70) cc_final: 0.8237 (t70) REVERT: J 162 ASN cc_start: 0.8948 (m110) cc_final: 0.8699 (m-40) REVERT: J 174 PHE cc_start: 0.8154 (t80) cc_final: 0.7946 (t80) REVERT: J 189 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6502 (mtm110) REVERT: J 204 ASN cc_start: 0.8381 (m110) cc_final: 0.7936 (m110) REVERT: J 205 LYS cc_start: 0.8537 (tptp) cc_final: 0.8115 (tptp) REVERT: J 208 GLN cc_start: 0.8280 (pt0) cc_final: 0.7879 (pt0) REVERT: K 15 TRP cc_start: 0.8332 (m100) cc_final: 0.7852 (m100) REVERT: K 22 LEU cc_start: 0.8569 (mm) cc_final: 0.8116 (mm) REVERT: K 34 GLU cc_start: 0.8817 (pt0) cc_final: 0.8376 (pp20) REVERT: K 35 ASP cc_start: 0.8707 (m-30) cc_final: 0.8370 (m-30) REVERT: K 132 MET cc_start: 0.7346 (ppp) cc_final: 0.6822 (ppp) REVERT: K 199 ASP cc_start: 0.9028 (m-30) cc_final: 0.8827 (m-30) REVERT: K 245 TRP cc_start: 0.8093 (m100) cc_final: 0.7715 (m100) REVERT: K 270 LYS cc_start: 0.7760 (mmtm) cc_final: 0.7265 (tmtt) REVERT: L 63 TRP cc_start: 0.6053 (m100) cc_final: 0.5605 (m100) REVERT: L 226 TYR cc_start: 0.6943 (p90) cc_final: 0.5984 (p90) REVERT: L 244 LEU cc_start: 0.8535 (mt) cc_final: 0.8304 (mt) REVERT: L 254 LYS cc_start: 0.8503 (tmtt) cc_final: 0.7752 (tmtt) REVERT: L 268 ASP cc_start: 0.6996 (t0) cc_final: 0.6762 (t70) REVERT: L 269 VAL cc_start: 0.7842 (m) cc_final: 0.7632 (m) REVERT: M 15 TRP cc_start: 0.8314 (m-10) cc_final: 0.8056 (m-10) REVERT: M 16 HIS cc_start: 0.7763 (m-70) cc_final: 0.7219 (m-70) REVERT: M 18 ASP cc_start: 0.7730 (t70) cc_final: 0.7330 (t70) REVERT: M 22 LEU cc_start: 0.8036 (pp) cc_final: 0.7798 (pp) REVERT: M 39 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7902 (tm-30) REVERT: M 78 TRP cc_start: 0.6880 (m-90) cc_final: 0.6131 (m-90) REVERT: M 100 ARG cc_start: 0.8783 (ptp90) cc_final: 0.8477 (ptt-90) REVERT: M 101 VAL cc_start: 0.8955 (t) cc_final: 0.8742 (t) REVERT: M 109 MET cc_start: 0.8799 (tmm) cc_final: 0.8130 (ttt) REVERT: M 158 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7696 (tm-30) REVERT: M 159 THR cc_start: 0.8655 (m) cc_final: 0.8070 (p) REVERT: M 174 PHE cc_start: 0.7339 (t80) cc_final: 0.7011 (t80) REVERT: M 178 LEU cc_start: 0.8872 (mt) cc_final: 0.8207 (mt) REVERT: M 202 ILE cc_start: 0.8816 (mm) cc_final: 0.8549 (mm) REVERT: M 205 LYS cc_start: 0.9092 (mttm) cc_final: 0.8826 (mtpp) REVERT: M 206 GLU cc_start: 0.8588 (pt0) cc_final: 0.7965 (pt0) REVERT: M 207 GLN cc_start: 0.8584 (mm110) cc_final: 0.8241 (mm110) REVERT: M 209 ARG cc_start: 0.8800 (tmt170) cc_final: 0.8384 (ttp80) REVERT: M 224 CYS cc_start: 0.5431 (p) cc_final: 0.5122 (p) REVERT: N 23 HIS cc_start: 0.7758 (t70) cc_final: 0.7423 (t70) REVERT: N 102 GLN cc_start: 0.8720 (mp10) cc_final: 0.8378 (mp10) REVERT: N 104 MET cc_start: 0.8391 (ptm) cc_final: 0.7797 (ppp) REVERT: N 105 LYS cc_start: 0.9401 (mtmm) cc_final: 0.9100 (mttt) REVERT: N 154 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7568 (mm-30) REVERT: N 157 HIS cc_start: 0.8026 (m90) cc_final: 0.7681 (m90) REVERT: N 161 LYS cc_start: 0.8880 (ptpp) cc_final: 0.8483 (ptpp) REVERT: N 162 ASN cc_start: 0.8641 (m110) cc_final: 0.8372 (m110) REVERT: N 164 LEU cc_start: 0.8611 (mt) cc_final: 0.8385 (mt) REVERT: N 165 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8092 (mm-30) REVERT: N 183 ILE cc_start: 0.7212 (mt) cc_final: 0.6971 (mt) REVERT: N 203 PHE cc_start: 0.8112 (t80) cc_final: 0.7805 (t80) REVERT: N 210 ILE cc_start: 0.8496 (pt) cc_final: 0.8134 (pt) REVERT: N 213 GLN cc_start: 0.8815 (mt0) cc_final: 0.8164 (mt0) REVERT: N 224 CYS cc_start: 0.8027 (p) cc_final: 0.7628 (p) REVERT: N 233 HIS cc_start: 0.7730 (m90) cc_final: 0.7416 (m-70) REVERT: N 243 VAL cc_start: 0.8594 (t) cc_final: 0.7770 (p) REVERT: N 256 ARG cc_start: 0.8449 (ttm110) cc_final: 0.7809 (ttm110) REVERT: N 270 LYS cc_start: 0.7914 (mptt) cc_final: 0.7200 (mmtm) REVERT: O 23 HIS cc_start: 0.7843 (t70) cc_final: 0.7296 (t70) REVERT: O 48 MET cc_start: -0.1542 (ppp) cc_final: -0.1934 (ppp) REVERT: O 62 HIS cc_start: 0.7650 (m-70) cc_final: 0.7230 (m-70) REVERT: O 104 MET cc_start: 0.8171 (pmm) cc_final: 0.7857 (pmm) REVERT: O 110 PHE cc_start: 0.8196 (m-80) cc_final: 0.7486 (m-80) REVERT: O 132 MET cc_start: 0.8055 (tmm) cc_final: 0.7588 (tmm) REVERT: O 155 ARG cc_start: 0.9170 (mtm110) cc_final: 0.8855 (ptp-110) REVERT: O 199 ASP cc_start: 0.8669 (m-30) cc_final: 0.8280 (m-30) REVERT: O 209 ARG cc_start: 0.8854 (ptm-80) cc_final: 0.8557 (ptm-80) REVERT: P 62 HIS cc_start: 0.7892 (t70) cc_final: 0.7299 (t70) REVERT: P 87 TYR cc_start: 0.8546 (t80) cc_final: 0.8327 (t80) REVERT: P 104 MET cc_start: 0.9143 (mmp) cc_final: 0.8644 (mmp) REVERT: P 106 TRP cc_start: 0.8412 (t60) cc_final: 0.7972 (t60) REVERT: P 115 LEU cc_start: 0.4860 (tp) cc_final: 0.4583 (tp) REVERT: P 170 MET cc_start: 0.7842 (mtt) cc_final: 0.7346 (mpp) REVERT: P 172 ASN cc_start: 0.8834 (m-40) cc_final: 0.8502 (p0) REVERT: P 207 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7917 (mm-40) REVERT: P 222 ARG cc_start: 0.6752 (mmm-85) cc_final: 0.5999 (mmm160) REVERT: P 223 PHE cc_start: 0.6871 (m-80) cc_final: 0.5741 (m-80) REVERT: P 233 HIS cc_start: 0.6695 (m-70) cc_final: 0.6461 (m-70) REVERT: P 238 GLN cc_start: 0.6970 (mp10) cc_final: 0.6709 (mp10) REVERT: P 272 ILE cc_start: 0.8102 (mm) cc_final: 0.7790 (mm) outliers start: 1 outliers final: 0 residues processed: 1200 average time/residue: 0.4814 time to fit residues: 897.4483 Evaluate side-chains 1117 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1117 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 372 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 360 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 347 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 377 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 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 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 102 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** D 158 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN G 102 GLN G 208 GLN H 157 HIS J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN N 242 GLN O 208 GLN O 211 GLN P 157 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.191597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.145342 restraints weight = 72623.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.150720 restraints weight = 45054.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154480 restraints weight = 31452.990| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34119 Z= 0.166 Angle : 0.685 12.989 46515 Z= 0.366 Chirality : 0.048 0.239 5006 Planarity : 0.005 0.064 5714 Dihedral : 14.762 173.640 5007 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 3851 helix: 0.97 (0.12), residues: 1882 sheet: -0.76 (0.18), residues: 811 loop : -1.78 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P 78 HIS 0.014 0.001 HIS E 157 PHE 0.043 0.002 PHE H 201 TYR 0.027 0.002 TYR F 225 ARG 0.009 0.001 ARG K 222 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 1746) hydrogen bonds : angle 5.28506 ( 5114) covalent geometry : bond 0.00348 (34119) covalent geometry : angle 0.68538 (46515) *********************** 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 1207 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1203 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7998 (t0) cc_final: 0.7779 (t0) REVERT: A 73 LYS cc_start: 0.7306 (mttp) cc_final: 0.6947 (mtmt) REVERT: A 79 VAL cc_start: 0.8146 (t) cc_final: 0.7694 (p) REVERT: A 80 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6536 (tm-30) REVERT: A 92 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8537 (mtpp) REVERT: A 97 GLN cc_start: 0.7674 (pm20) cc_final: 0.6987 (pm20) REVERT: A 98 GLU cc_start: 0.8173 (mp0) cc_final: 0.7716 (mp0) REVERT: A 104 MET cc_start: 0.8427 (ttm) cc_final: 0.7717 (ttm) REVERT: A 105 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8793 (mtpp) REVERT: A 113 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7802 (mmmm) REVERT: A 116 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 118 ASP cc_start: 0.7671 (p0) cc_final: 0.7410 (p0) REVERT: A 129 GLN cc_start: 0.8246 (tt0) cc_final: 0.7969 (tt0) REVERT: A 132 MET cc_start: 0.7843 (mmm) cc_final: 0.7522 (mmm) REVERT: A 135 LEU cc_start: 0.9153 (mt) cc_final: 0.8867 (mt) REVERT: A 155 ARG cc_start: 0.8331 (tpt90) cc_final: 0.7571 (mmm160) REVERT: A 158 GLN cc_start: 0.8641 (tt0) cc_final: 0.8113 (tt0) REVERT: A 161 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8324 (tptt) REVERT: A 164 LEU cc_start: 0.8470 (mt) cc_final: 0.8107 (mt) REVERT: A 183 ILE cc_start: 0.9020 (mt) cc_final: 0.8606 (mm) REVERT: A 190 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7229 (mtpt) REVERT: A 203 PHE cc_start: 0.8261 (t80) cc_final: 0.7806 (t80) REVERT: A 211 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7790 (tp-100) REVERT: A 254 LYS cc_start: 0.8016 (pptt) cc_final: 0.7501 (pptt) REVERT: A 260 ARG cc_start: 0.7416 (ptm160) cc_final: 0.7184 (ptm160) REVERT: B 13 ASN cc_start: 0.7386 (m110) cc_final: 0.7178 (m110) REVERT: B 15 TRP cc_start: 0.7851 (m100) cc_final: 0.7266 (m100) REVERT: B 40 CYS cc_start: 0.7673 (t) cc_final: 0.6976 (p) REVERT: B 63 TRP cc_start: 0.7874 (m100) cc_final: 0.6305 (m100) REVERT: B 64 GLN cc_start: 0.7081 (tp40) cc_final: 0.6474 (mp10) REVERT: B 86 ILE cc_start: 0.8740 (pt) cc_final: 0.8210 (mm) REVERT: B 89 GLU cc_start: 0.7671 (tt0) cc_final: 0.7075 (tt0) REVERT: B 90 ARG cc_start: 0.8577 (tpt-90) cc_final: 0.8227 (tpp80) REVERT: B 102 GLN cc_start: 0.8643 (mp10) cc_final: 0.8273 (mm-40) REVERT: B 104 MET cc_start: 0.8836 (mmp) cc_final: 0.8192 (mmp) REVERT: B 106 TRP cc_start: 0.8561 (t60) cc_final: 0.8283 (t60) REVERT: B 129 GLN cc_start: 0.8609 (pt0) cc_final: 0.8176 (pt0) REVERT: B 131 LEU cc_start: 0.8966 (tt) cc_final: 0.8425 (tt) REVERT: B 132 MET cc_start: 0.8794 (mmp) cc_final: 0.7960 (mmp) REVERT: B 137 ILE cc_start: 0.8578 (tt) cc_final: 0.8342 (tt) REVERT: B 138 GLU cc_start: 0.7922 (tp30) cc_final: 0.7680 (tp30) REVERT: B 139 HIS cc_start: 0.8602 (t70) cc_final: 0.8129 (t70) REVERT: B 175 GLU cc_start: 0.8645 (pm20) cc_final: 0.8309 (mp0) REVERT: B 178 LEU cc_start: 0.9123 (mm) cc_final: 0.8684 (mm) REVERT: B 186 ASN cc_start: 0.8206 (m-40) cc_final: 0.7877 (m-40) REVERT: B 198 MET cc_start: 0.8104 (tpt) cc_final: 0.7597 (tpp) REVERT: B 204 ASN cc_start: 0.7781 (p0) cc_final: 0.7431 (p0) REVERT: B 205 LYS cc_start: 0.8489 (tptp) cc_final: 0.8284 (tppp) REVERT: B 208 GLN cc_start: 0.8216 (pt0) cc_final: 0.7745 (pt0) REVERT: C 7 LEU cc_start: 0.8586 (tt) cc_final: 0.8167 (tt) REVERT: C 11 GLU cc_start: 0.8592 (tp30) cc_final: 0.7494 (tp30) REVERT: C 28 ILE cc_start: 0.8169 (tp) cc_final: 0.7933 (tp) REVERT: C 30 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8561 (ttp80) REVERT: C 36 ILE cc_start: 0.9046 (mm) cc_final: 0.8837 (mm) REVERT: C 38 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7987 (tm-30) REVERT: C 39 GLN cc_start: 0.8485 (tp40) cc_final: 0.7725 (tp40) REVERT: C 40 CYS cc_start: 0.8555 (m) cc_final: 0.7314 (t) REVERT: C 62 HIS cc_start: 0.7672 (t70) cc_final: 0.7450 (t70) REVERT: C 110 PHE cc_start: 0.7907 (m-80) cc_final: 0.7503 (m-80) REVERT: C 132 MET cc_start: 0.8447 (ppp) cc_final: 0.8215 (ppp) REVERT: C 162 ASN cc_start: 0.8839 (m-40) cc_final: 0.8467 (m-40) REVERT: C 186 ASN cc_start: 0.8103 (m-40) cc_final: 0.7862 (m110) REVERT: C 198 MET cc_start: 0.8426 (tpt) cc_final: 0.7875 (tpt) REVERT: C 202 ILE cc_start: 0.8259 (mt) cc_final: 0.7781 (mt) REVERT: C 206 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: C 233 HIS cc_start: 0.4617 (p90) cc_final: 0.4334 (p90) REVERT: C 245 TRP cc_start: 0.8283 (m-90) cc_final: 0.8041 (m-90) REVERT: C 270 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8115 (tmtt) REVERT: D 63 TRP cc_start: 0.6471 (m100) cc_final: 0.5910 (m100) REVERT: D 154 GLU cc_start: 0.6484 (mp0) cc_final: 0.6250 (pm20) REVERT: D 205 LYS cc_start: 0.8434 (mmpt) cc_final: 0.8157 (tppt) REVERT: D 209 ARG cc_start: 0.8674 (mmp-170) cc_final: 0.8456 (mmp-170) REVERT: D 218 GLN cc_start: 0.8425 (mm110) cc_final: 0.7913 (mm110) REVERT: D 223 PHE cc_start: 0.6196 (p90) cc_final: 0.5779 (p90) REVERT: D 226 TYR cc_start: 0.7072 (p90) cc_final: 0.6052 (p90) REVERT: D 254 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7912 (ttmm) REVERT: D 262 LEU cc_start: 0.8321 (mm) cc_final: 0.8048 (mm) REVERT: D 266 ASN cc_start: 0.8696 (m110) cc_final: 0.8230 (m110) REVERT: E 7 LEU cc_start: 0.8457 (tt) cc_final: 0.7928 (tt) REVERT: E 12 HIS cc_start: 0.8541 (t70) cc_final: 0.7323 (t70) REVERT: E 15 TRP cc_start: 0.8390 (m-10) cc_final: 0.8081 (m-10) REVERT: E 16 HIS cc_start: 0.7992 (m-70) cc_final: 0.7446 (m170) REVERT: E 18 ASP cc_start: 0.7976 (t70) cc_final: 0.7634 (t70) REVERT: E 132 MET cc_start: 0.6841 (mmm) cc_final: 0.6536 (mmm) REVERT: E 150 GLN cc_start: 0.7918 (mm110) cc_final: 0.7494 (mm110) REVERT: E 154 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8507 (mm-30) REVERT: E 158 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7575 (tm-30) REVERT: E 159 THR cc_start: 0.8348 (m) cc_final: 0.7721 (p) REVERT: E 178 LEU cc_start: 0.8876 (mt) cc_final: 0.8584 (mt) REVERT: E 206 GLU cc_start: 0.8638 (pt0) cc_final: 0.7504 (pp20) REVERT: E 209 ARG cc_start: 0.8618 (tmt170) cc_final: 0.8274 (ttp80) REVERT: E 236 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8430 (mm-30) REVERT: E 270 LYS cc_start: 0.8325 (mtmt) cc_final: 0.8115 (mtmt) REVERT: F 23 HIS cc_start: 0.7842 (t70) cc_final: 0.7435 (t70) REVERT: F 82 ASN cc_start: 0.8530 (m-40) cc_final: 0.8086 (m-40) REVERT: F 89 GLU cc_start: 0.6668 (tp30) cc_final: 0.6372 (tp30) REVERT: F 104 MET cc_start: 0.8083 (ptm) cc_final: 0.7583 (ppp) REVERT: F 105 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8943 (mttt) REVERT: F 129 GLN cc_start: 0.8243 (mt0) cc_final: 0.7930 (mt0) REVERT: F 131 LEU cc_start: 0.8625 (tp) cc_final: 0.8420 (mm) REVERT: F 154 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8195 (mm-30) REVERT: F 157 HIS cc_start: 0.7835 (m90) cc_final: 0.7571 (m90) REVERT: F 183 ILE cc_start: 0.6311 (mt) cc_final: 0.6093 (mt) REVERT: F 199 ASP cc_start: 0.8261 (m-30) cc_final: 0.8054 (m-30) REVERT: F 202 ILE cc_start: 0.8629 (mt) cc_final: 0.8123 (mt) REVERT: F 204 ASN cc_start: 0.8768 (p0) cc_final: 0.8414 (p0) REVERT: F 205 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8487 (mtmt) REVERT: F 224 CYS cc_start: 0.8132 (p) cc_final: 0.7796 (p) REVERT: F 230 LYS cc_start: 0.8451 (mmmt) cc_final: 0.8012 (mmmm) REVERT: F 233 HIS cc_start: 0.7826 (m-70) cc_final: 0.7555 (m-70) REVERT: F 242 GLN cc_start: 0.7740 (tt0) cc_final: 0.7125 (pp30) REVERT: F 243 VAL cc_start: 0.8502 (t) cc_final: 0.7904 (m) REVERT: F 244 LEU cc_start: 0.8285 (tt) cc_final: 0.7995 (tt) REVERT: G 7 LEU cc_start: 0.3890 (mp) cc_final: 0.3633 (tt) REVERT: G 48 MET cc_start: -0.0557 (ppp) cc_final: -0.1315 (ppp) REVERT: G 62 HIS cc_start: 0.7634 (t70) cc_final: 0.7011 (t70) REVERT: G 71 GLU cc_start: 0.7624 (tp30) cc_final: 0.7067 (tp30) REVERT: G 104 MET cc_start: 0.8077 (pmm) cc_final: 0.7831 (pmm) REVERT: G 106 TRP cc_start: 0.7401 (t60) cc_final: 0.7175 (t60) REVERT: G 131 LEU cc_start: 0.9324 (mt) cc_final: 0.9050 (mt) REVERT: G 154 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8673 (pp20) REVERT: G 168 ILE cc_start: 0.7838 (mt) cc_final: 0.7581 (pt) REVERT: G 171 PHE cc_start: 0.7078 (m-80) cc_final: 0.6558 (m-80) REVERT: G 175 GLU cc_start: 0.8684 (pm20) cc_final: 0.8270 (mp0) REVERT: G 197 PRO cc_start: 0.8273 (Cg_exo) cc_final: 0.8042 (Cg_endo) REVERT: G 201 PHE cc_start: 0.8439 (t80) cc_final: 0.8036 (t80) REVERT: G 207 GLN cc_start: 0.8477 (mp10) cc_final: 0.8256 (pt0) REVERT: G 209 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8297 (ttp80) REVERT: G 210 ILE cc_start: 0.8571 (pt) cc_final: 0.7940 (pt) REVERT: H 62 HIS cc_start: 0.7916 (t70) cc_final: 0.7200 (t70) REVERT: H 78 TRP cc_start: 0.7279 (m-10) cc_final: 0.6918 (m-10) REVERT: H 85 LEU cc_start: 0.8739 (tp) cc_final: 0.8388 (tp) REVERT: H 87 TYR cc_start: 0.8460 (t80) cc_final: 0.7843 (t80) REVERT: H 101 VAL cc_start: 0.8812 (p) cc_final: 0.8549 (p) REVERT: H 104 MET cc_start: 0.9120 (mmp) cc_final: 0.8426 (mmp) REVERT: H 106 TRP cc_start: 0.8379 (t60) cc_final: 0.7816 (t60) REVERT: H 109 MET cc_start: 0.7470 (mmp) cc_final: 0.7007 (mmm) REVERT: H 110 PHE cc_start: 0.7918 (m-10) cc_final: 0.7717 (m-10) REVERT: H 199 ASP cc_start: 0.7927 (m-30) cc_final: 0.7400 (m-30) REVERT: H 202 ILE cc_start: 0.9118 (mm) cc_final: 0.8893 (mm) REVERT: H 205 LYS cc_start: 0.8456 (mttp) cc_final: 0.7977 (mtmt) REVERT: H 207 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7783 (mm-40) REVERT: H 222 ARG cc_start: 0.6873 (mmm-85) cc_final: 0.6222 (mmm160) REVERT: H 223 PHE cc_start: 0.7044 (m-10) cc_final: 0.6289 (m-80) REVERT: H 256 ARG cc_start: 0.8156 (ppt170) cc_final: 0.7637 (ppt170) REVERT: H 270 LYS cc_start: 0.7658 (mmpt) cc_final: 0.7283 (mmtm) REVERT: I 60 ILE cc_start: 0.8794 (mt) cc_final: 0.8378 (mm) REVERT: I 62 HIS cc_start: 0.7822 (t70) cc_final: 0.7614 (t-90) REVERT: I 64 GLN cc_start: 0.6510 (pm20) cc_final: 0.5941 (pm20) REVERT: I 79 VAL cc_start: 0.8216 (t) cc_final: 0.7797 (p) REVERT: I 86 ILE cc_start: 0.8582 (pt) cc_final: 0.8252 (tp) REVERT: I 92 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8505 (mtpp) REVERT: I 97 GLN cc_start: 0.8023 (pm20) cc_final: 0.7669 (pm20) REVERT: I 100 ARG cc_start: 0.8323 (mtt90) cc_final: 0.7784 (mtm-85) REVERT: I 105 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8259 (mtmm) REVERT: I 113 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7742 (mmmm) REVERT: I 146 ASN cc_start: 0.8226 (t0) cc_final: 0.7904 (m-40) REVERT: I 152 LEU cc_start: 0.7388 (pt) cc_final: 0.6223 (mp) REVERT: I 155 ARG cc_start: 0.8291 (tpt90) cc_final: 0.7362 (mmm160) REVERT: I 158 GLN cc_start: 0.9105 (tt0) cc_final: 0.8472 (tt0) REVERT: I 163 THR cc_start: 0.8537 (m) cc_final: 0.8166 (p) REVERT: I 164 LEU cc_start: 0.8610 (mt) cc_final: 0.8376 (mt) REVERT: I 190 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7720 (mtpp) REVERT: I 203 PHE cc_start: 0.8312 (t80) cc_final: 0.8083 (t80) REVERT: I 207 GLN cc_start: 0.8232 (mm110) cc_final: 0.7755 (tp40) REVERT: I 211 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7913 (tp40) REVERT: I 238 GLN cc_start: 0.6607 (mt0) cc_final: 0.6404 (mt0) REVERT: I 244 LEU cc_start: 0.8596 (mt) cc_final: 0.8379 (mt) REVERT: I 251 ILE cc_start: 0.7984 (pt) cc_final: 0.7576 (mp) REVERT: J 13 ASN cc_start: 0.7693 (m-40) cc_final: 0.7468 (m110) REVERT: J 15 TRP cc_start: 0.8023 (m100) cc_final: 0.7450 (m100) REVERT: J 40 CYS cc_start: 0.7354 (t) cc_final: 0.6804 (p) REVERT: J 63 TRP cc_start: 0.7784 (m100) cc_final: 0.6038 (m100) REVERT: J 86 ILE cc_start: 0.8891 (pt) cc_final: 0.8298 (mm) REVERT: J 92 LYS cc_start: 0.8900 (tptp) cc_final: 0.8552 (tptp) REVERT: J 103 THR cc_start: 0.8807 (t) cc_final: 0.8455 (p) REVERT: J 104 MET cc_start: 0.8582 (mmt) cc_final: 0.8094 (mmt) REVERT: J 106 TRP cc_start: 0.8654 (t60) cc_final: 0.8341 (t60) REVERT: J 131 LEU cc_start: 0.8782 (tt) cc_final: 0.8272 (tt) REVERT: J 132 MET cc_start: 0.8725 (mmp) cc_final: 0.8419 (mmt) REVERT: J 137 ILE cc_start: 0.8442 (tt) cc_final: 0.7739 (tt) REVERT: J 139 HIS cc_start: 0.8638 (t70) cc_final: 0.8198 (t70) REVERT: J 150 GLN cc_start: 0.7803 (pt0) cc_final: 0.7524 (pt0) REVERT: J 162 ASN cc_start: 0.8915 (m110) cc_final: 0.8682 (m-40) REVERT: J 204 ASN cc_start: 0.8401 (m110) cc_final: 0.7956 (m110) REVERT: J 205 LYS cc_start: 0.8571 (tptp) cc_final: 0.8166 (tptp) REVERT: J 208 GLN cc_start: 0.8308 (pt0) cc_final: 0.7833 (pt0) REVERT: K 25 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8180 (tm-30) REVERT: K 34 GLU cc_start: 0.8800 (pt0) cc_final: 0.8385 (pp20) REVERT: K 35 ASP cc_start: 0.8716 (m-30) cc_final: 0.8357 (m-30) REVERT: K 39 GLN cc_start: 0.8528 (tp40) cc_final: 0.8023 (tp40) REVERT: K 132 MET cc_start: 0.7559 (ppp) cc_final: 0.7285 (ppp) REVERT: K 162 ASN cc_start: 0.8884 (m110) cc_final: 0.8625 (m-40) REVERT: K 245 TRP cc_start: 0.8202 (m100) cc_final: 0.7687 (m100) REVERT: K 270 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7406 (tmtt) REVERT: L 226 TYR cc_start: 0.6991 (p90) cc_final: 0.6123 (p90) REVERT: L 244 LEU cc_start: 0.8505 (mt) cc_final: 0.8288 (mt) REVERT: L 254 LYS cc_start: 0.8451 (tmtt) cc_final: 0.7711 (tmtt) REVERT: L 268 ASP cc_start: 0.6949 (t0) cc_final: 0.6701 (t70) REVERT: L 269 VAL cc_start: 0.7815 (m) cc_final: 0.7600 (m) REVERT: M 16 HIS cc_start: 0.7694 (m-70) cc_final: 0.6301 (m-70) REVERT: M 18 ASP cc_start: 0.7744 (t70) cc_final: 0.7287 (t70) REVERT: M 25 GLU cc_start: 0.8443 (tt0) cc_final: 0.8061 (tt0) REVERT: M 36 ILE cc_start: 0.8530 (mt) cc_final: 0.8277 (mt) REVERT: M 39 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7824 (tm-30) REVERT: M 78 TRP cc_start: 0.6290 (m-90) cc_final: 0.5971 (m-90) REVERT: M 89 GLU cc_start: 0.6943 (pm20) cc_final: 0.6644 (mp0) REVERT: M 109 MET cc_start: 0.8777 (tmm) cc_final: 0.8192 (ttt) REVERT: M 154 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8664 (mm-30) REVERT: M 158 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7551 (tm-30) REVERT: M 159 THR cc_start: 0.8648 (m) cc_final: 0.7961 (p) REVERT: M 174 PHE cc_start: 0.7386 (t80) cc_final: 0.7070 (t80) REVERT: M 178 LEU cc_start: 0.8843 (mt) cc_final: 0.8241 (mt) REVERT: M 205 LYS cc_start: 0.9086 (mttm) cc_final: 0.8804 (mtpp) REVERT: M 207 GLN cc_start: 0.8498 (mm110) cc_final: 0.8128 (mm110) REVERT: M 209 ARG cc_start: 0.8745 (tmt170) cc_final: 0.8356 (ttp80) REVERT: M 224 CYS cc_start: 0.5919 (p) cc_final: 0.5473 (p) REVERT: N 23 HIS cc_start: 0.7790 (t70) cc_final: 0.7482 (t70) REVERT: N 104 MET cc_start: 0.8393 (ptm) cc_final: 0.7695 (ppp) REVERT: N 157 HIS cc_start: 0.8045 (m90) cc_final: 0.7641 (m90) REVERT: N 158 GLN cc_start: 0.9012 (mp10) cc_final: 0.8758 (mp10) REVERT: N 161 LYS cc_start: 0.8937 (ptpp) cc_final: 0.8615 (ptpp) REVERT: N 162 ASN cc_start: 0.8839 (m110) cc_final: 0.8493 (m110) REVERT: N 164 LEU cc_start: 0.8674 (mt) cc_final: 0.8446 (mt) REVERT: N 165 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8049 (mm-30) REVERT: N 183 ILE cc_start: 0.7324 (mt) cc_final: 0.7090 (mt) REVERT: N 203 PHE cc_start: 0.8061 (t80) cc_final: 0.7740 (t80) REVERT: N 210 ILE cc_start: 0.8505 (pt) cc_final: 0.8155 (pt) REVERT: N 213 GLN cc_start: 0.8805 (mt0) cc_final: 0.8115 (mt0) REVERT: N 224 CYS cc_start: 0.8098 (p) cc_final: 0.7767 (p) REVERT: N 233 HIS cc_start: 0.7760 (m90) cc_final: 0.7293 (m90) REVERT: N 256 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7774 (ttm110) REVERT: N 260 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7333 (ptp-110) REVERT: N 267 LYS cc_start: 0.9011 (ptpt) cc_final: 0.8571 (pttt) REVERT: N 270 LYS cc_start: 0.7964 (mptt) cc_final: 0.7541 (mptt) REVERT: O 23 HIS cc_start: 0.7740 (t70) cc_final: 0.7495 (t70) REVERT: O 48 MET cc_start: -0.1739 (ppp) cc_final: -0.2188 (ppp) REVERT: O 62 HIS cc_start: 0.7669 (m-70) cc_final: 0.7047 (m-70) REVERT: O 110 PHE cc_start: 0.8267 (m-80) cc_final: 0.7504 (m-10) REVERT: O 132 MET cc_start: 0.8121 (tmm) cc_final: 0.7591 (tmm) REVERT: O 155 ARG cc_start: 0.9217 (mtm110) cc_final: 0.8777 (ptp-110) REVERT: O 209 ARG cc_start: 0.8861 (ptm-80) cc_final: 0.8660 (ptm-80) REVERT: P 62 HIS cc_start: 0.7914 (t70) cc_final: 0.7295 (t70) REVERT: P 87 TYR cc_start: 0.8532 (t80) cc_final: 0.8263 (t80) REVERT: P 104 MET cc_start: 0.9109 (mmp) cc_final: 0.8569 (mmp) REVERT: P 106 TRP cc_start: 0.8392 (t60) cc_final: 0.7958 (t60) REVERT: P 115 LEU cc_start: 0.5229 (tp) cc_final: 0.5002 (tp) REVERT: P 170 MET cc_start: 0.7826 (mtt) cc_final: 0.7314 (mpp) REVERT: P 172 ASN cc_start: 0.8847 (m-40) cc_final: 0.8513 (p0) REVERT: P 207 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7637 (mm-40) REVERT: P 222 ARG cc_start: 0.6625 (mmm-85) cc_final: 0.6011 (mmm160) REVERT: P 223 PHE cc_start: 0.6868 (m-80) cc_final: 0.5698 (m-80) REVERT: P 233 HIS cc_start: 0.6820 (m-70) cc_final: 0.6573 (m-70) REVERT: P 238 GLN cc_start: 0.7136 (mp10) cc_final: 0.6713 (mp10) REVERT: P 254 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8203 (mmmt) REVERT: P 270 LYS cc_start: 0.7608 (mptt) cc_final: 0.7396 (mmtm) REVERT: P 272 ILE cc_start: 0.8145 (mm) cc_final: 0.7848 (mm) outliers start: 4 outliers final: 2 residues processed: 1205 average time/residue: 0.5006 time to fit residues: 944.3753 Evaluate side-chains 1117 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1114 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 120 optimal weight: 0.0030 chunk 130 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 203 optimal weight: 0.5980 chunk 277 optimal weight: 0.9990 chunk 322 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 301 optimal weight: 0.7980 chunk 290 optimal weight: 2.9990 chunk 333 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN B 150 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN G 208 GLN G 211 GLN H 69 HIS ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN L 266 ASN M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 GLN O 208 GLN P 157 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.192322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.145836 restraints weight = 72665.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151309 restraints weight = 44925.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155126 restraints weight = 31270.386| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34119 Z= 0.146 Angle : 0.690 13.105 46515 Z= 0.367 Chirality : 0.048 0.292 5006 Planarity : 0.004 0.063 5714 Dihedral : 14.775 173.914 5007 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 3851 helix: 0.96 (0.12), residues: 1873 sheet: -0.73 (0.18), residues: 806 loop : -1.78 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP M 15 HIS 0.015 0.001 HIS G 157 PHE 0.030 0.002 PHE D 203 TYR 0.025 0.001 TYR N 134 ARG 0.018 0.001 ARG F 155 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 1746) hydrogen bonds : angle 5.27031 ( 5114) covalent geometry : bond 0.00309 (34119) covalent geometry : angle 0.68960 (46515) *********************** 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 1194 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1194 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8009 (t0) cc_final: 0.7790 (t0) REVERT: A 79 VAL cc_start: 0.8138 (t) cc_final: 0.7447 (p) REVERT: A 80 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6526 (tm-30) REVERT: A 85 LEU cc_start: 0.8078 (tt) cc_final: 0.7805 (tt) REVERT: A 92 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8528 (mtpp) REVERT: A 97 GLN cc_start: 0.7674 (pm20) cc_final: 0.6982 (pm20) REVERT: A 98 GLU cc_start: 0.8032 (mp0) cc_final: 0.7572 (mp0) REVERT: A 104 MET cc_start: 0.8573 (ttm) cc_final: 0.7879 (ttm) REVERT: A 105 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8818 (mtpp) REVERT: A 113 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7848 (mmmm) REVERT: A 116 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6865 (tm-30) REVERT: A 118 ASP cc_start: 0.7659 (p0) cc_final: 0.7379 (p0) REVERT: A 129 GLN cc_start: 0.8276 (tt0) cc_final: 0.8070 (tt0) REVERT: A 132 MET cc_start: 0.7572 (mmm) cc_final: 0.7363 (mmm) REVERT: A 152 LEU cc_start: 0.7506 (pt) cc_final: 0.6416 (mp) REVERT: A 153 VAL cc_start: 0.9014 (m) cc_final: 0.8784 (m) REVERT: A 155 ARG cc_start: 0.8291 (tpt90) cc_final: 0.7505 (mmm160) REVERT: A 158 GLN cc_start: 0.8619 (tt0) cc_final: 0.8079 (tt0) REVERT: A 161 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8254 (tppt) REVERT: A 164 LEU cc_start: 0.8440 (mt) cc_final: 0.8167 (mt) REVERT: A 183 ILE cc_start: 0.9012 (mt) cc_final: 0.8746 (mt) REVERT: A 190 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7217 (mtpp) REVERT: A 203 PHE cc_start: 0.8239 (t80) cc_final: 0.7759 (t80) REVERT: A 244 LEU cc_start: 0.8594 (mt) cc_final: 0.8383 (mt) REVERT: A 254 LYS cc_start: 0.7953 (pptt) cc_final: 0.7476 (pptt) REVERT: A 260 ARG cc_start: 0.7387 (ptm160) cc_final: 0.7129 (ptm160) REVERT: B 7 LEU cc_start: 0.8139 (mt) cc_final: 0.7928 (mt) REVERT: B 13 ASN cc_start: 0.7397 (m110) cc_final: 0.6976 (m110) REVERT: B 15 TRP cc_start: 0.7850 (m100) cc_final: 0.7229 (m100) REVERT: B 40 CYS cc_start: 0.7666 (t) cc_final: 0.6969 (p) REVERT: B 63 TRP cc_start: 0.7798 (m100) cc_final: 0.6408 (m100) REVERT: B 64 GLN cc_start: 0.6958 (tp40) cc_final: 0.6479 (mp10) REVERT: B 86 ILE cc_start: 0.8676 (pt) cc_final: 0.8248 (mm) REVERT: B 89 GLU cc_start: 0.7908 (tt0) cc_final: 0.7225 (tt0) REVERT: B 90 ARG cc_start: 0.8625 (tpt-90) cc_final: 0.8164 (tpp80) REVERT: B 100 ARG cc_start: 0.8733 (mtt180) cc_final: 0.8253 (mtt180) REVERT: B 102 GLN cc_start: 0.8798 (mp10) cc_final: 0.8306 (mm-40) REVERT: B 104 MET cc_start: 0.8821 (mmp) cc_final: 0.8245 (mmp) REVERT: B 106 TRP cc_start: 0.8589 (t60) cc_final: 0.8295 (t60) REVERT: B 129 GLN cc_start: 0.8598 (pt0) cc_final: 0.8146 (pt0) REVERT: B 131 LEU cc_start: 0.8914 (tt) cc_final: 0.8485 (tt) REVERT: B 132 MET cc_start: 0.8776 (mmp) cc_final: 0.7912 (mmp) REVERT: B 138 GLU cc_start: 0.7847 (tp30) cc_final: 0.7604 (tp30) REVERT: B 139 HIS cc_start: 0.8579 (t70) cc_final: 0.8127 (t70) REVERT: B 175 GLU cc_start: 0.8561 (pm20) cc_final: 0.8174 (mp0) REVERT: B 178 LEU cc_start: 0.9139 (mm) cc_final: 0.8801 (mm) REVERT: B 182 LEU cc_start: 0.8532 (mt) cc_final: 0.8281 (mt) REVERT: B 186 ASN cc_start: 0.8330 (m-40) cc_final: 0.8015 (m-40) REVERT: B 198 MET cc_start: 0.8143 (tpt) cc_final: 0.7683 (tpp) REVERT: B 204 ASN cc_start: 0.7891 (p0) cc_final: 0.7594 (p0) REVERT: B 205 LYS cc_start: 0.8434 (tptp) cc_final: 0.8227 (tppp) REVERT: B 208 GLN cc_start: 0.8252 (pt0) cc_final: 0.7742 (pt0) REVERT: C 7 LEU cc_start: 0.8587 (tt) cc_final: 0.8167 (tt) REVERT: C 11 GLU cc_start: 0.8621 (tp30) cc_final: 0.7579 (tp30) REVERT: C 25 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 28 ILE cc_start: 0.8143 (tp) cc_final: 0.7934 (tp) REVERT: C 36 ILE cc_start: 0.9043 (mm) cc_final: 0.8829 (mm) REVERT: C 38 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 39 GLN cc_start: 0.8444 (tp40) cc_final: 0.7717 (tp40) REVERT: C 40 CYS cc_start: 0.8536 (m) cc_final: 0.7278 (t) REVERT: C 110 PHE cc_start: 0.7793 (m-80) cc_final: 0.7484 (m-80) REVERT: C 132 MET cc_start: 0.8333 (ppp) cc_final: 0.8103 (ppp) REVERT: C 233 HIS cc_start: 0.4836 (p90) cc_final: 0.4534 (p90) REVERT: D 63 TRP cc_start: 0.6159 (m100) cc_final: 0.5676 (m100) REVERT: D 218 GLN cc_start: 0.8458 (mm110) cc_final: 0.7892 (mm110) REVERT: D 226 TYR cc_start: 0.7032 (p90) cc_final: 0.6119 (p90) REVERT: D 254 LYS cc_start: 0.8438 (ttmm) cc_final: 0.7978 (ttmm) REVERT: D 262 LEU cc_start: 0.8316 (mm) cc_final: 0.8045 (mm) REVERT: D 266 ASN cc_start: 0.8557 (m110) cc_final: 0.8135 (m110) REVERT: E 7 LEU cc_start: 0.8463 (tt) cc_final: 0.7814 (tt) REVERT: E 12 HIS cc_start: 0.8462 (t70) cc_final: 0.7220 (t70) REVERT: E 15 TRP cc_start: 0.8353 (m-10) cc_final: 0.8112 (m-10) REVERT: E 16 HIS cc_start: 0.7944 (m-70) cc_final: 0.7430 (m170) REVERT: E 18 ASP cc_start: 0.7971 (t70) cc_final: 0.7673 (t70) REVERT: E 89 GLU cc_start: 0.7926 (pm20) cc_final: 0.6823 (mp0) REVERT: E 103 THR cc_start: 0.8942 (t) cc_final: 0.8654 (p) REVERT: E 150 GLN cc_start: 0.7880 (mm110) cc_final: 0.7465 (mm110) REVERT: E 154 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8639 (mm-30) REVERT: E 158 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 159 THR cc_start: 0.8335 (m) cc_final: 0.7662 (p) REVERT: E 178 LEU cc_start: 0.8870 (mt) cc_final: 0.8566 (mt) REVERT: E 201 PHE cc_start: 0.8232 (t80) cc_final: 0.7872 (t80) REVERT: E 202 ILE cc_start: 0.8670 (mm) cc_final: 0.8371 (mm) REVERT: E 205 LYS cc_start: 0.8803 (mttt) cc_final: 0.8552 (mmtp) REVERT: E 206 GLU cc_start: 0.8440 (pt0) cc_final: 0.7544 (pt0) REVERT: F 23 HIS cc_start: 0.7865 (t70) cc_final: 0.7477 (t70) REVERT: F 75 ILE cc_start: 0.7238 (mm) cc_final: 0.7027 (mm) REVERT: F 82 ASN cc_start: 0.8429 (m-40) cc_final: 0.7948 (m-40) REVERT: F 89 GLU cc_start: 0.6619 (tp30) cc_final: 0.6418 (tp30) REVERT: F 104 MET cc_start: 0.8182 (ptm) cc_final: 0.7682 (ppp) REVERT: F 105 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8908 (mttt) REVERT: F 129 GLN cc_start: 0.8277 (mt0) cc_final: 0.7939 (mt0) REVERT: F 131 LEU cc_start: 0.8651 (tp) cc_final: 0.8374 (mm) REVERT: F 157 HIS cc_start: 0.7627 (m90) cc_final: 0.7258 (m90) REVERT: F 158 GLN cc_start: 0.9205 (mp10) cc_final: 0.8901 (mp10) REVERT: F 164 LEU cc_start: 0.8436 (mt) cc_final: 0.8216 (mt) REVERT: F 170 MET cc_start: 0.7768 (mpp) cc_final: 0.7515 (mpp) REVERT: F 198 MET cc_start: 0.8307 (ppp) cc_final: 0.8029 (ppp) REVERT: F 199 ASP cc_start: 0.8259 (m-30) cc_final: 0.8007 (m-30) REVERT: F 202 ILE cc_start: 0.8631 (mt) cc_final: 0.8128 (mt) REVERT: F 205 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8529 (mtmt) REVERT: F 208 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7764 (tm-30) REVERT: F 230 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7886 (mmmm) REVERT: F 233 HIS cc_start: 0.7847 (m-70) cc_final: 0.7591 (m90) REVERT: F 237 TRP cc_start: 0.7792 (m100) cc_final: 0.7586 (m-10) REVERT: F 242 GLN cc_start: 0.7723 (tt0) cc_final: 0.7060 (pp30) REVERT: F 243 VAL cc_start: 0.8468 (t) cc_final: 0.7573 (m) REVERT: F 244 LEU cc_start: 0.8294 (tt) cc_final: 0.7953 (tt) REVERT: G 48 MET cc_start: -0.0560 (ppp) cc_final: -0.1300 (ppp) REVERT: G 62 HIS cc_start: 0.7761 (t70) cc_final: 0.7114 (t70) REVERT: G 71 GLU cc_start: 0.7526 (tp30) cc_final: 0.6952 (tp30) REVERT: G 104 MET cc_start: 0.8112 (pmm) cc_final: 0.7870 (pmm) REVERT: G 131 LEU cc_start: 0.9335 (mt) cc_final: 0.9056 (mt) REVERT: G 155 ARG cc_start: 0.9192 (ttm110) cc_final: 0.8889 (ptp-110) REVERT: G 157 HIS cc_start: 0.8632 (p90) cc_final: 0.8361 (p90) REVERT: G 161 LYS cc_start: 0.9226 (mmtt) cc_final: 0.8937 (mmmt) REVERT: G 168 ILE cc_start: 0.7868 (mt) cc_final: 0.7566 (pt) REVERT: G 171 PHE cc_start: 0.7059 (m-80) cc_final: 0.6495 (m-80) REVERT: G 175 GLU cc_start: 0.8660 (pm20) cc_final: 0.8250 (mp0) REVERT: G 201 PHE cc_start: 0.8351 (t80) cc_final: 0.7942 (t80) REVERT: G 205 LYS cc_start: 0.8937 (mtmm) cc_final: 0.7888 (mtmm) REVERT: G 209 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8354 (ttp80) REVERT: G 210 ILE cc_start: 0.8673 (pt) cc_final: 0.7993 (pt) REVERT: H 62 HIS cc_start: 0.7915 (t70) cc_final: 0.7201 (t70) REVERT: H 78 TRP cc_start: 0.7258 (m-10) cc_final: 0.6198 (m-10) REVERT: H 85 LEU cc_start: 0.8660 (tp) cc_final: 0.8273 (tp) REVERT: H 87 TYR cc_start: 0.8455 (t80) cc_final: 0.7843 (t80) REVERT: H 101 VAL cc_start: 0.8805 (p) cc_final: 0.8528 (p) REVERT: H 104 MET cc_start: 0.9087 (mmp) cc_final: 0.8363 (mmp) REVERT: H 106 TRP cc_start: 0.8443 (t60) cc_final: 0.7200 (t60) REVERT: H 109 MET cc_start: 0.7380 (mmp) cc_final: 0.6878 (mmm) REVERT: H 110 PHE cc_start: 0.7948 (m-10) cc_final: 0.7257 (m-10) REVERT: H 170 MET cc_start: 0.7856 (mtt) cc_final: 0.7174 (mpp) REVERT: H 199 ASP cc_start: 0.7913 (m-30) cc_final: 0.7404 (m-30) REVERT: H 205 LYS cc_start: 0.8610 (mttp) cc_final: 0.8391 (mptt) REVERT: H 207 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7698 (mm-40) REVERT: H 222 ARG cc_start: 0.6938 (mmm-85) cc_final: 0.6303 (mmm160) REVERT: H 223 PHE cc_start: 0.7282 (m-10) cc_final: 0.6351 (m-80) REVERT: H 256 ARG cc_start: 0.8186 (ppt170) cc_final: 0.7662 (ppt170) REVERT: H 270 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7763 (mmtm) REVERT: I 30 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.6840 (mtm-85) REVERT: I 60 ILE cc_start: 0.8736 (mt) cc_final: 0.8371 (mm) REVERT: I 79 VAL cc_start: 0.8236 (t) cc_final: 0.7864 (p) REVERT: I 86 ILE cc_start: 0.8548 (pt) cc_final: 0.8267 (tp) REVERT: I 92 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8493 (mtpp) REVERT: I 97 GLN cc_start: 0.8031 (pm20) cc_final: 0.7679 (pm20) REVERT: I 113 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7689 (mmmm) REVERT: I 135 LEU cc_start: 0.9127 (mm) cc_final: 0.8729 (mm) REVERT: I 152 LEU cc_start: 0.7411 (pt) cc_final: 0.6324 (mp) REVERT: I 155 ARG cc_start: 0.8291 (tpt90) cc_final: 0.7344 (mmm160) REVERT: I 158 GLN cc_start: 0.9102 (tt0) cc_final: 0.8456 (tt0) REVERT: I 163 THR cc_start: 0.8304 (m) cc_final: 0.7855 (p) REVERT: I 183 ILE cc_start: 0.8940 (mt) cc_final: 0.8400 (mm) REVERT: I 190 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7640 (mtpt) REVERT: I 203 PHE cc_start: 0.8266 (t80) cc_final: 0.8024 (t80) REVERT: I 207 GLN cc_start: 0.8263 (mm110) cc_final: 0.7712 (tp40) REVERT: I 244 LEU cc_start: 0.8583 (mt) cc_final: 0.8366 (mt) REVERT: I 251 ILE cc_start: 0.7996 (pt) cc_final: 0.7566 (mp) REVERT: I 260 ARG cc_start: 0.7610 (ptp-170) cc_final: 0.7153 (ptp-170) REVERT: J 13 ASN cc_start: 0.7648 (m-40) cc_final: 0.7401 (m110) REVERT: J 40 CYS cc_start: 0.7361 (t) cc_final: 0.7024 (t) REVERT: J 63 TRP cc_start: 0.7529 (m100) cc_final: 0.5972 (m100) REVERT: J 86 ILE cc_start: 0.8936 (pt) cc_final: 0.8420 (mm) REVERT: J 92 LYS cc_start: 0.8924 (tptp) cc_final: 0.8598 (tptp) REVERT: J 102 GLN cc_start: 0.8644 (mp10) cc_final: 0.8151 (mp10) REVERT: J 103 THR cc_start: 0.8825 (t) cc_final: 0.8379 (p) REVERT: J 104 MET cc_start: 0.8480 (mmt) cc_final: 0.8087 (mmt) REVERT: J 106 TRP cc_start: 0.8547 (t60) cc_final: 0.8172 (t60) REVERT: J 131 LEU cc_start: 0.8773 (tt) cc_final: 0.8193 (tt) REVERT: J 132 MET cc_start: 0.8701 (mmp) cc_final: 0.8364 (mmt) REVERT: J 137 ILE cc_start: 0.8505 (tt) cc_final: 0.7702 (tt) REVERT: J 139 HIS cc_start: 0.8240 (t70) cc_final: 0.7890 (t70) REVERT: J 162 ASN cc_start: 0.8928 (m110) cc_final: 0.8680 (m-40) REVERT: J 164 LEU cc_start: 0.8715 (tp) cc_final: 0.8506 (tp) REVERT: J 178 LEU cc_start: 0.9209 (mm) cc_final: 0.8924 (mm) REVERT: J 189 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.6768 (mtm110) REVERT: J 204 ASN cc_start: 0.8407 (m110) cc_final: 0.7921 (m110) REVERT: J 205 LYS cc_start: 0.8577 (tptp) cc_final: 0.8164 (tptp) REVERT: J 208 GLN cc_start: 0.8305 (pt0) cc_final: 0.7849 (pt0) REVERT: K 11 GLU cc_start: 0.8425 (tp30) cc_final: 0.8211 (tp30) REVERT: K 30 ARG cc_start: 0.8803 (ttt180) cc_final: 0.8458 (ttt180) REVERT: K 34 GLU cc_start: 0.8804 (pt0) cc_final: 0.8352 (pp20) REVERT: K 35 ASP cc_start: 0.8736 (m-30) cc_final: 0.8365 (m-30) REVERT: K 109 MET cc_start: 0.8173 (tpp) cc_final: 0.7100 (ptp) REVERT: K 110 PHE cc_start: 0.7988 (m-80) cc_final: 0.7141 (m-80) REVERT: K 132 MET cc_start: 0.7688 (ppp) cc_final: 0.7449 (ppp) REVERT: K 245 TRP cc_start: 0.8234 (m100) cc_final: 0.7637 (m100) REVERT: K 270 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7548 (tmtt) REVERT: L 63 TRP cc_start: 0.5226 (m100) cc_final: 0.4942 (m100) REVERT: L 223 PHE cc_start: 0.5765 (p90) cc_final: 0.5322 (p90) REVERT: L 226 TYR cc_start: 0.7057 (p90) cc_final: 0.6180 (p90) REVERT: L 244 LEU cc_start: 0.8480 (mt) cc_final: 0.8230 (mt) REVERT: L 254 LYS cc_start: 0.8464 (tmtt) cc_final: 0.7750 (tmtt) REVERT: L 266 ASN cc_start: 0.8544 (m110) cc_final: 0.8278 (m110) REVERT: L 268 ASP cc_start: 0.6962 (t0) cc_final: 0.6722 (t70) REVERT: M 18 ASP cc_start: 0.7669 (t70) cc_final: 0.7217 (t70) REVERT: M 25 GLU cc_start: 0.8415 (tt0) cc_final: 0.8063 (tt0) REVERT: M 36 ILE cc_start: 0.8502 (mt) cc_final: 0.8295 (mt) REVERT: M 39 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7869 (tm-30) REVERT: M 78 TRP cc_start: 0.6687 (m-90) cc_final: 0.6067 (m-90) REVERT: M 89 GLU cc_start: 0.6933 (pm20) cc_final: 0.6672 (mp0) REVERT: M 152 LEU cc_start: 0.8774 (mm) cc_final: 0.7422 (mm) REVERT: M 154 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8581 (mm-30) REVERT: M 158 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7524 (tm-30) REVERT: M 159 THR cc_start: 0.8628 (m) cc_final: 0.7948 (p) REVERT: M 174 PHE cc_start: 0.7453 (t80) cc_final: 0.7147 (t80) REVERT: M 178 LEU cc_start: 0.8871 (mt) cc_final: 0.8323 (mt) REVERT: M 205 LYS cc_start: 0.9106 (mttm) cc_final: 0.8898 (mtpp) REVERT: M 207 GLN cc_start: 0.8515 (mm110) cc_final: 0.8237 (mm110) REVERT: M 224 CYS cc_start: 0.6424 (p) cc_final: 0.5886 (p) REVERT: N 23 HIS cc_start: 0.7845 (t70) cc_final: 0.7508 (t70) REVERT: N 104 MET cc_start: 0.8403 (ptm) cc_final: 0.7798 (ppp) REVERT: N 154 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8034 (mm-30) REVERT: N 157 HIS cc_start: 0.7991 (m90) cc_final: 0.7728 (m90) REVERT: N 161 LYS cc_start: 0.9156 (ptpp) cc_final: 0.8746 (ptpp) REVERT: N 164 LEU cc_start: 0.8708 (mt) cc_final: 0.8485 (mt) REVERT: N 165 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8061 (mm-30) REVERT: N 183 ILE cc_start: 0.7297 (mt) cc_final: 0.7057 (mt) REVERT: N 204 ASN cc_start: 0.8855 (p0) cc_final: 0.8594 (p0) REVERT: N 207 GLN cc_start: 0.8364 (mp10) cc_final: 0.8110 (mp10) REVERT: N 210 ILE cc_start: 0.8506 (pt) cc_final: 0.8152 (pt) REVERT: N 213 GLN cc_start: 0.8885 (mt0) cc_final: 0.8292 (mt0) REVERT: N 233 HIS cc_start: 0.7684 (m90) cc_final: 0.7260 (m90) REVERT: N 256 ARG cc_start: 0.8403 (ttm110) cc_final: 0.7778 (ttm110) REVERT: N 270 LYS cc_start: 0.7793 (mptt) cc_final: 0.7537 (mptt) REVERT: O 48 MET cc_start: -0.1692 (ppp) cc_final: -0.2166 (ppp) REVERT: O 62 HIS cc_start: 0.7767 (m-70) cc_final: 0.7004 (m-70) REVERT: O 109 MET cc_start: 0.7760 (tpt) cc_final: 0.7537 (tpp) REVERT: O 110 PHE cc_start: 0.8177 (m-80) cc_final: 0.7401 (m-10) REVERT: O 132 MET cc_start: 0.8136 (tmm) cc_final: 0.7560 (tmm) REVERT: O 152 LEU cc_start: 0.8834 (tp) cc_final: 0.8597 (tp) REVERT: O 205 LYS cc_start: 0.9242 (mmtm) cc_final: 0.8996 (mmtm) REVERT: P 62 HIS cc_start: 0.7903 (t70) cc_final: 0.7296 (t70) REVERT: P 87 TYR cc_start: 0.8495 (t80) cc_final: 0.8205 (t80) REVERT: P 104 MET cc_start: 0.9084 (mmp) cc_final: 0.8509 (mmp) REVERT: P 106 TRP cc_start: 0.8362 (t60) cc_final: 0.7978 (t60) REVERT: P 170 MET cc_start: 0.7808 (mtt) cc_final: 0.7299 (mpp) REVERT: P 172 ASN cc_start: 0.8869 (m-40) cc_final: 0.8519 (p0) REVERT: P 207 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7619 (mm-40) REVERT: P 222 ARG cc_start: 0.6582 (mmm-85) cc_final: 0.5973 (mmm160) REVERT: P 223 PHE cc_start: 0.6837 (m-80) cc_final: 0.5750 (m-80) REVERT: P 233 HIS cc_start: 0.6789 (m-70) cc_final: 0.6564 (m-70) REVERT: P 270 LYS cc_start: 0.7718 (mptt) cc_final: 0.7499 (mmtm) outliers start: 0 outliers final: 0 residues processed: 1194 average time/residue: 0.4872 time to fit residues: 903.7129 Evaluate side-chains 1111 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1111 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 136 optimal weight: 3.9990 chunk 373 optimal weight: 7.9990 chunk 267 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 chunk 339 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 300 optimal weight: 7.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 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** ** E 23 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 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN H 157 HIS ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN J 13 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN N 242 GLN O 208 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.192694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146239 restraints weight = 72415.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.151727 restraints weight = 44639.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155553 restraints weight = 31007.605| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34119 Z= 0.145 Angle : 0.712 13.219 46515 Z= 0.378 Chirality : 0.049 0.260 5006 Planarity : 0.005 0.078 5714 Dihedral : 14.780 174.176 5007 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3851 helix: 0.91 (0.12), residues: 1868 sheet: -0.70 (0.18), residues: 814 loop : -1.73 (0.16), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP P 78 HIS 0.025 0.001 HIS O 157 PHE 0.024 0.002 PHE N 201 TYR 0.021 0.001 TYR O 70 ARG 0.013 0.001 ARG F 155 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 1746) hydrogen bonds : angle 5.26076 ( 5114) covalent geometry : bond 0.00309 (34119) covalent geometry : angle 0.71209 (46515) *********************** 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 1184 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1184 time to evaluate : 3.272 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: A 11 GLU cc_start: 0.8306 (mp0) cc_final: 0.7881 (mp0) REVERT: A 73 LYS cc_start: 0.7269 (mptt) cc_final: 0.6673 (mtpt) REVERT: A 79 VAL cc_start: 0.8102 (t) cc_final: 0.7438 (p) REVERT: A 80 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 92 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8479 (mtpp) REVERT: A 97 GLN cc_start: 0.7671 (pm20) cc_final: 0.6923 (pm20) REVERT: A 98 GLU cc_start: 0.8031 (mp0) cc_final: 0.7346 (mp0) REVERT: A 104 MET cc_start: 0.8501 (ttm) cc_final: 0.7836 (ttm) REVERT: A 105 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8847 (mtpp) REVERT: A 129 GLN cc_start: 0.8290 (tt0) cc_final: 0.8072 (tt0) REVERT: A 132 MET cc_start: 0.7700 (mmm) cc_final: 0.7440 (mmm) REVERT: A 135 LEU cc_start: 0.9102 (mt) cc_final: 0.8765 (mt) REVERT: A 152 LEU cc_start: 0.7483 (pt) cc_final: 0.6401 (mp) REVERT: A 153 VAL cc_start: 0.8991 (m) cc_final: 0.8745 (m) REVERT: A 155 ARG cc_start: 0.8285 (tpt90) cc_final: 0.7499 (mmm160) REVERT: A 158 GLN cc_start: 0.8632 (tt0) cc_final: 0.8092 (tt0) REVERT: A 161 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8284 (tptt) REVERT: A 164 LEU cc_start: 0.8444 (mt) cc_final: 0.8229 (mt) REVERT: A 183 ILE cc_start: 0.8967 (mt) cc_final: 0.8415 (mm) REVERT: A 190 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7260 (mtpp) REVERT: A 203 PHE cc_start: 0.8314 (t80) cc_final: 0.7813 (t80) REVERT: A 254 LYS cc_start: 0.7978 (pptt) cc_final: 0.7524 (pptt) REVERT: A 260 ARG cc_start: 0.7374 (ptm160) cc_final: 0.7148 (ptm160) REVERT: B 13 ASN cc_start: 0.7376 (m110) cc_final: 0.7138 (m110) REVERT: B 15 TRP cc_start: 0.7716 (m100) cc_final: 0.7091 (m100) REVERT: B 40 CYS cc_start: 0.7478 (t) cc_final: 0.6888 (p) REVERT: B 63 TRP cc_start: 0.7785 (m100) cc_final: 0.6380 (m100) REVERT: B 64 GLN cc_start: 0.7008 (tp40) cc_final: 0.6468 (mp10) REVERT: B 86 ILE cc_start: 0.8731 (pt) cc_final: 0.8291 (mm) REVERT: B 89 GLU cc_start: 0.7956 (tt0) cc_final: 0.7357 (tt0) REVERT: B 97 GLN cc_start: 0.8992 (mp10) cc_final: 0.8418 (mp10) REVERT: B 100 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8242 (mtt180) REVERT: B 102 GLN cc_start: 0.8748 (mp10) cc_final: 0.8194 (mm-40) REVERT: B 104 MET cc_start: 0.8846 (mmp) cc_final: 0.8163 (mmp) REVERT: B 106 TRP cc_start: 0.8526 (t60) cc_final: 0.8253 (t60) REVERT: B 129 GLN cc_start: 0.8592 (pt0) cc_final: 0.8130 (pt0) REVERT: B 131 LEU cc_start: 0.8866 (tt) cc_final: 0.8296 (tt) REVERT: B 132 MET cc_start: 0.8773 (mmp) cc_final: 0.7866 (mmp) REVERT: B 138 GLU cc_start: 0.7855 (tp30) cc_final: 0.7622 (tp30) REVERT: B 139 HIS cc_start: 0.8577 (t70) cc_final: 0.8050 (t70) REVERT: B 178 LEU cc_start: 0.9152 (mm) cc_final: 0.8756 (mm) REVERT: B 182 LEU cc_start: 0.8494 (mt) cc_final: 0.8242 (mt) REVERT: B 186 ASN cc_start: 0.8321 (m-40) cc_final: 0.7952 (m-40) REVERT: B 198 MET cc_start: 0.8139 (tpt) cc_final: 0.7603 (tpp) REVERT: B 204 ASN cc_start: 0.7864 (p0) cc_final: 0.7661 (p0) REVERT: B 205 LYS cc_start: 0.8443 (tptp) cc_final: 0.8227 (tppp) REVERT: B 208 GLN cc_start: 0.8261 (pt0) cc_final: 0.7756 (pt0) REVERT: C 5 ILE cc_start: 0.9286 (mt) cc_final: 0.9045 (mt) REVERT: C 7 LEU cc_start: 0.8625 (tt) cc_final: 0.8140 (tt) REVERT: C 35 ASP cc_start: 0.8683 (m-30) cc_final: 0.8454 (m-30) REVERT: C 36 ILE cc_start: 0.9050 (mm) cc_final: 0.8833 (mm) REVERT: C 38 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 39 GLN cc_start: 0.8447 (tp40) cc_final: 0.7704 (tp40) REVERT: C 40 CYS cc_start: 0.8520 (m) cc_final: 0.7231 (t) REVERT: C 109 MET cc_start: 0.7993 (tpp) cc_final: 0.7112 (ptp) REVERT: C 110 PHE cc_start: 0.7871 (m-80) cc_final: 0.6795 (m-80) REVERT: C 245 TRP cc_start: 0.8255 (m-90) cc_final: 0.8043 (m-90) REVERT: D 63 TRP cc_start: 0.6036 (m100) cc_final: 0.5663 (m100) REVERT: D 154 GLU cc_start: 0.6802 (mp0) cc_final: 0.6507 (mp0) REVERT: D 218 GLN cc_start: 0.8458 (mm110) cc_final: 0.7923 (mm110) REVERT: D 223 PHE cc_start: 0.6021 (p90) cc_final: 0.5552 (p90) REVERT: D 226 TYR cc_start: 0.7041 (p90) cc_final: 0.6019 (p90) REVERT: D 254 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8044 (ttmm) REVERT: D 262 LEU cc_start: 0.8314 (mm) cc_final: 0.8056 (mm) REVERT: D 266 ASN cc_start: 0.8514 (m110) cc_final: 0.8103 (m110) REVERT: E 7 LEU cc_start: 0.8268 (tt) cc_final: 0.6985 (tt) REVERT: E 10 GLU cc_start: 0.8117 (pp20) cc_final: 0.7594 (pp20) REVERT: E 11 GLU cc_start: 0.8273 (pm20) cc_final: 0.7609 (pm20) REVERT: E 12 HIS cc_start: 0.8592 (t70) cc_final: 0.7727 (t70) REVERT: E 18 ASP cc_start: 0.7963 (t70) cc_final: 0.7681 (t70) REVERT: E 103 THR cc_start: 0.8895 (t) cc_final: 0.8670 (p) REVERT: E 132 MET cc_start: 0.6985 (tmm) cc_final: 0.6755 (tmm) REVERT: E 138 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6843 (tm-30) REVERT: E 150 GLN cc_start: 0.7910 (mm110) cc_final: 0.7478 (mm110) REVERT: E 154 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8549 (mm-30) REVERT: E 158 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7516 (tm-30) REVERT: E 159 THR cc_start: 0.8327 (m) cc_final: 0.7659 (p) REVERT: E 174 PHE cc_start: 0.7694 (t80) cc_final: 0.7334 (t80) REVERT: E 178 LEU cc_start: 0.8868 (mt) cc_final: 0.8256 (mt) REVERT: F 11 GLU cc_start: 0.7885 (mp0) cc_final: 0.7372 (mp0) REVERT: F 23 HIS cc_start: 0.8016 (t70) cc_final: 0.7595 (t70) REVERT: F 65 VAL cc_start: 0.7353 (t) cc_final: 0.6962 (p) REVERT: F 75 ILE cc_start: 0.7369 (mm) cc_final: 0.7155 (mm) REVERT: F 80 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7041 (tm-30) REVERT: F 82 ASN cc_start: 0.8182 (m-40) cc_final: 0.7918 (m-40) REVERT: F 89 GLU cc_start: 0.6862 (tp30) cc_final: 0.6642 (tp30) REVERT: F 104 MET cc_start: 0.8167 (ptm) cc_final: 0.7661 (ppp) REVERT: F 105 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8949 (mttt) REVERT: F 129 GLN cc_start: 0.8288 (mt0) cc_final: 0.7953 (mt0) REVERT: F 131 LEU cc_start: 0.8723 (tp) cc_final: 0.8418 (mm) REVERT: F 170 MET cc_start: 0.7708 (mpp) cc_final: 0.7498 (mpp) REVERT: F 198 MET cc_start: 0.8332 (ppp) cc_final: 0.8083 (ppp) REVERT: F 199 ASP cc_start: 0.8321 (m-30) cc_final: 0.8013 (m-30) REVERT: F 202 ILE cc_start: 0.8617 (mt) cc_final: 0.8080 (mt) REVERT: F 205 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8572 (mtmt) REVERT: F 206 GLU cc_start: 0.8370 (pp20) cc_final: 0.6727 (pp20) REVERT: F 208 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7816 (tm-30) REVERT: F 230 LYS cc_start: 0.8454 (mmmt) cc_final: 0.7895 (mmmm) REVERT: F 233 HIS cc_start: 0.7830 (m-70) cc_final: 0.7582 (m90) REVERT: F 243 VAL cc_start: 0.8472 (t) cc_final: 0.7817 (p) REVERT: F 267 LYS cc_start: 0.8833 (ptmt) cc_final: 0.8436 (pttt) REVERT: G 48 MET cc_start: -0.0539 (ppp) cc_final: -0.1293 (ppp) REVERT: G 62 HIS cc_start: 0.7825 (t70) cc_final: 0.7116 (t70) REVERT: G 71 GLU cc_start: 0.7303 (tp30) cc_final: 0.6750 (tp30) REVERT: G 106 TRP cc_start: 0.7360 (t60) cc_final: 0.7105 (t60) REVERT: G 131 LEU cc_start: 0.9235 (mt) cc_final: 0.8928 (mt) REVERT: G 150 GLN cc_start: 0.8425 (pp30) cc_final: 0.8217 (pp30) REVERT: G 157 HIS cc_start: 0.8811 (p90) cc_final: 0.8464 (p90) REVERT: G 158 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8743 (tp-100) REVERT: G 161 LYS cc_start: 0.9227 (mmtt) cc_final: 0.8842 (ptpt) REVERT: G 168 ILE cc_start: 0.7834 (mt) cc_final: 0.7612 (pt) REVERT: G 170 MET cc_start: 0.7518 (mmp) cc_final: 0.7259 (mmp) REVERT: G 171 PHE cc_start: 0.7025 (m-80) cc_final: 0.6448 (m-80) REVERT: G 175 GLU cc_start: 0.8652 (pm20) cc_final: 0.8284 (mp0) REVERT: G 209 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8278 (ttp80) REVERT: G 210 ILE cc_start: 0.8591 (pt) cc_final: 0.7936 (pt) REVERT: H 62 HIS cc_start: 0.7911 (t70) cc_final: 0.7213 (t70) REVERT: H 78 TRP cc_start: 0.7329 (m-10) cc_final: 0.6218 (m-10) REVERT: H 85 LEU cc_start: 0.8685 (tp) cc_final: 0.8256 (tp) REVERT: H 87 TYR cc_start: 0.8463 (t80) cc_final: 0.7922 (t80) REVERT: H 101 VAL cc_start: 0.8779 (p) cc_final: 0.8517 (p) REVERT: H 104 MET cc_start: 0.9067 (mmp) cc_final: 0.8315 (mmp) REVERT: H 106 TRP cc_start: 0.8426 (t60) cc_final: 0.7373 (t60) REVERT: H 109 MET cc_start: 0.7366 (mmp) cc_final: 0.6781 (mmm) REVERT: H 110 PHE cc_start: 0.7964 (m-10) cc_final: 0.7395 (m-10) REVERT: H 170 MET cc_start: 0.7855 (mtt) cc_final: 0.7173 (mpp) REVERT: H 202 ILE cc_start: 0.9093 (mm) cc_final: 0.8680 (pt) REVERT: H 206 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7633 (mp0) REVERT: H 222 ARG cc_start: 0.6954 (mmm-85) cc_final: 0.6280 (mmm160) REVERT: H 223 PHE cc_start: 0.7346 (m-10) cc_final: 0.6283 (m-80) REVERT: H 238 GLN cc_start: 0.7328 (mp10) cc_final: 0.6975 (mp10) REVERT: H 256 ARG cc_start: 0.8196 (ppt170) cc_final: 0.7710 (ppt170) REVERT: H 270 LYS cc_start: 0.8137 (mmpt) cc_final: 0.7755 (mmtm) REVERT: I 60 ILE cc_start: 0.8741 (mt) cc_final: 0.8350 (mm) REVERT: I 79 VAL cc_start: 0.8236 (t) cc_final: 0.7822 (p) REVERT: I 86 ILE cc_start: 0.8560 (pt) cc_final: 0.8268 (tp) REVERT: I 92 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8427 (mtpp) REVERT: I 97 GLN cc_start: 0.8060 (pm20) cc_final: 0.7692 (pm20) REVERT: I 113 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7646 (mmmm) REVERT: I 131 LEU cc_start: 0.9011 (mm) cc_final: 0.8774 (mm) REVERT: I 135 LEU cc_start: 0.8944 (mm) cc_final: 0.8647 (mm) REVERT: I 152 LEU cc_start: 0.7359 (pt) cc_final: 0.6350 (mp) REVERT: I 155 ARG cc_start: 0.8287 (tpt90) cc_final: 0.7371 (tpp-160) REVERT: I 163 THR cc_start: 0.8217 (m) cc_final: 0.7740 (p) REVERT: I 164 LEU cc_start: 0.8580 (mt) cc_final: 0.8249 (mt) REVERT: I 174 PHE cc_start: 0.7185 (t80) cc_final: 0.6785 (t80) REVERT: I 183 ILE cc_start: 0.8941 (mt) cc_final: 0.8434 (mm) REVERT: I 190 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7670 (mtpt) REVERT: I 203 PHE cc_start: 0.8117 (t80) cc_final: 0.7836 (t80) REVERT: I 207 GLN cc_start: 0.8252 (mm110) cc_final: 0.7537 (tp40) REVERT: I 244 LEU cc_start: 0.8558 (mt) cc_final: 0.8339 (mt) REVERT: I 251 ILE cc_start: 0.8076 (pt) cc_final: 0.7598 (mp) REVERT: I 260 ARG cc_start: 0.7594 (ptp-170) cc_final: 0.7130 (ptp-170) REVERT: I 267 LYS cc_start: 0.7517 (tmmt) cc_final: 0.7231 (pptt) REVERT: J 13 ASN cc_start: 0.7607 (m110) cc_final: 0.7364 (m110) REVERT: J 40 CYS cc_start: 0.7242 (t) cc_final: 0.7000 (t) REVERT: J 63 TRP cc_start: 0.7502 (m100) cc_final: 0.5894 (m100) REVERT: J 86 ILE cc_start: 0.8898 (pt) cc_final: 0.8440 (mm) REVERT: J 90 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8302 (tpp80) REVERT: J 92 LYS cc_start: 0.8947 (tptp) cc_final: 0.8607 (tptp) REVERT: J 103 THR cc_start: 0.8745 (t) cc_final: 0.8535 (t) REVERT: J 104 MET cc_start: 0.8526 (mmt) cc_final: 0.7966 (mmt) REVERT: J 106 TRP cc_start: 0.8471 (t60) cc_final: 0.8114 (t60) REVERT: J 113 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7220 (mmmt) REVERT: J 131 LEU cc_start: 0.8726 (tt) cc_final: 0.8223 (tt) REVERT: J 137 ILE cc_start: 0.8482 (tt) cc_final: 0.7655 (tt) REVERT: J 139 HIS cc_start: 0.8535 (t70) cc_final: 0.7871 (t70) REVERT: J 150 GLN cc_start: 0.7761 (pt0) cc_final: 0.7340 (pt0) REVERT: J 162 ASN cc_start: 0.8945 (m110) cc_final: 0.8700 (m-40) REVERT: J 164 LEU cc_start: 0.8666 (tp) cc_final: 0.8448 (tp) REVERT: J 178 LEU cc_start: 0.9255 (mm) cc_final: 0.9025 (mm) REVERT: J 189 ARG cc_start: 0.7495 (ttp-110) cc_final: 0.6645 (mtm180) REVERT: J 204 ASN cc_start: 0.8382 (m110) cc_final: 0.7858 (m110) REVERT: J 205 LYS cc_start: 0.8567 (tptp) cc_final: 0.8164 (tptp) REVERT: J 208 GLN cc_start: 0.8334 (pt0) cc_final: 0.7866 (pt0) REVERT: K 7 LEU cc_start: 0.8729 (tt) cc_final: 0.8456 (tt) REVERT: K 11 GLU cc_start: 0.8395 (tp30) cc_final: 0.8170 (tp30) REVERT: K 25 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8198 (tm-30) REVERT: K 30 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8461 (ttt180) REVERT: K 34 GLU cc_start: 0.8803 (pt0) cc_final: 0.8345 (pp20) REVERT: K 35 ASP cc_start: 0.8738 (m-30) cc_final: 0.8318 (m-30) REVERT: K 110 PHE cc_start: 0.7941 (m-80) cc_final: 0.7698 (m-80) REVERT: K 132 MET cc_start: 0.7774 (ppp) cc_final: 0.7563 (ppp) REVERT: K 245 TRP cc_start: 0.8216 (m100) cc_final: 0.7748 (m100) REVERT: L 63 TRP cc_start: 0.6905 (m100) cc_final: 0.6143 (m100) REVERT: L 223 PHE cc_start: 0.5673 (p90) cc_final: 0.5249 (p90) REVERT: L 226 TYR cc_start: 0.7064 (p90) cc_final: 0.6145 (p90) REVERT: L 244 LEU cc_start: 0.8497 (mt) cc_final: 0.8265 (mt) REVERT: L 254 LYS cc_start: 0.8433 (tmtt) cc_final: 0.7633 (tmtt) REVERT: L 266 ASN cc_start: 0.8668 (m110) cc_final: 0.8252 (m110) REVERT: L 268 ASP cc_start: 0.6975 (t0) cc_final: 0.6736 (t70) REVERT: L 269 VAL cc_start: 0.8227 (t) cc_final: 0.7983 (t) REVERT: M 18 ASP cc_start: 0.7692 (t70) cc_final: 0.7361 (t70) REVERT: M 25 GLU cc_start: 0.8550 (tt0) cc_final: 0.8222 (tt0) REVERT: M 36 ILE cc_start: 0.8727 (mt) cc_final: 0.8511 (mt) REVERT: M 39 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7846 (tm-30) REVERT: M 76 LEU cc_start: 0.8295 (mm) cc_final: 0.8083 (mm) REVERT: M 89 GLU cc_start: 0.6978 (pm20) cc_final: 0.6712 (mp0) REVERT: M 101 VAL cc_start: 0.9153 (t) cc_final: 0.8922 (t) REVERT: M 154 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8621 (mm-30) REVERT: M 158 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7481 (tm-30) REVERT: M 159 THR cc_start: 0.8615 (m) cc_final: 0.7956 (p) REVERT: M 174 PHE cc_start: 0.7424 (t80) cc_final: 0.7130 (t80) REVERT: M 178 LEU cc_start: 0.8858 (mt) cc_final: 0.8301 (mt) REVERT: M 198 MET cc_start: 0.8587 (mmp) cc_final: 0.8298 (mmp) REVERT: M 207 GLN cc_start: 0.8510 (mm110) cc_final: 0.8157 (mm110) REVERT: M 209 ARG cc_start: 0.8707 (tmt170) cc_final: 0.8352 (ttp80) REVERT: M 224 CYS cc_start: 0.6423 (p) cc_final: 0.5941 (p) REVERT: N 23 HIS cc_start: 0.8008 (t70) cc_final: 0.7671 (t70) REVERT: N 104 MET cc_start: 0.8151 (ptm) cc_final: 0.7520 (ppp) REVERT: N 157 HIS cc_start: 0.8002 (m90) cc_final: 0.7622 (m90) REVERT: N 158 GLN cc_start: 0.9002 (mp10) cc_final: 0.8793 (mp10) REVERT: N 161 LYS cc_start: 0.9149 (ptpp) cc_final: 0.8863 (ptpp) REVERT: N 164 LEU cc_start: 0.8688 (mt) cc_final: 0.8470 (mt) REVERT: N 165 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8058 (mm-30) REVERT: N 183 ILE cc_start: 0.7385 (mt) cc_final: 0.7154 (mt) REVERT: N 206 GLU cc_start: 0.8052 (pp20) cc_final: 0.6664 (pp20) REVERT: N 213 GLN cc_start: 0.8810 (mt0) cc_final: 0.8452 (mt0) REVERT: N 233 HIS cc_start: 0.7633 (m90) cc_final: 0.7236 (m90) REVERT: N 256 ARG cc_start: 0.8376 (ttm110) cc_final: 0.7733 (ttm110) REVERT: N 260 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7503 (ptp-110) REVERT: N 267 LYS cc_start: 0.8998 (ptpt) cc_final: 0.8404 (pttt) REVERT: N 270 LYS cc_start: 0.7773 (mptt) cc_final: 0.7552 (mptt) REVERT: O 23 HIS cc_start: 0.7780 (t70) cc_final: 0.7156 (t70) REVERT: O 48 MET cc_start: -0.1709 (ppp) cc_final: -0.2156 (ppp) REVERT: O 62 HIS cc_start: 0.7795 (m-70) cc_final: 0.7325 (m-70) REVERT: O 109 MET cc_start: 0.7743 (tpt) cc_final: 0.7514 (tpp) REVERT: O 110 PHE cc_start: 0.8086 (m-80) cc_final: 0.7286 (m-10) REVERT: O 115 LEU cc_start: 0.8667 (tp) cc_final: 0.8463 (tp) REVERT: O 132 MET cc_start: 0.8156 (tmm) cc_final: 0.7561 (tmm) REVERT: O 154 GLU cc_start: 0.9109 (pp20) cc_final: 0.8884 (pp20) REVERT: O 155 ARG cc_start: 0.9189 (mtm110) cc_final: 0.8819 (ptp-110) REVERT: O 157 HIS cc_start: 0.8861 (p90) cc_final: 0.8565 (p90) REVERT: O 161 LYS cc_start: 0.8723 (ptpp) cc_final: 0.8519 (ptpp) REVERT: O 162 ASN cc_start: 0.8908 (t0) cc_final: 0.8622 (t0) REVERT: O 193 LEU cc_start: 0.8663 (mm) cc_final: 0.8407 (mm) REVERT: O 205 LYS cc_start: 0.9222 (mmtm) cc_final: 0.8976 (mmtm) REVERT: O 207 GLN cc_start: 0.8545 (mp10) cc_final: 0.8323 (mp10) REVERT: P 62 HIS cc_start: 0.7908 (t70) cc_final: 0.7295 (t70) REVERT: P 87 TYR cc_start: 0.8594 (t80) cc_final: 0.8304 (t80) REVERT: P 104 MET cc_start: 0.9057 (mmp) cc_final: 0.8463 (mmp) REVERT: P 106 TRP cc_start: 0.8304 (t60) cc_final: 0.7986 (t60) REVERT: P 170 MET cc_start: 0.7807 (mtt) cc_final: 0.7299 (mpp) REVERT: P 172 ASN cc_start: 0.8889 (m-40) cc_final: 0.8535 (p0) REVERT: P 199 ASP cc_start: 0.8161 (m-30) cc_final: 0.7611 (m-30) REVERT: P 207 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7631 (mm-40) REVERT: P 222 ARG cc_start: 0.6329 (mmm-85) cc_final: 0.5760 (mmm160) REVERT: P 223 PHE cc_start: 0.6892 (m-80) cc_final: 0.5808 (m-80) REVERT: P 238 GLN cc_start: 0.6958 (mp10) cc_final: 0.6637 (mp10) REVERT: P 266 ASN cc_start: 0.6411 (p0) cc_final: 0.6015 (m-40) outliers start: 0 outliers final: 0 residues processed: 1184 average time/residue: 0.4636 time to fit residues: 854.4747 Evaluate side-chains 1111 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1111 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 289 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 274 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 305 optimal weight: 0.2980 chunk 128 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 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** ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN G 208 GLN H 157 HIS ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 HIS ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 GLN O 208 GLN O 211 GLN P 148 GLN P 157 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.193555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147520 restraints weight = 70209.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153219 restraints weight = 42651.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.157086 restraints weight = 29258.093| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34119 Z= 0.157 Angle : 0.744 14.652 46515 Z= 0.397 Chirality : 0.050 0.503 5006 Planarity : 0.005 0.094 5714 Dihedral : 14.797 174.536 5007 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 3851 helix: 0.79 (0.12), residues: 1873 sheet: -0.77 (0.18), residues: 822 loop : -1.73 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP M 63 HIS 0.023 0.001 HIS O 157 PHE 0.058 0.002 PHE M 201 TYR 0.032 0.001 TYR B 70 ARG 0.010 0.001 ARG D 256 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 1746) hydrogen bonds : angle 5.40479 ( 5114) covalent geometry : bond 0.00334 (34119) covalent geometry : angle 0.74401 (46515) *********************** 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 1186 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1186 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8238 (mp0) cc_final: 0.7994 (mp0) REVERT: A 45 GLU cc_start: 0.7963 (tt0) cc_final: 0.7657 (tp30) REVERT: A 73 LYS cc_start: 0.7311 (mptt) cc_final: 0.6593 (mtpt) REVERT: A 79 VAL cc_start: 0.8113 (t) cc_final: 0.7592 (p) REVERT: A 80 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6559 (tm-30) REVERT: A 92 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8515 (mtpp) REVERT: A 98 GLU cc_start: 0.8086 (mp0) cc_final: 0.7711 (mp0) REVERT: A 104 MET cc_start: 0.8628 (ttm) cc_final: 0.8205 (ttm) REVERT: A 105 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8887 (mtpp) REVERT: A 129 GLN cc_start: 0.8453 (tt0) cc_final: 0.8181 (tt0) REVERT: A 132 MET cc_start: 0.7754 (mmm) cc_final: 0.7540 (mmm) REVERT: A 155 ARG cc_start: 0.8322 (tpt90) cc_final: 0.6971 (mmm160) REVERT: A 158 GLN cc_start: 0.8635 (tt0) cc_final: 0.8074 (pt0) REVERT: A 161 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8282 (tppt) REVERT: A 190 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7336 (mtpp) REVERT: A 203 PHE cc_start: 0.8397 (t80) cc_final: 0.7887 (t80) REVERT: A 244 LEU cc_start: 0.8562 (mt) cc_final: 0.8345 (mt) REVERT: A 254 LYS cc_start: 0.7983 (pptt) cc_final: 0.7657 (pptt) REVERT: A 260 ARG cc_start: 0.7353 (ptm160) cc_final: 0.7137 (ptm160) REVERT: A 267 LYS cc_start: 0.8202 (tmmt) cc_final: 0.7989 (pptt) REVERT: B 13 ASN cc_start: 0.7524 (m110) cc_final: 0.7254 (m110) REVERT: B 15 TRP cc_start: 0.7742 (m100) cc_final: 0.7132 (m100) REVERT: B 40 CYS cc_start: 0.7610 (t) cc_final: 0.6949 (p) REVERT: B 63 TRP cc_start: 0.7802 (m100) cc_final: 0.6492 (m100) REVERT: B 64 GLN cc_start: 0.6745 (tp40) cc_final: 0.6338 (mp10) REVERT: B 86 ILE cc_start: 0.8631 (pt) cc_final: 0.8230 (mm) REVERT: B 89 GLU cc_start: 0.7994 (tt0) cc_final: 0.7191 (tt0) REVERT: B 90 ARG cc_start: 0.8663 (tpt-90) cc_final: 0.8331 (tpp80) REVERT: B 97 GLN cc_start: 0.8885 (mp10) cc_final: 0.8414 (mp10) REVERT: B 100 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8264 (mtt180) REVERT: B 104 MET cc_start: 0.8850 (mmp) cc_final: 0.8289 (mmp) REVERT: B 106 TRP cc_start: 0.8527 (t60) cc_final: 0.8234 (t60) REVERT: B 129 GLN cc_start: 0.8591 (pt0) cc_final: 0.8158 (pt0) REVERT: B 131 LEU cc_start: 0.8935 (tt) cc_final: 0.8493 (tt) REVERT: B 132 MET cc_start: 0.8815 (mmp) cc_final: 0.7900 (mmp) REVERT: B 138 GLU cc_start: 0.7859 (tp30) cc_final: 0.7632 (tp30) REVERT: B 139 HIS cc_start: 0.8600 (t70) cc_final: 0.8112 (t70) REVERT: B 178 LEU cc_start: 0.9086 (mm) cc_final: 0.8659 (mm) REVERT: B 186 ASN cc_start: 0.8291 (m-40) cc_final: 0.7990 (m-40) REVERT: B 198 MET cc_start: 0.8136 (tpt) cc_final: 0.7596 (tpp) REVERT: B 204 ASN cc_start: 0.7935 (p0) cc_final: 0.7642 (p0) REVERT: B 205 LYS cc_start: 0.8502 (tptp) cc_final: 0.8271 (tppp) REVERT: B 208 GLN cc_start: 0.8245 (pt0) cc_final: 0.7794 (pt0) REVERT: C 5 ILE cc_start: 0.9278 (mt) cc_final: 0.9002 (mt) REVERT: C 11 GLU cc_start: 0.8637 (tp30) cc_final: 0.7593 (tp30) REVERT: C 28 ILE cc_start: 0.7919 (tp) cc_final: 0.7634 (tp) REVERT: C 35 ASP cc_start: 0.8803 (m-30) cc_final: 0.8244 (m-30) REVERT: C 38 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 39 GLN cc_start: 0.8453 (tp40) cc_final: 0.7716 (tp40) REVERT: C 40 CYS cc_start: 0.8585 (m) cc_final: 0.7297 (t) REVERT: C 109 MET cc_start: 0.8018 (tpp) cc_final: 0.7138 (ptp) REVERT: C 110 PHE cc_start: 0.7912 (m-80) cc_final: 0.6792 (m-80) REVERT: C 132 MET cc_start: 0.7838 (ppp) cc_final: 0.7265 (ppp) REVERT: C 186 ASN cc_start: 0.8283 (m-40) cc_final: 0.8080 (m110) REVERT: C 245 TRP cc_start: 0.8320 (m-90) cc_final: 0.8112 (m-90) REVERT: D 63 TRP cc_start: 0.6013 (m100) cc_final: 0.5677 (m100) REVERT: D 154 GLU cc_start: 0.6734 (mp0) cc_final: 0.6426 (mp0) REVERT: D 209 ARG cc_start: 0.8583 (mmp-170) cc_final: 0.8295 (mmp80) REVERT: D 218 GLN cc_start: 0.8468 (mm110) cc_final: 0.7911 (mm110) REVERT: D 223 PHE cc_start: 0.6080 (p90) cc_final: 0.5609 (p90) REVERT: D 224 CYS cc_start: 0.7277 (p) cc_final: 0.7050 (p) REVERT: D 226 TYR cc_start: 0.7109 (p90) cc_final: 0.6067 (p90) REVERT: D 254 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8026 (ttmm) REVERT: D 262 LEU cc_start: 0.8272 (mm) cc_final: 0.8036 (mm) REVERT: D 266 ASN cc_start: 0.8474 (m110) cc_final: 0.8087 (m110) REVERT: E 3 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8005 (mt-10) REVERT: E 7 LEU cc_start: 0.8215 (tt) cc_final: 0.7128 (tt) REVERT: E 10 GLU cc_start: 0.8266 (pp20) cc_final: 0.7642 (pp20) REVERT: E 11 GLU cc_start: 0.8489 (pm20) cc_final: 0.7662 (pm20) REVERT: E 16 HIS cc_start: 0.7746 (m170) cc_final: 0.7471 (m90) REVERT: E 89 GLU cc_start: 0.7884 (pm20) cc_final: 0.6741 (mp0) REVERT: E 103 THR cc_start: 0.8911 (t) cc_final: 0.8645 (p) REVERT: E 132 MET cc_start: 0.7141 (tmm) cc_final: 0.6897 (tmm) REVERT: E 138 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6840 (tm-30) REVERT: E 150 GLN cc_start: 0.7925 (mm110) cc_final: 0.7489 (mm110) REVERT: E 154 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8565 (mm-30) REVERT: E 158 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7520 (tm-30) REVERT: E 159 THR cc_start: 0.8355 (m) cc_final: 0.7664 (p) REVERT: E 174 PHE cc_start: 0.7778 (t80) cc_final: 0.7406 (t80) REVERT: E 178 LEU cc_start: 0.8858 (mt) cc_final: 0.8420 (mt) REVERT: E 202 ILE cc_start: 0.8821 (mp) cc_final: 0.8418 (mp) REVERT: E 206 GLU cc_start: 0.8450 (pt0) cc_final: 0.8121 (pt0) REVERT: E 208 GLN cc_start: 0.8822 (pp30) cc_final: 0.8617 (pp30) REVERT: E 209 ARG cc_start: 0.8649 (tmt170) cc_final: 0.8220 (ttp80) REVERT: F 11 GLU cc_start: 0.7944 (mp0) cc_final: 0.7373 (mp0) REVERT: F 23 HIS cc_start: 0.7861 (t70) cc_final: 0.7444 (t70) REVERT: F 65 VAL cc_start: 0.7359 (t) cc_final: 0.6981 (p) REVERT: F 89 GLU cc_start: 0.6832 (tp30) cc_final: 0.6600 (tp30) REVERT: F 102 GLN cc_start: 0.8769 (mp10) cc_final: 0.8278 (mp10) REVERT: F 104 MET cc_start: 0.8219 (ptm) cc_final: 0.7671 (ppp) REVERT: F 105 LYS cc_start: 0.9238 (mtmm) cc_final: 0.8973 (mttt) REVERT: F 129 GLN cc_start: 0.8316 (mt0) cc_final: 0.7986 (mt0) REVERT: F 131 LEU cc_start: 0.8661 (tp) cc_final: 0.8339 (mm) REVERT: F 158 GLN cc_start: 0.9218 (mp10) cc_final: 0.9011 (mp10) REVERT: F 197 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.7995 (Cg_endo) REVERT: F 198 MET cc_start: 0.8342 (ppp) cc_final: 0.8133 (ppp) REVERT: F 199 ASP cc_start: 0.8251 (m-30) cc_final: 0.7914 (m-30) REVERT: F 202 ILE cc_start: 0.8591 (mt) cc_final: 0.7447 (mt) REVERT: F 205 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8506 (mtmt) REVERT: F 207 GLN cc_start: 0.8471 (mp10) cc_final: 0.8126 (mp-120) REVERT: F 208 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8046 (tm-30) REVERT: F 230 LYS cc_start: 0.8504 (mmmt) cc_final: 0.7917 (mmmm) REVERT: F 233 HIS cc_start: 0.7865 (m-70) cc_final: 0.7604 (m90) REVERT: F 243 VAL cc_start: 0.8049 (t) cc_final: 0.7642 (m) REVERT: F 267 LYS cc_start: 0.8789 (ptmt) cc_final: 0.8268 (pttt) REVERT: G 48 MET cc_start: -0.0533 (ppp) cc_final: -0.1311 (ppp) REVERT: G 62 HIS cc_start: 0.7932 (t70) cc_final: 0.7084 (t70) REVERT: G 71 GLU cc_start: 0.7316 (tp30) cc_final: 0.6849 (tp30) REVERT: G 106 TRP cc_start: 0.7320 (t60) cc_final: 0.7088 (t60) REVERT: G 131 LEU cc_start: 0.9289 (mt) cc_final: 0.9002 (mt) REVERT: G 150 GLN cc_start: 0.8476 (pp30) cc_final: 0.8199 (pp30) REVERT: G 152 LEU cc_start: 0.8770 (tp) cc_final: 0.8544 (tp) REVERT: G 157 HIS cc_start: 0.8868 (p90) cc_final: 0.8494 (p90) REVERT: G 158 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8742 (tp-100) REVERT: G 161 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8803 (ptpt) REVERT: G 168 ILE cc_start: 0.7827 (mt) cc_final: 0.7518 (pt) REVERT: G 170 MET cc_start: 0.7480 (mmp) cc_final: 0.7188 (mmp) REVERT: G 171 PHE cc_start: 0.7009 (m-80) cc_final: 0.6475 (m-80) REVERT: G 175 GLU cc_start: 0.8675 (pm20) cc_final: 0.8262 (mm-30) REVERT: G 193 LEU cc_start: 0.8990 (mm) cc_final: 0.8789 (mm) REVERT: G 209 ARG cc_start: 0.8917 (ttp80) cc_final: 0.8355 (ttp80) REVERT: G 210 ILE cc_start: 0.8664 (pt) cc_final: 0.7990 (pt) REVERT: H 62 HIS cc_start: 0.7909 (t70) cc_final: 0.7188 (t70) REVERT: H 78 TRP cc_start: 0.7277 (m-10) cc_final: 0.5943 (m-10) REVERT: H 85 LEU cc_start: 0.8610 (tp) cc_final: 0.8295 (tp) REVERT: H 87 TYR cc_start: 0.8469 (t80) cc_final: 0.7932 (t80) REVERT: H 101 VAL cc_start: 0.8777 (p) cc_final: 0.8517 (p) REVERT: H 104 MET cc_start: 0.9083 (mmp) cc_final: 0.8333 (mmp) REVERT: H 106 TRP cc_start: 0.8436 (t60) cc_final: 0.7452 (t60) REVERT: H 109 MET cc_start: 0.7387 (mmp) cc_final: 0.6813 (mmm) REVERT: H 110 PHE cc_start: 0.7972 (m-10) cc_final: 0.7429 (m-10) REVERT: H 170 MET cc_start: 0.7881 (mtt) cc_final: 0.7184 (mpp) REVERT: H 199 ASP cc_start: 0.7961 (m-30) cc_final: 0.7452 (m-30) REVERT: H 222 ARG cc_start: 0.7077 (mmm-85) cc_final: 0.6390 (mmm160) REVERT: H 223 PHE cc_start: 0.7347 (m-10) cc_final: 0.6290 (m-80) REVERT: H 256 ARG cc_start: 0.8190 (ppt170) cc_final: 0.7703 (ppt170) REVERT: H 267 LYS cc_start: 0.8257 (ptmm) cc_final: 0.8030 (ptmm) REVERT: H 270 LYS cc_start: 0.8199 (mmpt) cc_final: 0.7802 (mmtm) REVERT: I 60 ILE cc_start: 0.8739 (mt) cc_final: 0.8310 (mm) REVERT: I 79 VAL cc_start: 0.8250 (t) cc_final: 0.7895 (p) REVERT: I 82 ASN cc_start: 0.8574 (t0) cc_final: 0.8359 (t0) REVERT: I 85 LEU cc_start: 0.8076 (tp) cc_final: 0.7781 (tp) REVERT: I 86 ILE cc_start: 0.8540 (pt) cc_final: 0.8221 (tp) REVERT: I 92 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8484 (mtpp) REVERT: I 97 GLN cc_start: 0.8069 (pm20) cc_final: 0.7729 (pm20) REVERT: I 113 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7621 (mmmm) REVERT: I 135 LEU cc_start: 0.9099 (mm) cc_final: 0.8617 (mm) REVERT: I 152 LEU cc_start: 0.7411 (pt) cc_final: 0.6503 (mp) REVERT: I 155 ARG cc_start: 0.8264 (tpt90) cc_final: 0.7398 (tpp-160) REVERT: I 163 THR cc_start: 0.8161 (m) cc_final: 0.7689 (p) REVERT: I 164 LEU cc_start: 0.8577 (mt) cc_final: 0.8262 (mt) REVERT: I 174 PHE cc_start: 0.7246 (t80) cc_final: 0.6835 (t80) REVERT: I 183 ILE cc_start: 0.8900 (mt) cc_final: 0.8614 (mt) REVERT: I 186 ASN cc_start: 0.7351 (m-40) cc_final: 0.7149 (m-40) REVERT: I 190 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7686 (mtpt) REVERT: I 203 PHE cc_start: 0.8149 (t80) cc_final: 0.7909 (t80) REVERT: I 207 GLN cc_start: 0.8272 (mm110) cc_final: 0.7723 (tp40) REVERT: I 238 GLN cc_start: 0.6903 (mt0) cc_final: 0.6620 (mt0) REVERT: I 260 ARG cc_start: 0.7554 (ptp-170) cc_final: 0.7119 (ptp-170) REVERT: I 267 LYS cc_start: 0.7635 (tmmt) cc_final: 0.7334 (pptt) REVERT: J 13 ASN cc_start: 0.7645 (m110) cc_final: 0.7432 (m-40) REVERT: J 15 TRP cc_start: 0.8024 (m100) cc_final: 0.7437 (m100) REVERT: J 40 CYS cc_start: 0.7425 (t) cc_final: 0.7132 (t) REVERT: J 86 ILE cc_start: 0.8859 (pt) cc_final: 0.8488 (mm) REVERT: J 104 MET cc_start: 0.8617 (mmt) cc_final: 0.8078 (mmt) REVERT: J 106 TRP cc_start: 0.8513 (t60) cc_final: 0.8160 (t60) REVERT: J 131 LEU cc_start: 0.8764 (tt) cc_final: 0.8271 (tt) REVERT: J 132 MET cc_start: 0.8470 (tpp) cc_final: 0.7334 (tpp) REVERT: J 137 ILE cc_start: 0.8009 (tt) cc_final: 0.7345 (tt) REVERT: J 139 HIS cc_start: 0.8207 (t70) cc_final: 0.7859 (t70) REVERT: J 150 GLN cc_start: 0.7809 (pt0) cc_final: 0.7409 (pt0) REVERT: J 162 ASN cc_start: 0.8936 (m110) cc_final: 0.8698 (m-40) REVERT: J 164 LEU cc_start: 0.8656 (tp) cc_final: 0.8448 (tp) REVERT: J 178 LEU cc_start: 0.9266 (mm) cc_final: 0.8975 (mm) REVERT: J 189 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.6662 (mtm180) REVERT: J 204 ASN cc_start: 0.8433 (m110) cc_final: 0.7909 (m110) REVERT: J 205 LYS cc_start: 0.8601 (tptp) cc_final: 0.8192 (tptp) REVERT: J 208 GLN cc_start: 0.8364 (pt0) cc_final: 0.7885 (pt0) REVERT: K 34 GLU cc_start: 0.8803 (pt0) cc_final: 0.8334 (pp20) REVERT: K 35 ASP cc_start: 0.8735 (m-30) cc_final: 0.8333 (m-30) REVERT: K 109 MET cc_start: 0.8092 (tpp) cc_final: 0.6989 (ptp) REVERT: K 110 PHE cc_start: 0.7962 (m-80) cc_final: 0.7138 (m-80) REVERT: K 132 MET cc_start: 0.7814 (ppp) cc_final: 0.7571 (ppp) REVERT: K 204 ASN cc_start: 0.8543 (m110) cc_final: 0.8298 (m110) REVERT: K 245 TRP cc_start: 0.8219 (m100) cc_final: 0.7685 (m100) REVERT: K 255 ASP cc_start: 0.7029 (t0) cc_final: 0.6824 (t0) REVERT: L 63 TRP cc_start: 0.6862 (m100) cc_final: 0.6138 (m100) REVERT: L 223 PHE cc_start: 0.5738 (p90) cc_final: 0.5378 (p90) REVERT: L 224 CYS cc_start: 0.7350 (p) cc_final: 0.7143 (p) REVERT: L 226 TYR cc_start: 0.7159 (p90) cc_final: 0.6141 (p90) REVERT: L 244 LEU cc_start: 0.8499 (mt) cc_final: 0.8221 (mt) REVERT: L 254 LYS cc_start: 0.8506 (tmtt) cc_final: 0.7740 (tmtt) REVERT: L 266 ASN cc_start: 0.8601 (m110) cc_final: 0.8190 (m110) REVERT: L 268 ASP cc_start: 0.7013 (t0) cc_final: 0.6729 (t70) REVERT: L 269 VAL cc_start: 0.8214 (t) cc_final: 0.7977 (t) REVERT: M 7 LEU cc_start: 0.8619 (tt) cc_final: 0.8408 (tt) REVERT: M 18 ASP cc_start: 0.7775 (t70) cc_final: 0.7395 (t70) REVERT: M 25 GLU cc_start: 0.8528 (tt0) cc_final: 0.8242 (tt0) REVERT: M 36 ILE cc_start: 0.8704 (mt) cc_final: 0.8499 (mt) REVERT: M 39 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7852 (tm-30) REVERT: M 89 GLU cc_start: 0.7408 (pm20) cc_final: 0.6758 (mp0) REVERT: M 101 VAL cc_start: 0.9163 (t) cc_final: 0.8943 (t) REVERT: M 154 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8640 (mm-30) REVERT: M 158 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7555 (tm-30) REVERT: M 159 THR cc_start: 0.8645 (m) cc_final: 0.8048 (p) REVERT: M 174 PHE cc_start: 0.7479 (t80) cc_final: 0.7155 (t80) REVERT: M 178 LEU cc_start: 0.8753 (mt) cc_final: 0.8174 (mt) REVERT: M 205 LYS cc_start: 0.8611 (mttp) cc_final: 0.8328 (mtmm) REVERT: M 207 GLN cc_start: 0.8591 (mm110) cc_final: 0.8179 (mm110) REVERT: M 209 ARG cc_start: 0.8751 (tmt170) cc_final: 0.8387 (ttp80) REVERT: M 224 CYS cc_start: 0.6457 (p) cc_final: 0.5893 (p) REVERT: N 11 GLU cc_start: 0.8099 (mp0) cc_final: 0.7839 (mp0) REVERT: N 23 HIS cc_start: 0.7823 (t70) cc_final: 0.7500 (t70) REVERT: N 102 GLN cc_start: 0.8748 (mp10) cc_final: 0.8235 (mp10) REVERT: N 104 MET cc_start: 0.8176 (ptm) cc_final: 0.7571 (ppp) REVERT: N 105 LYS cc_start: 0.9292 (mtmm) cc_final: 0.9053 (mttt) REVERT: N 154 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8284 (mm-30) REVERT: N 157 HIS cc_start: 0.8117 (m90) cc_final: 0.7755 (m90) REVERT: N 162 ASN cc_start: 0.8890 (m110) cc_final: 0.8522 (m110) REVERT: N 164 LEU cc_start: 0.8752 (mt) cc_final: 0.8516 (mt) REVERT: N 165 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8023 (mm-30) REVERT: N 183 ILE cc_start: 0.6982 (mt) cc_final: 0.6755 (mt) REVERT: N 206 GLU cc_start: 0.7739 (pp20) cc_final: 0.7212 (pp20) REVERT: N 213 GLN cc_start: 0.8847 (mt0) cc_final: 0.8347 (mt0) REVERT: N 233 HIS cc_start: 0.7736 (m90) cc_final: 0.7312 (m90) REVERT: N 256 ARG cc_start: 0.8442 (ttm110) cc_final: 0.7781 (ttm110) REVERT: O 23 HIS cc_start: 0.7811 (t70) cc_final: 0.7170 (t70) REVERT: O 48 MET cc_start: -0.1737 (ppp) cc_final: -0.2181 (ppp) REVERT: O 62 HIS cc_start: 0.7768 (m-70) cc_final: 0.7138 (m-70) REVERT: O 110 PHE cc_start: 0.8050 (m-80) cc_final: 0.7364 (m-10) REVERT: O 115 LEU cc_start: 0.8678 (tp) cc_final: 0.8469 (tp) REVERT: O 132 MET cc_start: 0.8167 (tmm) cc_final: 0.7546 (tmm) REVERT: O 152 LEU cc_start: 0.8808 (tp) cc_final: 0.8589 (tp) REVERT: O 193 LEU cc_start: 0.8694 (mm) cc_final: 0.8436 (mm) REVERT: O 205 LYS cc_start: 0.9248 (mmtm) cc_final: 0.9003 (mmtm) REVERT: O 211 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8194 (tp40) REVERT: P 62 HIS cc_start: 0.7932 (t70) cc_final: 0.7296 (t70) REVERT: P 87 TYR cc_start: 0.8502 (t80) cc_final: 0.8241 (t80) REVERT: P 104 MET cc_start: 0.9058 (mmp) cc_final: 0.8460 (mmp) REVERT: P 106 TRP cc_start: 0.8326 (t60) cc_final: 0.8022 (t60) REVERT: P 170 MET cc_start: 0.7757 (mtt) cc_final: 0.7115 (mpp) REVERT: P 172 ASN cc_start: 0.8913 (m-40) cc_final: 0.8557 (p0) REVERT: P 198 MET cc_start: 0.8403 (ppp) cc_final: 0.8160 (ppp) REVERT: P 199 ASP cc_start: 0.8109 (m-30) cc_final: 0.7533 (m-30) REVERT: P 202 ILE cc_start: 0.9198 (pt) cc_final: 0.8784 (pt) REVERT: P 205 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8550 (mtmm) REVERT: P 207 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7655 (mm-40) REVERT: P 222 ARG cc_start: 0.6571 (mmm-85) cc_final: 0.5982 (mmm160) REVERT: P 223 PHE cc_start: 0.6846 (m-80) cc_final: 0.5704 (m-80) REVERT: P 266 ASN cc_start: 0.6481 (p0) cc_final: 0.6087 (m-40) outliers start: 0 outliers final: 0 residues processed: 1186 average time/residue: 0.4641 time to fit residues: 857.1737 Evaluate side-chains 1109 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1109 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 107 optimal weight: 0.1980 chunk 269 optimal weight: 10.0000 chunk 201 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 155 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 207 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 HIS ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 157 HIS ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 GLN ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 HIS M 69 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN P 157 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.192860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.147068 restraints weight = 70332.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152679 restraints weight = 42575.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.156537 restraints weight = 29208.451| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34119 Z= 0.159 Angle : 0.756 13.453 46515 Z= 0.404 Chirality : 0.051 0.504 5006 Planarity : 0.005 0.082 5714 Dihedral : 14.824 174.930 5007 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3851 helix: 0.72 (0.12), residues: 1871 sheet: -0.82 (0.18), residues: 821 loop : -1.75 (0.16), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 15 HIS 0.020 0.001 HIS O 157 PHE 0.050 0.002 PHE M 201 TYR 0.021 0.001 TYR F 134 ARG 0.011 0.001 ARG D 256 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1746) hydrogen bonds : angle 5.43932 ( 5114) covalent geometry : bond 0.00339 (34119) covalent geometry : angle 0.75624 (46515) ********************** 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 1185 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1183 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8287 (mp0) cc_final: 0.7962 (mp0) REVERT: A 20 VAL cc_start: 0.8526 (m) cc_final: 0.8245 (t) REVERT: A 60 ILE cc_start: 0.8735 (mm) cc_final: 0.8373 (mm) REVERT: A 73 LYS cc_start: 0.7394 (mptt) cc_final: 0.6706 (mtpt) REVERT: A 79 VAL cc_start: 0.8045 (t) cc_final: 0.7538 (p) REVERT: A 80 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6478 (tm-30) REVERT: A 92 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8529 (mtpp) REVERT: A 98 GLU cc_start: 0.8084 (mp0) cc_final: 0.7697 (mp0) REVERT: A 104 MET cc_start: 0.8660 (ttm) cc_final: 0.8229 (ttm) REVERT: A 105 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8862 (mtpp) REVERT: A 129 GLN cc_start: 0.8459 (tt0) cc_final: 0.8221 (tt0) REVERT: A 135 LEU cc_start: 0.9145 (mt) cc_final: 0.8860 (mt) REVERT: A 152 LEU cc_start: 0.7026 (pt) cc_final: 0.5655 (tt) REVERT: A 155 ARG cc_start: 0.8306 (tpt90) cc_final: 0.7668 (mmm160) REVERT: A 158 GLN cc_start: 0.8637 (tt0) cc_final: 0.8338 (tt0) REVERT: A 161 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8227 (tppt) REVERT: A 164 LEU cc_start: 0.8422 (mt) cc_final: 0.8150 (mt) REVERT: A 183 ILE cc_start: 0.8890 (mt) cc_final: 0.8437 (mm) REVERT: A 190 LYS cc_start: 0.8380 (mtmm) cc_final: 0.7695 (mtpp) REVERT: A 203 PHE cc_start: 0.8302 (t80) cc_final: 0.7806 (t80) REVERT: A 254 LYS cc_start: 0.8007 (pptt) cc_final: 0.7751 (pptt) REVERT: A 267 LYS cc_start: 0.8172 (tmmt) cc_final: 0.7962 (pptt) REVERT: B 13 ASN cc_start: 0.7570 (m110) cc_final: 0.7295 (m110) REVERT: B 15 TRP cc_start: 0.7776 (m100) cc_final: 0.7193 (m100) REVERT: B 40 CYS cc_start: 0.7628 (t) cc_final: 0.6951 (p) REVERT: B 63 TRP cc_start: 0.7782 (m100) cc_final: 0.6478 (m100) REVERT: B 64 GLN cc_start: 0.6837 (tp40) cc_final: 0.6358 (mp10) REVERT: B 75 ILE cc_start: 0.7923 (mp) cc_final: 0.7651 (mm) REVERT: B 86 ILE cc_start: 0.8656 (pt) cc_final: 0.8239 (mm) REVERT: B 89 GLU cc_start: 0.7993 (tt0) cc_final: 0.7183 (tt0) REVERT: B 90 ARG cc_start: 0.8659 (tpt-90) cc_final: 0.8177 (tpp80) REVERT: B 100 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8127 (mtt-85) REVERT: B 104 MET cc_start: 0.8913 (mmp) cc_final: 0.8224 (mmp) REVERT: B 106 TRP cc_start: 0.8493 (t60) cc_final: 0.8181 (t60) REVERT: B 129 GLN cc_start: 0.8612 (pt0) cc_final: 0.8188 (pt0) REVERT: B 131 LEU cc_start: 0.8897 (tt) cc_final: 0.8455 (tt) REVERT: B 132 MET cc_start: 0.8778 (mmp) cc_final: 0.7865 (mmp) REVERT: B 138 GLU cc_start: 0.7870 (tp30) cc_final: 0.7650 (tp30) REVERT: B 139 HIS cc_start: 0.8614 (t70) cc_final: 0.8102 (t70) REVERT: B 158 GLN cc_start: 0.8412 (mp-120) cc_final: 0.8136 (mp-120) REVERT: B 178 LEU cc_start: 0.9067 (mm) cc_final: 0.8804 (mm) REVERT: B 186 ASN cc_start: 0.8240 (m-40) cc_final: 0.7921 (m-40) REVERT: B 198 MET cc_start: 0.8180 (tpt) cc_final: 0.7520 (tpp) REVERT: B 204 ASN cc_start: 0.7924 (p0) cc_final: 0.7672 (p0) REVERT: B 205 LYS cc_start: 0.8509 (tptp) cc_final: 0.8273 (tppp) REVERT: B 208 GLN cc_start: 0.8263 (pt0) cc_final: 0.7763 (pt0) REVERT: C 7 LEU cc_start: 0.8604 (tt) cc_final: 0.8403 (tt) REVERT: C 11 GLU cc_start: 0.8723 (tp30) cc_final: 0.8352 (tp30) REVERT: C 15 TRP cc_start: 0.8731 (m100) cc_final: 0.8293 (m-10) REVERT: C 28 ILE cc_start: 0.7615 (tp) cc_final: 0.7371 (tp) REVERT: C 34 GLU cc_start: 0.8359 (pp20) cc_final: 0.7888 (pp20) REVERT: C 38 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8076 (tm-30) REVERT: C 39 GLN cc_start: 0.8479 (tp40) cc_final: 0.7723 (tp40) REVERT: C 40 CYS cc_start: 0.8576 (m) cc_final: 0.7299 (t) REVERT: C 106 TRP cc_start: 0.6615 (t60) cc_final: 0.6133 (t60) REVERT: C 110 PHE cc_start: 0.7772 (m-80) cc_final: 0.7033 (m-80) REVERT: C 209 ARG cc_start: 0.8661 (ptt90) cc_final: 0.8429 (ptt90) REVERT: C 245 TRP cc_start: 0.8274 (m-90) cc_final: 0.7982 (m-90) REVERT: D 63 TRP cc_start: 0.5887 (m100) cc_final: 0.5656 (m100) REVERT: D 154 GLU cc_start: 0.6774 (mp0) cc_final: 0.6458 (mp0) REVERT: D 218 GLN cc_start: 0.8470 (mm110) cc_final: 0.7944 (mm110) REVERT: D 220 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7423 (pptt) REVERT: D 223 PHE cc_start: 0.6056 (p90) cc_final: 0.5645 (p90) REVERT: D 224 CYS cc_start: 0.7293 (p) cc_final: 0.7081 (p) REVERT: D 226 TYR cc_start: 0.7161 (p90) cc_final: 0.6095 (p90) REVERT: D 254 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8101 (ttmm) REVERT: D 266 ASN cc_start: 0.8528 (m110) cc_final: 0.8122 (m110) REVERT: E 7 LEU cc_start: 0.8107 (tt) cc_final: 0.7026 (tt) REVERT: E 10 GLU cc_start: 0.8341 (pp20) cc_final: 0.7646 (pp20) REVERT: E 11 GLU cc_start: 0.8281 (pm20) cc_final: 0.7644 (pm20) REVERT: E 16 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7728 (m90) REVERT: E 18 ASP cc_start: 0.8030 (t70) cc_final: 0.7771 (t70) REVERT: E 89 GLU cc_start: 0.7865 (pm20) cc_final: 0.6671 (mp0) REVERT: E 103 THR cc_start: 0.8910 (t) cc_final: 0.8648 (p) REVERT: E 133 LYS cc_start: 0.9196 (ptpp) cc_final: 0.8839 (pttm) REVERT: E 138 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6948 (tm-30) REVERT: E 150 GLN cc_start: 0.7836 (mm110) cc_final: 0.7446 (mm110) REVERT: E 154 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8584 (mm-30) REVERT: E 158 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7486 (tm-30) REVERT: E 159 THR cc_start: 0.8351 (m) cc_final: 0.7648 (p) REVERT: E 174 PHE cc_start: 0.7824 (t80) cc_final: 0.7434 (t80) REVERT: E 178 LEU cc_start: 0.8843 (mt) cc_final: 0.8244 (mt) REVERT: E 201 PHE cc_start: 0.8427 (t80) cc_final: 0.7966 (t80) REVERT: E 205 LYS cc_start: 0.8834 (mttt) cc_final: 0.8625 (mmtp) REVERT: F 23 HIS cc_start: 0.7820 (t70) cc_final: 0.7400 (t70) REVERT: F 65 VAL cc_start: 0.7385 (t) cc_final: 0.7084 (p) REVERT: F 104 MET cc_start: 0.8287 (ptm) cc_final: 0.7776 (ppp) REVERT: F 105 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8692 (mttm) REVERT: F 131 LEU cc_start: 0.8602 (tp) cc_final: 0.8162 (mm) REVERT: F 157 HIS cc_start: 0.7776 (m90) cc_final: 0.7543 (m90) REVERT: F 158 GLN cc_start: 0.9132 (mp10) cc_final: 0.8891 (mm-40) REVERT: F 197 PRO cc_start: 0.8190 (Cg_exo) cc_final: 0.7932 (Cg_endo) REVERT: F 198 MET cc_start: 0.8260 (ppp) cc_final: 0.7927 (ppp) REVERT: F 199 ASP cc_start: 0.8306 (m-30) cc_final: 0.8040 (m-30) REVERT: F 202 ILE cc_start: 0.8546 (mt) cc_final: 0.7685 (mt) REVERT: F 205 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8381 (mtmt) REVERT: F 208 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8186 (tm-30) REVERT: F 230 LYS cc_start: 0.8549 (mmmt) cc_final: 0.7960 (mmmm) REVERT: F 233 HIS cc_start: 0.7849 (m-70) cc_final: 0.7603 (m90) REVERT: F 243 VAL cc_start: 0.8028 (t) cc_final: 0.7718 (m) REVERT: F 260 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7406 (ptp-110) REVERT: F 267 LYS cc_start: 0.8827 (ptmt) cc_final: 0.8420 (pttt) REVERT: G 48 MET cc_start: -0.0574 (ppp) cc_final: -0.1331 (ppp) REVERT: G 70 TYR cc_start: 0.8040 (t80) cc_final: 0.7800 (t80) REVERT: G 97 GLN cc_start: 0.9018 (tt0) cc_final: 0.8773 (tp-100) REVERT: G 106 TRP cc_start: 0.7210 (t60) cc_final: 0.6978 (t60) REVERT: G 107 TYR cc_start: 0.8380 (t80) cc_final: 0.7709 (t80) REVERT: G 114 SER cc_start: 0.8673 (p) cc_final: 0.7968 (p) REVERT: G 131 LEU cc_start: 0.9289 (mt) cc_final: 0.9006 (mt) REVERT: G 150 GLN cc_start: 0.8437 (pp30) cc_final: 0.8145 (pp30) REVERT: G 157 HIS cc_start: 0.8800 (p90) cc_final: 0.8410 (p90) REVERT: G 161 LYS cc_start: 0.9211 (mmtt) cc_final: 0.8925 (mmmt) REVERT: G 168 ILE cc_start: 0.7777 (mt) cc_final: 0.7464 (pt) REVERT: G 171 PHE cc_start: 0.7033 (m-80) cc_final: 0.6537 (m-80) REVERT: G 175 GLU cc_start: 0.8667 (pm20) cc_final: 0.8247 (mm-30) REVERT: G 205 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8810 (mttp) REVERT: G 209 ARG cc_start: 0.8917 (ttp80) cc_final: 0.8343 (ttp80) REVERT: H 78 TRP cc_start: 0.7274 (m-10) cc_final: 0.5953 (m-10) REVERT: H 85 LEU cc_start: 0.8679 (tp) cc_final: 0.8324 (tp) REVERT: H 87 TYR cc_start: 0.8337 (t80) cc_final: 0.7817 (t80) REVERT: H 101 VAL cc_start: 0.8771 (p) cc_final: 0.8485 (p) REVERT: H 104 MET cc_start: 0.9081 (mmp) cc_final: 0.8323 (mmp) REVERT: H 106 TRP cc_start: 0.8380 (t60) cc_final: 0.7444 (t60) REVERT: H 109 MET cc_start: 0.7346 (mmp) cc_final: 0.6808 (mmm) REVERT: H 110 PHE cc_start: 0.7926 (m-10) cc_final: 0.7444 (m-10) REVERT: H 170 MET cc_start: 0.7894 (mtt) cc_final: 0.7199 (mpp) REVERT: H 199 ASP cc_start: 0.7936 (m-30) cc_final: 0.7688 (m-30) REVERT: H 222 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6385 (mmm160) REVERT: H 223 PHE cc_start: 0.7281 (m-10) cc_final: 0.6361 (m-80) REVERT: H 238 GLN cc_start: 0.7561 (mp10) cc_final: 0.7180 (mp10) REVERT: H 256 ARG cc_start: 0.8177 (ppt170) cc_final: 0.7684 (ppt170) REVERT: H 270 LYS cc_start: 0.8175 (mmpt) cc_final: 0.7814 (mmtm) REVERT: I 60 ILE cc_start: 0.8730 (mt) cc_final: 0.8281 (mm) REVERT: I 79 VAL cc_start: 0.8258 (t) cc_final: 0.7844 (p) REVERT: I 82 ASN cc_start: 0.8557 (t0) cc_final: 0.8303 (t0) REVERT: I 85 LEU cc_start: 0.8116 (tp) cc_final: 0.7761 (tp) REVERT: I 86 ILE cc_start: 0.8555 (pt) cc_final: 0.8266 (tp) REVERT: I 92 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8505 (mtpp) REVERT: I 97 GLN cc_start: 0.8061 (pm20) cc_final: 0.7741 (pm20) REVERT: I 113 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7667 (mmmm) REVERT: I 135 LEU cc_start: 0.8947 (mm) cc_final: 0.8683 (mm) REVERT: I 152 LEU cc_start: 0.7517 (pt) cc_final: 0.6615 (mp) REVERT: I 155 ARG cc_start: 0.8290 (tpt90) cc_final: 0.7398 (mmm160) REVERT: I 158 GLN cc_start: 0.9078 (tt0) cc_final: 0.8427 (tt0) REVERT: I 163 THR cc_start: 0.8166 (m) cc_final: 0.7700 (p) REVERT: I 164 LEU cc_start: 0.8570 (mt) cc_final: 0.8289 (mt) REVERT: I 174 PHE cc_start: 0.7429 (t80) cc_final: 0.7035 (t80) REVERT: I 183 ILE cc_start: 0.8925 (mt) cc_final: 0.8654 (mt) REVERT: I 186 ASN cc_start: 0.7275 (m-40) cc_final: 0.6842 (m-40) REVERT: I 190 LYS cc_start: 0.8583 (mtmm) cc_final: 0.7803 (mtpp) REVERT: I 203 PHE cc_start: 0.8131 (t80) cc_final: 0.7675 (t80) REVERT: I 238 GLN cc_start: 0.6914 (mt0) cc_final: 0.6642 (mt0) REVERT: I 253 VAL cc_start: 0.8073 (t) cc_final: 0.7830 (m) REVERT: I 260 ARG cc_start: 0.7532 (ptp-170) cc_final: 0.7079 (ptp-170) REVERT: J 13 ASN cc_start: 0.7567 (m110) cc_final: 0.7336 (m110) REVERT: J 15 TRP cc_start: 0.8138 (m100) cc_final: 0.7469 (m100) REVERT: J 40 CYS cc_start: 0.7497 (t) cc_final: 0.7180 (t) REVERT: J 62 HIS cc_start: 0.6960 (t-90) cc_final: 0.6688 (t-90) REVERT: J 64 GLN cc_start: 0.7294 (tp40) cc_final: 0.7021 (tp40) REVERT: J 86 ILE cc_start: 0.8844 (pt) cc_final: 0.8472 (mm) REVERT: J 104 MET cc_start: 0.8591 (mmt) cc_final: 0.7971 (mmt) REVERT: J 106 TRP cc_start: 0.8395 (t60) cc_final: 0.8089 (t60) REVERT: J 131 LEU cc_start: 0.8838 (tt) cc_final: 0.8282 (tt) REVERT: J 132 MET cc_start: 0.8439 (tpp) cc_final: 0.7342 (tpp) REVERT: J 135 LEU cc_start: 0.9058 (mt) cc_final: 0.8840 (mt) REVERT: J 137 ILE cc_start: 0.8021 (tt) cc_final: 0.7289 (tt) REVERT: J 139 HIS cc_start: 0.8469 (t70) cc_final: 0.7597 (t70) REVERT: J 150 GLN cc_start: 0.8001 (pt0) cc_final: 0.7670 (pt0) REVERT: J 162 ASN cc_start: 0.8958 (m110) cc_final: 0.8738 (m110) REVERT: J 178 LEU cc_start: 0.9274 (mm) cc_final: 0.9031 (mm) REVERT: J 189 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.6717 (mtm180) REVERT: J 204 ASN cc_start: 0.8414 (m110) cc_final: 0.7807 (m110) REVERT: J 205 LYS cc_start: 0.8613 (tptp) cc_final: 0.8226 (tptp) REVERT: J 208 GLN cc_start: 0.8362 (pt0) cc_final: 0.7860 (pt0) REVERT: K 34 GLU cc_start: 0.8738 (pt0) cc_final: 0.8358 (pp20) REVERT: K 35 ASP cc_start: 0.8644 (m-30) cc_final: 0.8296 (m-30) REVERT: K 38 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8074 (tm-30) REVERT: K 109 MET cc_start: 0.8105 (tpp) cc_final: 0.7033 (ptp) REVERT: K 110 PHE cc_start: 0.7945 (m-80) cc_final: 0.7108 (m-80) REVERT: K 132 MET cc_start: 0.7870 (ppp) cc_final: 0.7619 (ppp) REVERT: K 245 TRP cc_start: 0.8220 (m100) cc_final: 0.7658 (m100) REVERT: K 255 ASP cc_start: 0.7054 (t0) cc_final: 0.6836 (t0) REVERT: L 63 TRP cc_start: 0.7254 (m100) cc_final: 0.6392 (m100) REVERT: L 209 ARG cc_start: 0.8483 (mmp-170) cc_final: 0.8199 (mmm160) REVERT: L 223 PHE cc_start: 0.5711 (p90) cc_final: 0.5366 (p90) REVERT: L 226 TYR cc_start: 0.7211 (p90) cc_final: 0.6158 (p90) REVERT: L 244 LEU cc_start: 0.8505 (mt) cc_final: 0.8212 (mt) REVERT: L 254 LYS cc_start: 0.8485 (tmtt) cc_final: 0.7849 (tmtt) REVERT: L 268 ASP cc_start: 0.6999 (t0) cc_final: 0.6706 (t70) REVERT: L 269 VAL cc_start: 0.8200 (t) cc_final: 0.7942 (t) REVERT: M 10 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7655 (tm-30) REVERT: M 18 ASP cc_start: 0.7708 (t70) cc_final: 0.7427 (t70) REVERT: M 25 GLU cc_start: 0.8662 (tt0) cc_final: 0.8274 (tt0) REVERT: M 39 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7875 (tm-30) REVERT: M 89 GLU cc_start: 0.7012 (pm20) cc_final: 0.6792 (mp0) REVERT: M 101 VAL cc_start: 0.9160 (t) cc_final: 0.8934 (t) REVERT: M 154 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8578 (mm-30) REVERT: M 158 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7551 (tm-30) REVERT: M 159 THR cc_start: 0.8633 (m) cc_final: 0.8026 (p) REVERT: M 174 PHE cc_start: 0.7620 (t80) cc_final: 0.7258 (t80) REVERT: M 178 LEU cc_start: 0.8774 (mt) cc_final: 0.8345 (mt) REVERT: M 205 LYS cc_start: 0.8692 (mttp) cc_final: 0.8435 (mtmm) REVERT: M 207 GLN cc_start: 0.8575 (mm110) cc_final: 0.8173 (mm110) REVERT: M 209 ARG cc_start: 0.8699 (tmt170) cc_final: 0.8373 (ttp80) REVERT: M 224 CYS cc_start: 0.6526 (p) cc_final: 0.5986 (p) REVERT: N 11 GLU cc_start: 0.8061 (mp0) cc_final: 0.7693 (mp0) REVERT: N 23 HIS cc_start: 0.7804 (t70) cc_final: 0.7564 (t70) REVERT: N 102 GLN cc_start: 0.8752 (mp10) cc_final: 0.8249 (mp-120) REVERT: N 104 MET cc_start: 0.8333 (ptm) cc_final: 0.7602 (ppp) REVERT: N 105 LYS cc_start: 0.9305 (mtmm) cc_final: 0.9049 (mttt) REVERT: N 154 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8160 (mm-30) REVERT: N 157 HIS cc_start: 0.8085 (m90) cc_final: 0.7750 (m90) REVERT: N 158 GLN cc_start: 0.9028 (mp10) cc_final: 0.8775 (mp10) REVERT: N 162 ASN cc_start: 0.8834 (m110) cc_final: 0.8470 (m110) REVERT: N 164 LEU cc_start: 0.8731 (mt) cc_final: 0.8477 (mt) REVERT: N 165 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7944 (mm-30) REVERT: N 170 MET cc_start: 0.7920 (mpp) cc_final: 0.7620 (mpp) REVERT: N 183 ILE cc_start: 0.7076 (mt) cc_final: 0.6875 (mt) REVERT: N 206 GLU cc_start: 0.7871 (pp20) cc_final: 0.7160 (pp20) REVERT: N 213 GLN cc_start: 0.8802 (mt0) cc_final: 0.8301 (mt0) REVERT: N 233 HIS cc_start: 0.7729 (m90) cc_final: 0.7312 (m90) REVERT: N 256 ARG cc_start: 0.8391 (ttm110) cc_final: 0.7719 (ttm110) REVERT: N 260 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7581 (ptp-110) REVERT: O 23 HIS cc_start: 0.7768 (t70) cc_final: 0.7162 (t70) REVERT: O 48 MET cc_start: -0.1736 (ppp) cc_final: -0.2179 (ppp) REVERT: O 62 HIS cc_start: 0.7590 (m-70) cc_final: 0.6861 (m-70) REVERT: O 109 MET cc_start: 0.7677 (tpp) cc_final: 0.7424 (tpt) REVERT: O 110 PHE cc_start: 0.7971 (m-80) cc_final: 0.7435 (m-80) REVERT: O 152 LEU cc_start: 0.8842 (tp) cc_final: 0.8516 (tp) REVERT: O 157 HIS cc_start: 0.8817 (p90) cc_final: 0.8559 (p90) REVERT: O 170 MET cc_start: 0.7695 (mmp) cc_final: 0.7458 (mmp) REVERT: O 171 PHE cc_start: 0.7794 (m-10) cc_final: 0.7321 (m-80) REVERT: O 193 LEU cc_start: 0.8702 (mm) cc_final: 0.8443 (mm) REVERT: O 205 LYS cc_start: 0.9263 (mmtm) cc_final: 0.9014 (mmtm) REVERT: O 211 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8206 (tp40) REVERT: P 62 HIS cc_start: 0.8041 (t70) cc_final: 0.7376 (t70) REVERT: P 87 TYR cc_start: 0.8516 (t80) cc_final: 0.8266 (t80) REVERT: P 104 MET cc_start: 0.9025 (mmp) cc_final: 0.8398 (mmp) REVERT: P 106 TRP cc_start: 0.8304 (t60) cc_final: 0.7977 (t60) REVERT: P 170 MET cc_start: 0.7774 (mtt) cc_final: 0.7124 (mpp) REVERT: P 172 ASN cc_start: 0.8934 (m-40) cc_final: 0.8593 (p0) REVERT: P 198 MET cc_start: 0.8458 (ppp) cc_final: 0.8163 (ppp) REVERT: P 199 ASP cc_start: 0.8095 (m-30) cc_final: 0.7485 (m-30) REVERT: P 202 ILE cc_start: 0.9165 (pt) cc_final: 0.8499 (pt) REVERT: P 222 ARG cc_start: 0.6596 (mmm-85) cc_final: 0.6002 (mmm160) REVERT: P 223 PHE cc_start: 0.6822 (m-80) cc_final: 0.5787 (m-80) REVERT: P 233 HIS cc_start: 0.6531 (m-70) cc_final: 0.6306 (m-70) REVERT: P 238 GLN cc_start: 0.7061 (mp10) cc_final: 0.6729 (mp10) outliers start: 2 outliers final: 1 residues processed: 1183 average time/residue: 0.5302 time to fit residues: 990.8566 Evaluate side-chains 1119 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1117 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 218 optimal weight: 0.0070 chunk 63 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 334 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 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** E 23 HIS E 204 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 HIS ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN G 208 GLN H 157 HIS ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 ASN ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 HIS M 23 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN P 157 HIS ** P 213 GLN ** 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 = 0.4436 r_free = 0.4436 target = 0.190643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144845 restraints weight = 70387.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150373 restraints weight = 42703.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154248 restraints weight = 29396.674| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34119 Z= 0.172 Angle : 0.756 13.177 46515 Z= 0.403 Chirality : 0.050 0.270 5006 Planarity : 0.005 0.061 5714 Dihedral : 14.857 175.484 5007 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 3851 helix: 0.71 (0.12), residues: 1871 sheet: -0.82 (0.18), residues: 824 loop : -1.80 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP M 63 HIS 0.018 0.001 HIS O 157 PHE 0.041 0.002 PHE D 110 TYR 0.031 0.001 TYR F 134 ARG 0.012 0.001 ARG F 209 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 1746) hydrogen bonds : angle 5.49765 ( 5114) covalent geometry : bond 0.00364 (34119) covalent geometry : angle 0.75571 (46515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17104.27 seconds wall clock time: 294 minutes 57.53 seconds (17697.53 seconds total)