Starting phenix.real_space_refine on Fri Mar 22 11:24:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/03_2024/7zpp_14860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/03_2024/7zpp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/03_2024/7zpp_14860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/03_2024/7zpp_14860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/03_2024/7zpp_14860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/03_2024/7zpp_14860.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.76, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 13.58 Conformation dependent library (CDL) restraints added in 5.4 seconds 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7254 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 62 sheets defined 52.2% alpha, 18.3% beta 20 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 11.41 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: 12.40 Time building geometry restraints manager: 14.66 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: 97.45 - 105.45: 1008 105.45 - 113.46: 18832 113.46 - 121.46: 18222 121.46 - 129.47: 8055 129.47 - 137.47: 398 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 2.440 nonbonded pdb=" OG1 THR A 95 " pdb=" OE1 GLU A 98 " model vdw 2.167 2.440 nonbonded pdb=" O ASP G 18 " pdb=" OG SER G 21 " model vdw 2.170 2.440 nonbonded pdb=" O ASP O 18 " pdb=" OG SER O 21 " model vdw 2.170 2.440 nonbonded pdb=" ND1 HIS M 23 " pdb=" O ILE M 28 " model vdw 2.195 2.520 ... (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 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: 1.650 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: 0.020 Extract box with map and model: 7.620 Check model and map are aligned: 0.480 Set scattering table: 0.320 Process input model: 93.170 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.190 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.790 ------------------------------------------------------------------------------- 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= 0.169 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 1225 time to evaluate : 3.389 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: 0.5021 time to fit residues: 956.5491 Evaluate side-chains 1048 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1048 time to evaluate : 3.271 ------------------------------------------------------------------------------- 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: 0.0270 chunk 294 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 352 optimal weight: 10.0000 overall best weight: 1.5642 ------------------------------------------------------------------------------- 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** B 16 HIS B 139 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 129 GLN C 186 ASN ** 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 186 ASN D 266 ASN E 23 HIS E 102 GLN E 204 ASN ** F 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS G 148 GLN G 208 GLN G 211 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS H 242 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 HIS J 16 HIS ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 242 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 129 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 HIS M 102 GLN N 213 GLN ** N 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 HIS O 102 GLN O 208 GLN O 211 GLN ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34119 Z= 0.339 Angle : 0.756 14.421 46515 Z= 0.402 Chirality : 0.049 0.229 5006 Planarity : 0.006 0.076 5714 Dihedral : 14.601 174.352 5007 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 0.27 % Allowed : 5.14 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.13), residues: 3851 helix: 1.21 (0.12), residues: 1872 sheet: -0.53 (0.17), residues: 869 loop : -1.58 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP H 78 HIS 0.019 0.002 HIS N 62 PHE 0.040 0.002 PHE F 26 TYR 0.037 0.002 TYR E 70 ARG 0.014 0.001 ARG G 155 *********************** 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 1194 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1185 time to evaluate : 3.500 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: A 15 TRP cc_start: 0.6872 (m-90) cc_final: 0.5987 (m-90) REVERT: A 66 ASP cc_start: 0.7624 (t0) cc_final: 0.7363 (t70) REVERT: A 79 VAL cc_start: 0.8001 (t) cc_final: 0.7576 (m) REVERT: A 92 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8510 (mtpp) REVERT: A 98 GLU cc_start: 0.8043 (mp0) cc_final: 0.7807 (mp0) REVERT: A 100 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7676 (mtm180) REVERT: A 104 MET cc_start: 0.8331 (ttm) cc_final: 0.7670 (ttm) REVERT: A 107 TYR cc_start: 0.8436 (t80) cc_final: 0.8175 (t80) REVERT: A 118 ASP cc_start: 0.7951 (p0) cc_final: 0.7569 (p0) REVERT: A 132 MET cc_start: 0.7572 (mmm) cc_final: 0.7322 (mmm) REVERT: A 150 GLN cc_start: 0.8098 (mp10) cc_final: 0.7683 (mp10) REVERT: A 158 GLN cc_start: 0.8733 (tt0) cc_final: 0.8487 (tt0) REVERT: A 164 LEU cc_start: 0.8286 (mt) cc_final: 0.8026 (mt) REVERT: A 178 LEU cc_start: 0.7937 (tp) cc_final: 0.7723 (tp) REVERT: A 184 THR cc_start: 0.8392 (m) cc_final: 0.7955 (p) REVERT: A 201 PHE cc_start: 0.8505 (t80) cc_final: 0.8189 (t80) REVERT: A 203 PHE cc_start: 0.8222 (t80) cc_final: 0.7785 (t80) REVERT: A 208 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 254 LYS cc_start: 0.8124 (pptt) cc_final: 0.7493 (pptt) REVERT: A 260 ARG cc_start: 0.6735 (ptm160) cc_final: 0.6533 (ptm160) REVERT: B 86 ILE cc_start: 0.8825 (pt) cc_final: 0.8498 (mm) REVERT: B 89 GLU cc_start: 0.7617 (tt0) cc_final: 0.7268 (tt0) REVERT: B 92 LYS cc_start: 0.8589 (tppt) cc_final: 0.8188 (tptp) REVERT: B 100 ARG cc_start: 0.8333 (mtt180) cc_final: 0.7648 (mtt-85) REVERT: B 104 MET cc_start: 0.8425 (mmp) cc_final: 0.8194 (mmp) REVERT: B 105 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8679 (mtpp) REVERT: B 129 GLN cc_start: 0.8418 (pt0) cc_final: 0.7997 (pt0) REVERT: B 131 LEU cc_start: 0.8874 (tt) cc_final: 0.8474 (tt) REVERT: B 132 MET cc_start: 0.8092 (mmp) cc_final: 0.7366 (mmp) REVERT: B 184 THR cc_start: 0.8749 (p) cc_final: 0.8494 (p) REVERT: B 198 MET cc_start: 0.8029 (tpt) cc_final: 0.7682 (tpp) REVERT: B 204 ASN cc_start: 0.7143 (p0) cc_final: 0.6755 (p0) REVERT: B 205 LYS cc_start: 0.8416 (tptp) cc_final: 0.8214 (tppp) REVERT: B 208 GLN cc_start: 0.7758 (pt0) cc_final: 0.7481 (pt0) REVERT: C 34 GLU cc_start: 0.8353 (pt0) cc_final: 0.7599 (pp20) REVERT: C 35 ASP cc_start: 0.8321 (m-30) cc_final: 0.7666 (m-30) REVERT: C 106 TRP cc_start: 0.5536 (t60) cc_final: 0.5209 (t60) REVERT: C 110 PHE cc_start: 0.7227 (m-80) cc_final: 0.6754 (m-80) REVERT: C 132 MET cc_start: 0.7734 (ppp) cc_final: 0.6964 (ppp) REVERT: C 157 HIS cc_start: 0.7151 (m90) cc_final: 0.6926 (m90) REVERT: C 186 ASN cc_start: 0.6510 (m-40) cc_final: 0.6238 (m110) REVERT: C 206 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7023 (pm20) REVERT: C 209 ARG cc_start: 0.7985 (ptt90) cc_final: 0.7479 (ptt90) REVERT: D 218 GLN cc_start: 0.8167 (mm110) cc_final: 0.7876 (mm110) REVERT: D 223 PHE cc_start: 0.6173 (p90) cc_final: 0.5791 (p90) REVERT: D 226 TYR cc_start: 0.6535 (p90) cc_final: 0.6041 (p90) REVERT: D 266 ASN cc_start: 0.8317 (m110) cc_final: 0.8113 (m-40) REVERT: D 269 VAL cc_start: 0.8031 (m) cc_final: 0.7813 (m) REVERT: E 7 LEU cc_start: 0.7693 (tt) cc_final: 0.7473 (tt) REVERT: E 10 GLU cc_start: 0.7411 (tp30) cc_final: 0.7072 (tp30) REVERT: E 12 HIS cc_start: 0.7248 (t70) cc_final: 0.6255 (t70) REVERT: E 15 TRP cc_start: 0.8115 (m-10) cc_final: 0.7694 (m-10) REVERT: E 16 HIS cc_start: 0.7355 (m-70) cc_final: 0.7021 (m170) REVERT: E 36 ILE cc_start: 0.8315 (mt) cc_final: 0.8112 (mm) REVERT: E 150 GLN cc_start: 0.7403 (mm110) cc_final: 0.7182 (mm-40) REVERT: E 159 THR cc_start: 0.8418 (m) cc_final: 0.7695 (p) REVERT: E 165 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7308 (mm-30) REVERT: E 178 LEU cc_start: 0.8498 (mt) cc_final: 0.8267 (mt) REVERT: E 199 ASP cc_start: 0.8261 (m-30) cc_final: 0.7163 (m-30) REVERT: E 200 ILE cc_start: 0.8359 (mp) cc_final: 0.8138 (mp) REVERT: E 206 GLU cc_start: 0.8386 (pt0) cc_final: 0.7731 (pt0) REVERT: E 207 GLN cc_start: 0.8055 (mm110) cc_final: 0.7394 (mm-40) REVERT: F 65 VAL cc_start: 0.7125 (t) cc_final: 0.6786 (p) REVERT: F 161 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7672 (ptpp) REVERT: F 183 ILE cc_start: 0.6030 (mt) cc_final: 0.5593 (mt) REVERT: F 198 MET cc_start: 0.7890 (ppp) cc_final: 0.7661 (ppp) REVERT: F 199 ASP cc_start: 0.7990 (m-30) cc_final: 0.7789 (m-30) REVERT: F 202 ILE cc_start: 0.8309 (mt) cc_final: 0.7820 (mt) REVERT: F 203 PHE cc_start: 0.7302 (t80) cc_final: 0.6870 (t80) REVERT: F 242 GLN cc_start: 0.7060 (tt0) cc_final: 0.6666 (pp30) REVERT: F 243 VAL cc_start: 0.8371 (t) cc_final: 0.7134 (m) REVERT: F 256 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7545 (ttm110) REVERT: F 260 ARG cc_start: 0.7428 (mtm110) cc_final: 0.7209 (ttp-110) REVERT: G 48 MET cc_start: -0.0459 (ppp) cc_final: -0.1376 (ppp) REVERT: G 85 LEU cc_start: 0.7183 (tp) cc_final: 0.6820 (tp) REVERT: G 132 MET cc_start: 0.7612 (tmm) cc_final: 0.7352 (tmm) REVERT: G 157 HIS cc_start: 0.7877 (m90) cc_final: 0.7651 (m90) REVERT: G 164 LEU cc_start: 0.8242 (mt) cc_final: 0.8027 (mt) REVERT: G 183 ILE cc_start: 0.7198 (mt) cc_final: 0.6937 (mt) REVERT: G 197 PRO cc_start: 0.8311 (Cg_exo) cc_final: 0.8067 (Cg_endo) REVERT: G 210 ILE cc_start: 0.8515 (pt) cc_final: 0.8184 (pt) REVERT: H 62 HIS cc_start: 0.6889 (t-90) cc_final: 0.6228 (t-170) REVERT: H 100 ARG cc_start: 0.5194 (mtt90) cc_final: 0.4511 (mtm-85) REVERT: H 110 PHE cc_start: 0.7883 (m-10) cc_final: 0.7584 (m-10) REVERT: I 60 ILE cc_start: 0.8822 (mt) cc_final: 0.8237 (mm) REVERT: I 66 ASP cc_start: 0.7792 (t0) cc_final: 0.7452 (t70) REVERT: I 79 VAL cc_start: 0.7881 (t) cc_final: 0.7534 (m) REVERT: I 86 ILE cc_start: 0.8491 (pt) cc_final: 0.8008 (mp) REVERT: I 92 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8425 (mtpp) REVERT: I 100 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7622 (mtm-85) REVERT: I 102 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8488 (mm-40) REVERT: I 118 ASP cc_start: 0.8090 (p0) cc_final: 0.7521 (p0) REVERT: I 129 GLN cc_start: 0.7568 (tt0) cc_final: 0.7310 (tt0) REVERT: I 155 ARG cc_start: 0.8330 (tpt90) cc_final: 0.7325 (mmm160) REVERT: I 158 GLN cc_start: 0.8761 (tt0) cc_final: 0.8313 (tt0) REVERT: I 164 LEU cc_start: 0.8509 (mt) cc_final: 0.8273 (mt) REVERT: I 178 LEU cc_start: 0.8150 (tp) cc_final: 0.7630 (tp) REVERT: I 182 LEU cc_start: 0.8481 (mt) cc_final: 0.8271 (mt) REVERT: I 184 THR cc_start: 0.8641 (m) cc_final: 0.8191 (p) REVERT: I 190 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7353 (mtpp) REVERT: I 203 PHE cc_start: 0.8325 (t80) cc_final: 0.7834 (t80) REVERT: I 208 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7943 (tm-30) REVERT: I 272 ILE cc_start: 0.7991 (mt) cc_final: 0.7661 (mm) REVERT: J 70 TYR cc_start: 0.7604 (t80) cc_final: 0.6695 (t80) REVERT: J 73 LYS cc_start: 0.8197 (mttt) cc_final: 0.7171 (mttt) REVERT: J 86 ILE cc_start: 0.8945 (pt) cc_final: 0.8471 (mm) REVERT: J 92 LYS cc_start: 0.8681 (tptp) cc_final: 0.8324 (tptp) REVERT: J 105 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8867 (ttpt) REVERT: J 131 LEU cc_start: 0.8499 (tt) cc_final: 0.8147 (tt) REVERT: J 132 MET cc_start: 0.8275 (mmp) cc_final: 0.7550 (mmp) REVERT: J 160 LEU cc_start: 0.8745 (tt) cc_final: 0.8341 (tt) REVERT: J 161 LYS cc_start: 0.8791 (ptpt) cc_final: 0.8394 (pttm) REVERT: J 162 ASN cc_start: 0.8701 (m110) cc_final: 0.8441 (m-40) REVERT: J 178 LEU cc_start: 0.8976 (mm) cc_final: 0.8664 (mm) REVERT: J 201 PHE cc_start: 0.9001 (t80) cc_final: 0.8609 (t80) REVERT: J 203 PHE cc_start: 0.8365 (t80) cc_final: 0.6888 (t80) REVERT: J 204 ASN cc_start: 0.7197 (m110) cc_final: 0.6893 (p0) REVERT: J 205 LYS cc_start: 0.8456 (tptp) cc_final: 0.7726 (tptp) REVERT: J 207 GLN cc_start: 0.7721 (mp10) cc_final: 0.7456 (mt0) REVERT: J 208 GLN cc_start: 0.7716 (pt0) cc_final: 0.7284 (pt0) REVERT: K 15 TRP cc_start: 0.8394 (m100) cc_final: 0.8024 (m100) REVERT: K 34 GLU cc_start: 0.8352 (pt0) cc_final: 0.7777 (pp20) REVERT: K 35 ASP cc_start: 0.8255 (m-30) cc_final: 0.8014 (m-30) REVERT: K 36 ILE cc_start: 0.8955 (mm) cc_final: 0.8739 (mm) REVERT: K 38 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7497 (tm-30) REVERT: K 110 PHE cc_start: 0.7180 (m-80) cc_final: 0.6797 (m-80) REVERT: K 132 MET cc_start: 0.6605 (ppp) cc_final: 0.6212 (ppp) REVERT: K 157 HIS cc_start: 0.7958 (m-70) cc_final: 0.7412 (m-70) REVERT: K 206 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: K 244 LEU cc_start: 0.8252 (mm) cc_final: 0.8010 (mm) REVERT: L 209 ARG cc_start: 0.8098 (mmp80) cc_final: 0.7756 (mmp80) REVERT: L 226 TYR cc_start: 0.6748 (p90) cc_final: 0.5918 (p90) REVERT: L 244 LEU cc_start: 0.8520 (mt) cc_final: 0.8277 (mt) REVERT: L 259 ASP cc_start: 0.8513 (m-30) cc_final: 0.8134 (m-30) REVERT: M 7 LEU cc_start: 0.7623 (tt) cc_final: 0.7284 (tt) REVERT: M 12 HIS cc_start: 0.7240 (t-90) cc_final: 0.6280 (t-170) REVERT: M 14 LYS cc_start: 0.8302 (mttp) cc_final: 0.7991 (mtmt) REVERT: M 15 TRP cc_start: 0.8006 (m-10) cc_final: 0.7693 (m-10) REVERT: M 16 HIS cc_start: 0.7324 (m-70) cc_final: 0.6847 (m170) REVERT: M 76 LEU cc_start: 0.6513 (tp) cc_final: 0.5898 (tp) REVERT: M 158 GLN cc_start: 0.7088 (tm-30) cc_final: 0.6566 (tm-30) REVERT: M 159 THR cc_start: 0.8470 (m) cc_final: 0.7485 (p) REVERT: M 199 ASP cc_start: 0.8375 (m-30) cc_final: 0.7226 (m-30) REVERT: M 202 ILE cc_start: 0.8950 (mm) cc_final: 0.8476 (mm) REVERT: M 205 LYS cc_start: 0.8918 (mttm) cc_final: 0.8368 (mtmt) REVERT: N 21 SER cc_start: 0.7431 (m) cc_final: 0.7197 (m) REVERT: N 65 VAL cc_start: 0.6892 (t) cc_final: 0.6612 (p) REVERT: N 104 MET cc_start: 0.8145 (ptm) cc_final: 0.7881 (ptm) REVERT: N 183 ILE cc_start: 0.6376 (mt) cc_final: 0.6030 (mt) REVERT: N 198 MET cc_start: 0.7618 (ppp) cc_final: 0.7158 (ppp) REVERT: N 199 ASP cc_start: 0.7897 (m-30) cc_final: 0.7599 (m-30) REVERT: N 203 PHE cc_start: 0.7311 (t80) cc_final: 0.6927 (t80) REVERT: N 208 GLN cc_start: 0.8010 (tt0) cc_final: 0.7725 (tt0) REVERT: N 213 GLN cc_start: 0.8767 (mt0) cc_final: 0.8537 (mt0) REVERT: N 230 LYS cc_start: 0.8387 (mttt) cc_final: 0.7584 (ttpp) REVERT: N 236 GLU cc_start: 0.7705 (pm20) cc_final: 0.7451 (pm20) REVERT: N 237 TRP cc_start: 0.8171 (m100) cc_final: 0.7780 (m100) REVERT: N 242 GLN cc_start: 0.7335 (tt0) cc_final: 0.7040 (pp30) REVERT: N 243 VAL cc_start: 0.8468 (t) cc_final: 0.7459 (m) REVERT: N 244 LEU cc_start: 0.8162 (tt) cc_final: 0.7857 (tt) REVERT: N 256 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7426 (ttm110) REVERT: N 270 LYS cc_start: 0.8037 (mptt) cc_final: 0.6716 (mptt) REVERT: O 23 HIS cc_start: 0.6426 (t70) cc_final: 0.5792 (t70) REVERT: O 29 PRO cc_start: 0.5044 (Cg_exo) cc_final: 0.4775 (Cg_endo) REVERT: O 48 MET cc_start: -0.1081 (ppp) cc_final: -0.2068 (ppp) REVERT: O 85 LEU cc_start: 0.7240 (tp) cc_final: 0.6969 (tp) REVERT: O 104 MET cc_start: 0.7752 (pmm) cc_final: 0.7424 (pmm) REVERT: O 132 MET cc_start: 0.7642 (tmm) cc_final: 0.7064 (tmm) REVERT: O 157 HIS cc_start: 0.7938 (m90) cc_final: 0.7678 (m90) REVERT: O 209 ARG cc_start: 0.8268 (ptm-80) cc_final: 0.8005 (ptm-80) REVERT: O 211 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7746 (tp40) REVERT: P 62 HIS cc_start: 0.7011 (t-90) cc_final: 0.6430 (t-170) REVERT: P 100 ARG cc_start: 0.4997 (mtt90) cc_final: 0.4664 (mtm-85) REVERT: P 101 VAL cc_start: 0.8825 (p) cc_final: 0.8587 (p) REVERT: P 132 MET cc_start: 0.4990 (tmm) cc_final: 0.4733 (tmm) REVERT: P 170 MET cc_start: 0.7656 (mtt) cc_final: 0.7383 (mpp) REVERT: P 254 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8123 (mmtt) outliers start: 9 outliers final: 3 residues processed: 1189 average time/residue: 0.4841 time to fit residues: 893.5359 Evaluate side-chains 1105 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1100 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 0.0060 chunk 109 optimal weight: 0.0770 chunk 293 optimal weight: 0.1980 chunk 239 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 381 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 350 optimal weight: 0.6980 chunk 120 optimal weight: 0.4980 chunk 283 optimal weight: 0.8980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 ASN B 102 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 69 HIS ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS H 207 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 GLN O 208 GLN P 62 HIS ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5666 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34119 Z= 0.189 Angle : 0.646 14.436 46515 Z= 0.337 Chirality : 0.046 0.224 5006 Planarity : 0.004 0.058 5714 Dihedral : 14.540 173.639 5007 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 0.18 % Allowed : 3.43 % Favored : 96.39 % 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: 0.10 (0.13), residues: 3851 helix: 1.29 (0.12), residues: 1870 sheet: -0.37 (0.17), residues: 843 loop : -1.58 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 78 HIS 0.012 0.001 HIS F 62 PHE 0.030 0.002 PHE D 203 TYR 0.022 0.001 TYR E 70 ARG 0.005 0.000 ARG M 209 *********************** 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 1188 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1182 time to evaluate : 3.498 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: A 15 TRP cc_start: 0.6762 (m-90) cc_final: 0.5644 (m-90) REVERT: A 48 MET cc_start: 0.4931 (mmm) cc_final: 0.4261 (mmm) REVERT: A 79 VAL cc_start: 0.7809 (t) cc_final: 0.7186 (p) REVERT: A 92 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8430 (mtpp) REVERT: A 104 MET cc_start: 0.8221 (ttm) cc_final: 0.7980 (ttm) REVERT: A 107 TYR cc_start: 0.8362 (t80) cc_final: 0.8015 (t80) REVERT: A 118 ASP cc_start: 0.7841 (p0) cc_final: 0.7501 (p0) REVERT: A 135 LEU cc_start: 0.8673 (mt) cc_final: 0.8117 (mt) REVERT: A 152 LEU cc_start: 0.7465 (pt) cc_final: 0.6367 (mp) REVERT: A 155 ARG cc_start: 0.8425 (tpt90) cc_final: 0.7345 (mmm160) REVERT: A 158 GLN cc_start: 0.8728 (tt0) cc_final: 0.8377 (tt0) REVERT: A 161 LYS cc_start: 0.8595 (tptt) cc_final: 0.8346 (tptt) REVERT: A 184 THR cc_start: 0.8290 (m) cc_final: 0.7921 (p) REVERT: A 198 MET cc_start: 0.7999 (ttm) cc_final: 0.7666 (ttm) REVERT: A 201 PHE cc_start: 0.8437 (t80) cc_final: 0.7897 (t80) REVERT: A 203 PHE cc_start: 0.8115 (t80) cc_final: 0.7652 (t80) REVERT: A 262 LEU cc_start: 0.7467 (tt) cc_final: 0.7252 (tp) REVERT: B 40 CYS cc_start: 0.7420 (t) cc_final: 0.7179 (p) REVERT: B 63 TRP cc_start: 0.7738 (m100) cc_final: 0.6468 (m100) REVERT: B 64 GLN cc_start: 0.6935 (tp40) cc_final: 0.6647 (mp10) REVERT: B 65 VAL cc_start: 0.8740 (t) cc_final: 0.8367 (t) REVERT: B 86 ILE cc_start: 0.8811 (pt) cc_final: 0.8293 (mm) REVERT: B 89 GLU cc_start: 0.7477 (tt0) cc_final: 0.7244 (tt0) REVERT: B 100 ARG cc_start: 0.8431 (mtt180) cc_final: 0.7706 (mtt-85) REVERT: B 105 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8551 (mtpp) REVERT: B 129 GLN cc_start: 0.8360 (pt0) cc_final: 0.7988 (pt0) REVERT: B 131 LEU cc_start: 0.8821 (tt) cc_final: 0.8421 (tt) REVERT: B 132 MET cc_start: 0.8125 (mmp) cc_final: 0.7395 (mmp) REVERT: B 198 MET cc_start: 0.7852 (tpt) cc_final: 0.7445 (tpp) REVERT: B 204 ASN cc_start: 0.7087 (p0) cc_final: 0.6670 (p0) REVERT: B 207 GLN cc_start: 0.7759 (mm110) cc_final: 0.7464 (mm-40) REVERT: B 208 GLN cc_start: 0.7623 (pt0) cc_final: 0.7410 (pt0) REVERT: C 11 GLU cc_start: 0.7331 (tp30) cc_final: 0.6038 (tp30) REVERT: C 28 ILE cc_start: 0.7748 (tp) cc_final: 0.7444 (tp) REVERT: C 34 GLU cc_start: 0.8333 (pt0) cc_final: 0.7626 (pp20) REVERT: C 35 ASP cc_start: 0.8238 (m-30) cc_final: 0.7406 (m-30) REVERT: C 106 TRP cc_start: 0.5369 (t60) cc_final: 0.5160 (t60) REVERT: C 110 PHE cc_start: 0.7194 (m-80) cc_final: 0.6841 (m-80) REVERT: C 132 MET cc_start: 0.7707 (ppp) cc_final: 0.7024 (ppp) REVERT: C 157 HIS cc_start: 0.7008 (m90) cc_final: 0.6663 (m170) REVERT: C 162 ASN cc_start: 0.8316 (m-40) cc_final: 0.7285 (m-40) REVERT: C 186 ASN cc_start: 0.6324 (m-40) cc_final: 0.6067 (m110) REVERT: C 209 ARG cc_start: 0.8111 (ptt90) cc_final: 0.7238 (ptt90) REVERT: D 226 TYR cc_start: 0.6555 (p90) cc_final: 0.5962 (p90) REVERT: D 254 LYS cc_start: 0.8134 (tptt) cc_final: 0.7845 (tppt) REVERT: D 261 TYR cc_start: 0.7248 (m-80) cc_final: 0.6998 (m-80) REVERT: D 266 ASN cc_start: 0.8313 (m110) cc_final: 0.8022 (m-40) REVERT: D 269 VAL cc_start: 0.7961 (m) cc_final: 0.7757 (m) REVERT: E 10 GLU cc_start: 0.7336 (tp30) cc_final: 0.6921 (tp30) REVERT: E 12 HIS cc_start: 0.7272 (t70) cc_final: 0.6323 (t70) REVERT: E 150 GLN cc_start: 0.7491 (mm110) cc_final: 0.6693 (mm110) REVERT: E 159 THR cc_start: 0.8275 (m) cc_final: 0.7650 (t) REVERT: E 201 PHE cc_start: 0.7513 (t80) cc_final: 0.7247 (t80) REVERT: E 204 ASN cc_start: 0.7694 (t0) cc_final: 0.7476 (t0) REVERT: E 206 GLU cc_start: 0.8164 (pt0) cc_final: 0.7072 (pp20) REVERT: E 210 ILE cc_start: 0.8801 (mt) cc_final: 0.8589 (mm) REVERT: F 183 ILE cc_start: 0.6144 (mt) cc_final: 0.5745 (mt) REVERT: F 198 MET cc_start: 0.7602 (ppp) cc_final: 0.7217 (ppp) REVERT: F 199 ASP cc_start: 0.7817 (m-30) cc_final: 0.7528 (m-30) REVERT: F 202 ILE cc_start: 0.8084 (mt) cc_final: 0.7809 (mt) REVERT: F 203 PHE cc_start: 0.7277 (t80) cc_final: 0.6726 (t80) REVERT: F 205 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7594 (mtmt) REVERT: F 230 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7768 (mmmm) REVERT: F 231 ARG cc_start: 0.7668 (mpp-170) cc_final: 0.7167 (mpp-170) REVERT: F 242 GLN cc_start: 0.6781 (tt0) cc_final: 0.6444 (pp30) REVERT: F 243 VAL cc_start: 0.8248 (t) cc_final: 0.7289 (p) REVERT: F 244 LEU cc_start: 0.7858 (tt) cc_final: 0.7525 (tt) REVERT: F 256 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7484 (ttm110) REVERT: G 48 MET cc_start: -0.0281 (ppp) cc_final: -0.1251 (ppp) REVERT: G 85 LEU cc_start: 0.6942 (tp) cc_final: 0.6508 (tp) REVERT: G 110 PHE cc_start: 0.7093 (m-10) cc_final: 0.6890 (m-10) REVERT: G 132 MET cc_start: 0.7533 (tmm) cc_final: 0.7194 (tmm) REVERT: G 157 HIS cc_start: 0.7759 (m90) cc_final: 0.7503 (m90) REVERT: G 175 GLU cc_start: 0.8313 (pm20) cc_final: 0.8090 (pm20) REVERT: G 183 ILE cc_start: 0.6751 (mt) cc_final: 0.6512 (mt) REVERT: G 197 PRO cc_start: 0.8132 (Cg_exo) cc_final: 0.7872 (Cg_endo) REVERT: G 210 ILE cc_start: 0.8205 (pt) cc_final: 0.7868 (pt) REVERT: H 62 HIS cc_start: 0.7085 (t-90) cc_final: 0.6269 (t-170) REVERT: H 109 MET cc_start: 0.7466 (mtm) cc_final: 0.6828 (ptp) REVERT: H 205 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7579 (mtmt) REVERT: H 207 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7318 (mm-40) REVERT: I 60 ILE cc_start: 0.8622 (mt) cc_final: 0.8099 (mm) REVERT: I 66 ASP cc_start: 0.7659 (t0) cc_final: 0.7297 (t70) REVERT: I 79 VAL cc_start: 0.7797 (t) cc_final: 0.7323 (p) REVERT: I 86 ILE cc_start: 0.8444 (pt) cc_final: 0.7905 (mp) REVERT: I 92 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8422 (mtpp) REVERT: I 97 GLN cc_start: 0.7801 (pm20) cc_final: 0.7439 (pm20) REVERT: I 98 GLU cc_start: 0.7938 (mp0) cc_final: 0.7715 (mp0) REVERT: I 100 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7287 (mtm-85) REVERT: I 102 GLN cc_start: 0.8803 (mm-40) cc_final: 0.7977 (mm-40) REVERT: I 105 LYS cc_start: 0.8830 (mtpp) cc_final: 0.7983 (mtmm) REVERT: I 129 GLN cc_start: 0.7544 (tt0) cc_final: 0.7292 (tt0) REVERT: I 132 MET cc_start: 0.7871 (mmm) cc_final: 0.7521 (mmm) REVERT: I 155 ARG cc_start: 0.8361 (tpt90) cc_final: 0.7257 (mmm160) REVERT: I 158 GLN cc_start: 0.8800 (tt0) cc_final: 0.8289 (tt0) REVERT: I 164 LEU cc_start: 0.8492 (mt) cc_final: 0.8287 (mt) REVERT: I 168 ILE cc_start: 0.8821 (tp) cc_final: 0.8604 (tp) REVERT: I 178 LEU cc_start: 0.7943 (tp) cc_final: 0.7741 (tp) REVERT: I 183 ILE cc_start: 0.8906 (mt) cc_final: 0.8568 (mm) REVERT: I 184 THR cc_start: 0.8576 (m) cc_final: 0.8186 (p) REVERT: I 198 MET cc_start: 0.8347 (ttm) cc_final: 0.8042 (tpp) REVERT: I 201 PHE cc_start: 0.8523 (t80) cc_final: 0.8315 (t80) REVERT: I 203 PHE cc_start: 0.8226 (t80) cc_final: 0.7777 (t80) REVERT: I 208 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7897 (tm-30) REVERT: I 264 ILE cc_start: 0.7253 (mm) cc_final: 0.6966 (mm) REVERT: J 40 CYS cc_start: 0.7038 (t) cc_final: 0.6831 (p) REVERT: J 63 TRP cc_start: 0.7649 (m100) cc_final: 0.6461 (m100) REVERT: J 64 GLN cc_start: 0.7161 (tp40) cc_final: 0.6877 (mm-40) REVERT: J 65 VAL cc_start: 0.8804 (t) cc_final: 0.8425 (t) REVERT: J 86 ILE cc_start: 0.8913 (pt) cc_final: 0.8244 (mm) REVERT: J 92 LYS cc_start: 0.8670 (tptp) cc_final: 0.8345 (tptp) REVERT: J 101 VAL cc_start: 0.8872 (t) cc_final: 0.8549 (t) REVERT: J 104 MET cc_start: 0.8154 (mmp) cc_final: 0.7739 (mmp) REVERT: J 105 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8793 (mtpt) REVERT: J 116 GLN cc_start: 0.6404 (tm-30) cc_final: 0.6047 (tm-30) REVERT: J 131 LEU cc_start: 0.8453 (tt) cc_final: 0.8222 (tt) REVERT: J 132 MET cc_start: 0.8423 (mmp) cc_final: 0.8155 (mmt) REVERT: J 137 ILE cc_start: 0.8298 (tt) cc_final: 0.7606 (tt) REVERT: J 139 HIS cc_start: 0.8086 (t70) cc_final: 0.7737 (t70) REVERT: J 160 LEU cc_start: 0.8614 (tt) cc_final: 0.8258 (tt) REVERT: J 184 THR cc_start: 0.8846 (p) cc_final: 0.8474 (p) REVERT: J 186 ASN cc_start: 0.7587 (m-40) cc_final: 0.6810 (m-40) REVERT: J 201 PHE cc_start: 0.8906 (t80) cc_final: 0.8495 (t80) REVERT: J 204 ASN cc_start: 0.7169 (m110) cc_final: 0.6817 (p0) REVERT: J 205 LYS cc_start: 0.8387 (tptp) cc_final: 0.7573 (tptp) REVERT: J 208 GLN cc_start: 0.7633 (pt0) cc_final: 0.7250 (pt0) REVERT: K 14 LYS cc_start: 0.8256 (mmtm) cc_final: 0.8015 (mmtm) REVERT: K 15 TRP cc_start: 0.8430 (m100) cc_final: 0.7872 (m100) REVERT: K 34 GLU cc_start: 0.8309 (pt0) cc_final: 0.7764 (pp20) REVERT: K 35 ASP cc_start: 0.8091 (m-30) cc_final: 0.7861 (m-30) REVERT: K 36 ILE cc_start: 0.8892 (mm) cc_final: 0.8687 (mm) REVERT: K 110 PHE cc_start: 0.7110 (m-80) cc_final: 0.6707 (m-80) REVERT: K 132 MET cc_start: 0.6575 (ppp) cc_final: 0.6184 (ppp) REVERT: K 209 ARG cc_start: 0.8238 (ptt90) cc_final: 0.7859 (ptt90) REVERT: L 226 TYR cc_start: 0.6648 (p90) cc_final: 0.5894 (p90) REVERT: L 266 ASN cc_start: 0.8422 (m-40) cc_final: 0.8082 (m-40) REVERT: L 269 VAL cc_start: 0.7912 (m) cc_final: 0.7655 (m) REVERT: M 13 ASN cc_start: 0.8324 (m110) cc_final: 0.7965 (m110) REVERT: M 15 TRP cc_start: 0.7702 (m-10) cc_final: 0.7268 (m-10) REVERT: M 16 HIS cc_start: 0.7059 (m-70) cc_final: 0.6751 (m170) REVERT: M 18 ASP cc_start: 0.6999 (t70) cc_final: 0.6724 (t70) REVERT: M 159 THR cc_start: 0.8385 (m) cc_final: 0.7483 (p) REVERT: M 201 PHE cc_start: 0.7500 (t80) cc_final: 0.7134 (t80) REVERT: M 205 LYS cc_start: 0.8809 (mttm) cc_final: 0.8367 (mtpp) REVERT: N 65 VAL cc_start: 0.7171 (t) cc_final: 0.6864 (p) REVERT: N 104 MET cc_start: 0.7956 (ptm) cc_final: 0.7594 (ppp) REVERT: N 183 ILE cc_start: 0.6561 (mt) cc_final: 0.6208 (mt) REVERT: N 198 MET cc_start: 0.7577 (ppp) cc_final: 0.7202 (ppp) REVERT: N 203 PHE cc_start: 0.7154 (t80) cc_final: 0.6658 (t80) REVERT: N 210 ILE cc_start: 0.8161 (pt) cc_final: 0.7727 (pt) REVERT: N 213 GLN cc_start: 0.8715 (mt0) cc_final: 0.8161 (mt0) REVERT: N 233 HIS cc_start: 0.7573 (m-70) cc_final: 0.7293 (m-70) REVERT: N 243 VAL cc_start: 0.8306 (t) cc_final: 0.7611 (p) REVERT: N 244 LEU cc_start: 0.8052 (tt) cc_final: 0.7806 (tt) REVERT: N 256 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7414 (ttm110) REVERT: O 23 HIS cc_start: 0.6369 (t70) cc_final: 0.5666 (t70) REVERT: O 29 PRO cc_start: 0.4704 (Cg_exo) cc_final: 0.4439 (Cg_endo) REVERT: O 48 MET cc_start: -0.1825 (ppp) cc_final: -0.2239 (ppp) REVERT: O 110 PHE cc_start: 0.7017 (m-10) cc_final: 0.6800 (m-10) REVERT: O 132 MET cc_start: 0.7562 (tmm) cc_final: 0.6797 (tmm) REVERT: O 157 HIS cc_start: 0.7765 (m90) cc_final: 0.7468 (m90) REVERT: O 193 LEU cc_start: 0.8441 (mm) cc_final: 0.8174 (mm) REVERT: O 209 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7898 (ptm-80) REVERT: O 211 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7553 (tp40) REVERT: P 62 HIS cc_start: 0.7020 (t70) cc_final: 0.6492 (t70) REVERT: P 132 MET cc_start: 0.5724 (tmm) cc_final: 0.5083 (tmm) REVERT: P 168 ILE cc_start: 0.8622 (pt) cc_final: 0.8292 (mt) REVERT: P 170 MET cc_start: 0.7653 (mtt) cc_final: 0.7385 (mpp) REVERT: P 254 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7596 (tppt) outliers start: 6 outliers final: 1 residues processed: 1182 average time/residue: 0.4769 time to fit residues: 872.4914 Evaluate side-chains 1082 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1081 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 chunk 375 optimal weight: 0.9990 chunk 185 optimal weight: 0.0050 chunk 335 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 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 44 GLN D 116 GLN D 150 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN F 150 GLN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN G 102 GLN G 208 GLN G 211 GLN H 102 GLN H 157 HIS ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 GLN M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34119 Z= 0.230 Angle : 0.655 12.835 46515 Z= 0.349 Chirality : 0.047 0.218 5006 Planarity : 0.005 0.061 5714 Dihedral : 14.655 173.849 5007 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.01 (0.13), residues: 3851 helix: 1.29 (0.12), residues: 1870 sheet: -0.50 (0.18), residues: 768 loop : -1.69 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 63 HIS 0.013 0.001 HIS C 233 PHE 0.032 0.002 PHE E 26 TYR 0.021 0.002 TYR D 134 ARG 0.008 0.000 ARG C 222 *********************** 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 1175 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1173 time to evaluate : 3.498 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: A 45 GLU cc_start: 0.7522 (pp20) cc_final: 0.7137 (tm-30) REVERT: A 48 MET cc_start: 0.5161 (mmm) cc_final: 0.4875 (mmm) REVERT: A 66 ASP cc_start: 0.7729 (t0) cc_final: 0.7450 (t70) REVERT: A 79 VAL cc_start: 0.7920 (t) cc_final: 0.7267 (p) REVERT: A 82 ASN cc_start: 0.8323 (t0) cc_final: 0.8081 (p0) REVERT: A 92 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8467 (mtpp) REVERT: A 104 MET cc_start: 0.8388 (ttm) cc_final: 0.7920 (ttm) REVERT: A 107 TYR cc_start: 0.8356 (t80) cc_final: 0.8104 (t80) REVERT: A 116 GLN cc_start: 0.7406 (tm-30) cc_final: 0.6672 (tm-30) REVERT: A 118 ASP cc_start: 0.7743 (p0) cc_final: 0.7500 (p0) REVERT: A 129 GLN cc_start: 0.7845 (tt0) cc_final: 0.7596 (tt0) REVERT: A 132 MET cc_start: 0.7921 (mmm) cc_final: 0.7429 (mmm) REVERT: A 152 LEU cc_start: 0.7473 (pt) cc_final: 0.6483 (mp) REVERT: A 153 VAL cc_start: 0.8862 (m) cc_final: 0.8602 (m) REVERT: A 155 ARG cc_start: 0.8321 (tpt90) cc_final: 0.7298 (mmm160) REVERT: A 158 GLN cc_start: 0.8735 (tt0) cc_final: 0.8380 (tt0) REVERT: A 160 LEU cc_start: 0.8543 (tt) cc_final: 0.8316 (tt) REVERT: A 164 LEU cc_start: 0.8250 (mt) cc_final: 0.7976 (mt) REVERT: A 184 THR cc_start: 0.8532 (m) cc_final: 0.8191 (p) REVERT: A 190 LYS cc_start: 0.7377 (mtmm) cc_final: 0.6911 (mtpp) REVERT: A 201 PHE cc_start: 0.8505 (t80) cc_final: 0.7974 (t80) REVERT: A 203 PHE cc_start: 0.8291 (t80) cc_final: 0.7855 (t80) REVERT: A 254 LYS cc_start: 0.8287 (pptt) cc_final: 0.7988 (pptt) REVERT: B 40 CYS cc_start: 0.7467 (t) cc_final: 0.7166 (p) REVERT: B 63 TRP cc_start: 0.7734 (m100) cc_final: 0.6623 (m100) REVERT: B 64 GLN cc_start: 0.7002 (tp40) cc_final: 0.6801 (mm-40) REVERT: B 65 VAL cc_start: 0.8727 (t) cc_final: 0.8482 (t) REVERT: B 86 ILE cc_start: 0.8785 (pt) cc_final: 0.8304 (mm) REVERT: B 92 LYS cc_start: 0.8555 (tppp) cc_final: 0.8241 (tppp) REVERT: B 98 GLU cc_start: 0.7935 (pm20) cc_final: 0.7648 (pm20) REVERT: B 100 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7671 (mtt-85) REVERT: B 103 THR cc_start: 0.8711 (p) cc_final: 0.8490 (p) REVERT: B 105 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8624 (mtpp) REVERT: B 129 GLN cc_start: 0.8385 (pt0) cc_final: 0.7997 (pt0) REVERT: B 131 LEU cc_start: 0.8838 (tt) cc_final: 0.8416 (tt) REVERT: B 132 MET cc_start: 0.8269 (mmp) cc_final: 0.7583 (mmp) REVERT: B 164 LEU cc_start: 0.8627 (tp) cc_final: 0.8393 (tp) REVERT: B 165 GLU cc_start: 0.7425 (tp30) cc_final: 0.7132 (tp30) REVERT: B 198 MET cc_start: 0.7935 (tpt) cc_final: 0.7551 (tpp) REVERT: B 204 ASN cc_start: 0.7104 (p0) cc_final: 0.6639 (p0) REVERT: B 208 GLN cc_start: 0.7665 (pt0) cc_final: 0.7256 (pt0) REVERT: C 11 GLU cc_start: 0.7413 (tp30) cc_final: 0.6153 (tp30) REVERT: C 110 PHE cc_start: 0.7207 (m-80) cc_final: 0.6877 (m-80) REVERT: C 132 MET cc_start: 0.7836 (ppp) cc_final: 0.7115 (ppp) REVERT: C 157 HIS cc_start: 0.7145 (m90) cc_final: 0.6792 (m170) REVERT: C 162 ASN cc_start: 0.8459 (m-40) cc_final: 0.7428 (m-40) REVERT: C 186 ASN cc_start: 0.6648 (m-40) cc_final: 0.6405 (m110) REVERT: C 209 ARG cc_start: 0.7998 (ptt90) cc_final: 0.7468 (ptt90) REVERT: D 218 GLN cc_start: 0.8183 (mm110) cc_final: 0.7806 (mm110) REVERT: D 223 PHE cc_start: 0.5793 (p90) cc_final: 0.5531 (p90) REVERT: D 226 TYR cc_start: 0.6844 (p90) cc_final: 0.6161 (p90) REVERT: D 269 VAL cc_start: 0.7987 (m) cc_final: 0.7723 (m) REVERT: E 10 GLU cc_start: 0.7149 (tp30) cc_final: 0.6782 (tp30) REVERT: E 16 HIS cc_start: 0.7046 (m-70) cc_final: 0.6811 (m170) REVERT: E 150 GLN cc_start: 0.7656 (mm110) cc_final: 0.6972 (mm110) REVERT: E 159 THR cc_start: 0.8263 (m) cc_final: 0.7501 (p) REVERT: E 178 LEU cc_start: 0.8853 (mt) cc_final: 0.8357 (mt) REVERT: E 201 PHE cc_start: 0.7570 (t80) cc_final: 0.7309 (t80) REVERT: E 204 ASN cc_start: 0.7978 (t0) cc_final: 0.7681 (t0) REVERT: E 205 LYS cc_start: 0.8759 (mttt) cc_final: 0.8284 (mmtp) REVERT: E 206 GLU cc_start: 0.8229 (pt0) cc_final: 0.6930 (pp20) REVERT: F 65 VAL cc_start: 0.7015 (t) cc_final: 0.6592 (p) REVERT: F 77 VAL cc_start: 0.6887 (m) cc_final: 0.6547 (m) REVERT: F 82 ASN cc_start: 0.8338 (m110) cc_final: 0.8089 (m-40) REVERT: F 183 ILE cc_start: 0.6261 (mt) cc_final: 0.5893 (mt) REVERT: F 198 MET cc_start: 0.7750 (ppp) cc_final: 0.7437 (ppp) REVERT: F 199 ASP cc_start: 0.7864 (m-30) cc_final: 0.7538 (m-30) REVERT: F 202 ILE cc_start: 0.8277 (mt) cc_final: 0.7882 (mt) REVERT: F 203 PHE cc_start: 0.7256 (t80) cc_final: 0.6886 (t80) REVERT: F 230 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7914 (mmmm) REVERT: F 242 GLN cc_start: 0.6661 (tt0) cc_final: 0.6397 (pp30) REVERT: F 243 VAL cc_start: 0.8330 (t) cc_final: 0.7068 (m) REVERT: F 244 LEU cc_start: 0.8023 (tt) cc_final: 0.7623 (tt) REVERT: F 256 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7539 (ttm110) REVERT: G 48 MET cc_start: -0.0396 (ppp) cc_final: -0.1360 (ppp) REVERT: G 74 ILE cc_start: 0.5575 (mt) cc_final: 0.5373 (mt) REVERT: G 110 PHE cc_start: 0.7293 (m-10) cc_final: 0.7024 (m-10) REVERT: G 130 LEU cc_start: 0.8541 (pp) cc_final: 0.8341 (pp) REVERT: G 132 MET cc_start: 0.7555 (tmm) cc_final: 0.7182 (tmm) REVERT: G 157 HIS cc_start: 0.7838 (m90) cc_final: 0.7454 (m90) REVERT: G 175 GLU cc_start: 0.8162 (pm20) cc_final: 0.7961 (pm20) REVERT: G 183 ILE cc_start: 0.6804 (mt) cc_final: 0.6568 (mt) REVERT: G 199 ASP cc_start: 0.8532 (m-30) cc_final: 0.8302 (m-30) REVERT: G 202 ILE cc_start: 0.8660 (mt) cc_final: 0.8138 (mt) REVERT: G 209 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7674 (ttp80) REVERT: G 210 ILE cc_start: 0.8456 (pt) cc_final: 0.7452 (pt) REVERT: H 62 HIS cc_start: 0.6989 (t-90) cc_final: 0.6218 (t-170) REVERT: H 109 MET cc_start: 0.7421 (mtm) cc_final: 0.6828 (ptp) REVERT: H 168 ILE cc_start: 0.8446 (pt) cc_final: 0.8229 (mt) REVERT: I 60 ILE cc_start: 0.8646 (mt) cc_final: 0.8143 (mm) REVERT: I 66 ASP cc_start: 0.7810 (t0) cc_final: 0.7439 (t70) REVERT: I 79 VAL cc_start: 0.7871 (t) cc_final: 0.7325 (p) REVERT: I 86 ILE cc_start: 0.8444 (pt) cc_final: 0.7994 (mm) REVERT: I 92 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8390 (mtpp) REVERT: I 97 GLN cc_start: 0.8061 (pm20) cc_final: 0.7768 (pm20) REVERT: I 98 GLU cc_start: 0.8003 (mp0) cc_final: 0.7737 (mp0) REVERT: I 100 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7453 (mtm-85) REVERT: I 102 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8029 (mm-40) REVERT: I 105 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8114 (mtmm) REVERT: I 118 ASP cc_start: 0.7799 (p0) cc_final: 0.7565 (p0) REVERT: I 129 GLN cc_start: 0.7569 (tt0) cc_final: 0.7360 (tt0) REVERT: I 146 ASN cc_start: 0.7735 (m110) cc_final: 0.7492 (m-40) REVERT: I 155 ARG cc_start: 0.8291 (tpt90) cc_final: 0.7289 (mmm160) REVERT: I 158 GLN cc_start: 0.8741 (tt0) cc_final: 0.8297 (tt0) REVERT: I 162 ASN cc_start: 0.8653 (t0) cc_final: 0.8406 (m-40) REVERT: I 163 THR cc_start: 0.8491 (m) cc_final: 0.8104 (p) REVERT: I 198 MET cc_start: 0.8331 (ttm) cc_final: 0.8025 (tpp) REVERT: I 203 PHE cc_start: 0.8232 (t80) cc_final: 0.7755 (t80) REVERT: I 208 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8027 (tm-30) REVERT: I 258 THR cc_start: 0.8780 (p) cc_final: 0.8498 (p) REVERT: I 264 ILE cc_start: 0.7418 (mm) cc_final: 0.7124 (mm) REVERT: J 40 CYS cc_start: 0.7049 (t) cc_final: 0.6818 (p) REVERT: J 63 TRP cc_start: 0.7702 (m100) cc_final: 0.6229 (m100) REVERT: J 86 ILE cc_start: 0.8928 (pt) cc_final: 0.8347 (mm) REVERT: J 92 LYS cc_start: 0.8743 (tptp) cc_final: 0.8397 (tptp) REVERT: J 104 MET cc_start: 0.8143 (mmp) cc_final: 0.7921 (mmp) REVERT: J 105 LYS cc_start: 0.9104 (mtpt) cc_final: 0.8800 (mtpt) REVERT: J 131 LEU cc_start: 0.8535 (tt) cc_final: 0.8314 (tt) REVERT: J 132 MET cc_start: 0.8410 (mmp) cc_final: 0.7750 (mmp) REVERT: J 139 HIS cc_start: 0.8181 (t70) cc_final: 0.7855 (t70) REVERT: J 160 LEU cc_start: 0.8629 (tt) cc_final: 0.8300 (tt) REVERT: J 161 LYS cc_start: 0.8729 (ptpt) cc_final: 0.8483 (pttm) REVERT: J 182 LEU cc_start: 0.8200 (mt) cc_final: 0.7938 (mt) REVERT: J 201 PHE cc_start: 0.8928 (t80) cc_final: 0.8569 (t80) REVERT: J 204 ASN cc_start: 0.7151 (m110) cc_final: 0.6751 (p0) REVERT: J 205 LYS cc_start: 0.8480 (tptp) cc_final: 0.7629 (tptp) REVERT: J 207 GLN cc_start: 0.7500 (mp10) cc_final: 0.7065 (mt0) REVERT: J 208 GLN cc_start: 0.7673 (pt0) cc_final: 0.7179 (pt0) REVERT: K 15 TRP cc_start: 0.8453 (m100) cc_final: 0.7949 (m100) REVERT: K 34 GLU cc_start: 0.8304 (pt0) cc_final: 0.7742 (pp20) REVERT: K 132 MET cc_start: 0.6677 (ppp) cc_final: 0.6275 (ppp) REVERT: K 157 HIS cc_start: 0.7868 (m-70) cc_final: 0.7420 (m90) REVERT: K 209 ARG cc_start: 0.8283 (ptt90) cc_final: 0.7999 (ptt90) REVERT: L 209 ARG cc_start: 0.8316 (mmp-170) cc_final: 0.8000 (mmp80) REVERT: L 226 TYR cc_start: 0.6914 (p90) cc_final: 0.6163 (p90) REVERT: L 248 ASP cc_start: 0.8228 (p0) cc_final: 0.7998 (p0) REVERT: L 266 ASN cc_start: 0.8566 (m-40) cc_final: 0.8188 (m-40) REVERT: L 269 VAL cc_start: 0.7850 (m) cc_final: 0.7481 (m) REVERT: M 7 LEU cc_start: 0.8017 (tt) cc_final: 0.7232 (tt) REVERT: M 16 HIS cc_start: 0.7031 (m-70) cc_final: 0.6702 (m170) REVERT: M 76 LEU cc_start: 0.6484 (mm) cc_final: 0.6264 (mm) REVERT: M 109 MET cc_start: 0.8513 (tmm) cc_final: 0.7925 (ttt) REVERT: M 110 PHE cc_start: 0.7028 (m-80) cc_final: 0.6741 (m-80) REVERT: M 159 THR cc_start: 0.8353 (m) cc_final: 0.7446 (p) REVERT: M 178 LEU cc_start: 0.8690 (mt) cc_final: 0.8484 (mt) REVERT: M 202 ILE cc_start: 0.8704 (mm) cc_final: 0.8306 (mm) REVERT: M 205 LYS cc_start: 0.8931 (mttm) cc_final: 0.8493 (mtpp) REVERT: M 206 GLU cc_start: 0.8251 (pt0) cc_final: 0.7481 (pt0) REVERT: M 220 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7172 (mmtt) REVERT: N 65 VAL cc_start: 0.7198 (t) cc_final: 0.6967 (p) REVERT: N 98 GLU cc_start: 0.7136 (mp0) cc_final: 0.6897 (mp0) REVERT: N 104 MET cc_start: 0.7954 (ptm) cc_final: 0.7543 (ppp) REVERT: N 154 GLU cc_start: 0.7550 (mp0) cc_final: 0.7120 (mp0) REVERT: N 183 ILE cc_start: 0.6714 (mt) cc_final: 0.6373 (mt) REVERT: N 198 MET cc_start: 0.7512 (ppp) cc_final: 0.7202 (ppp) REVERT: N 202 ILE cc_start: 0.8081 (mt) cc_final: 0.7818 (mt) REVERT: N 207 GLN cc_start: 0.7825 (mp10) cc_final: 0.7369 (mm-40) REVERT: N 210 ILE cc_start: 0.8270 (pt) cc_final: 0.7838 (pt) REVERT: N 213 GLN cc_start: 0.8754 (mt0) cc_final: 0.8292 (mt0) REVERT: N 230 LYS cc_start: 0.8379 (mttt) cc_final: 0.7877 (tptp) REVERT: N 233 HIS cc_start: 0.7529 (m-70) cc_final: 0.7319 (m-70) REVERT: N 243 VAL cc_start: 0.8206 (t) cc_final: 0.7360 (m) REVERT: N 256 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7423 (ttm110) REVERT: N 270 LYS cc_start: 0.7992 (mptt) cc_final: 0.7425 (mptt) REVERT: O 23 HIS cc_start: 0.6489 (t70) cc_final: 0.5712 (t70) REVERT: O 48 MET cc_start: -0.1846 (ppp) cc_final: -0.2253 (ppp) REVERT: O 104 MET cc_start: 0.7464 (pmm) cc_final: 0.7262 (pmm) REVERT: O 109 MET cc_start: 0.6775 (tpp) cc_final: 0.6410 (tpt) REVERT: O 132 MET cc_start: 0.7587 (tmm) cc_final: 0.7050 (tmm) REVERT: O 193 LEU cc_start: 0.8444 (mm) cc_final: 0.8195 (mm) REVERT: O 211 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7526 (tp40) REVERT: P 62 HIS cc_start: 0.7216 (t70) cc_final: 0.6570 (t70) REVERT: P 115 LEU cc_start: 0.4137 (tp) cc_final: 0.3696 (tp) REVERT: P 132 MET cc_start: 0.5881 (tmm) cc_final: 0.5558 (tmm) REVERT: P 168 ILE cc_start: 0.8537 (pt) cc_final: 0.8103 (tp) REVERT: P 170 MET cc_start: 0.7618 (mtt) cc_final: 0.7371 (mpp) REVERT: P 238 GLN cc_start: 0.5555 (mp-120) cc_final: 0.5252 (mp10) outliers start: 2 outliers final: 0 residues processed: 1173 average time/residue: 0.4832 time to fit residues: 883.8289 Evaluate side-chains 1093 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1093 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 154 optimal weight: 0.0670 chunk 320 optimal weight: 0.9990 chunk 259 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 336 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS G 102 GLN G 208 GLN G 211 GLN H 157 HIS H 242 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 GLN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 GLN O 208 GLN ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.4360 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= 0.199 Angle : 0.650 12.721 46515 Z= 0.342 Chirality : 0.046 0.201 5006 Planarity : 0.005 0.074 5714 Dihedral : 14.634 173.953 5007 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.13), residues: 3851 helix: 1.29 (0.12), residues: 1876 sheet: -0.54 (0.17), residues: 854 loop : -1.69 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP P 78 HIS 0.008 0.001 HIS F 62 PHE 0.028 0.002 PHE E 26 TYR 0.022 0.001 TYR O 70 ARG 0.017 0.001 ARG K 222 *********************** 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 1190 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1188 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7631 (pp20) cc_final: 0.7174 (tm-30) REVERT: A 48 MET cc_start: 0.6156 (mmm) cc_final: 0.5750 (mmm) REVERT: A 66 ASP cc_start: 0.7695 (t0) cc_final: 0.7364 (t70) REVERT: A 79 VAL cc_start: 0.7976 (t) cc_final: 0.7382 (p) REVERT: A 86 ILE cc_start: 0.8417 (pt) cc_final: 0.7801 (mm) REVERT: A 92 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8460 (mtpp) REVERT: A 97 GLN cc_start: 0.7726 (pm20) cc_final: 0.7268 (pm20) REVERT: A 104 MET cc_start: 0.8322 (ttm) cc_final: 0.7754 (ttm) REVERT: A 107 TYR cc_start: 0.8313 (t80) cc_final: 0.7622 (t80) REVERT: A 113 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7652 (mmmm) REVERT: A 118 ASP cc_start: 0.7804 (p0) cc_final: 0.7579 (p0) REVERT: A 129 GLN cc_start: 0.7839 (tt0) cc_final: 0.7621 (tt0) REVERT: A 132 MET cc_start: 0.7896 (mmm) cc_final: 0.7393 (mmm) REVERT: A 135 LEU cc_start: 0.8800 (mt) cc_final: 0.8511 (mt) REVERT: A 155 ARG cc_start: 0.8331 (tpt90) cc_final: 0.7208 (tpp-160) REVERT: A 161 LYS cc_start: 0.8608 (tptt) cc_final: 0.8376 (tptt) REVERT: A 164 LEU cc_start: 0.8223 (mt) cc_final: 0.7955 (mt) REVERT: A 175 GLU cc_start: 0.8649 (pm20) cc_final: 0.8310 (pm20) REVERT: A 183 ILE cc_start: 0.8926 (mt) cc_final: 0.8470 (mm) REVERT: A 184 THR cc_start: 0.8491 (m) cc_final: 0.8140 (p) REVERT: A 190 LYS cc_start: 0.7483 (mtmm) cc_final: 0.6838 (mtpt) REVERT: A 201 PHE cc_start: 0.8515 (t80) cc_final: 0.8012 (t80) REVERT: A 203 PHE cc_start: 0.8273 (t80) cc_final: 0.7826 (t80) REVERT: A 254 LYS cc_start: 0.8234 (pptt) cc_final: 0.7874 (pptt) REVERT: B 40 CYS cc_start: 0.7414 (t) cc_final: 0.7165 (p) REVERT: B 41 ASP cc_start: 0.8364 (p0) cc_final: 0.8159 (p0) REVERT: B 63 TRP cc_start: 0.7707 (m100) cc_final: 0.6643 (m100) REVERT: B 65 VAL cc_start: 0.8692 (t) cc_final: 0.8418 (t) REVERT: B 86 ILE cc_start: 0.8780 (pt) cc_final: 0.8327 (mm) REVERT: B 89 GLU cc_start: 0.7432 (tt0) cc_final: 0.6993 (tt0) REVERT: B 92 LYS cc_start: 0.8527 (tppp) cc_final: 0.8255 (tppp) REVERT: B 100 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7670 (mtt-85) REVERT: B 105 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8618 (mtpp) REVERT: B 129 GLN cc_start: 0.8356 (pt0) cc_final: 0.7978 (pt0) REVERT: B 131 LEU cc_start: 0.8730 (tt) cc_final: 0.8331 (tt) REVERT: B 132 MET cc_start: 0.8329 (mmp) cc_final: 0.7566 (mmp) REVERT: B 137 ILE cc_start: 0.8448 (tt) cc_final: 0.8236 (tt) REVERT: B 139 HIS cc_start: 0.8304 (t70) cc_final: 0.8049 (t70) REVERT: B 198 MET cc_start: 0.7897 (tpt) cc_final: 0.7518 (tpp) REVERT: B 204 ASN cc_start: 0.7005 (p0) cc_final: 0.6562 (p0) REVERT: B 207 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7542 (mm-40) REVERT: B 208 GLN cc_start: 0.7680 (pt0) cc_final: 0.7242 (pt0) REVERT: C 11 GLU cc_start: 0.7463 (tp30) cc_final: 0.6147 (tp30) REVERT: C 30 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7452 (ttt180) REVERT: C 157 HIS cc_start: 0.7096 (m90) cc_final: 0.6757 (m-70) REVERT: C 165 GLU cc_start: 0.6918 (pt0) cc_final: 0.6648 (pt0) REVERT: C 186 ASN cc_start: 0.6736 (m-40) cc_final: 0.6485 (m110) REVERT: C 208 GLN cc_start: 0.8356 (mt0) cc_final: 0.8060 (mt0) REVERT: C 209 ARG cc_start: 0.8208 (ptt90) cc_final: 0.7310 (ptt90) REVERT: C 258 THR cc_start: 0.7719 (p) cc_final: 0.6848 (p) REVERT: D 218 GLN cc_start: 0.8194 (mm110) cc_final: 0.7729 (mm110) REVERT: D 226 TYR cc_start: 0.6383 (p90) cc_final: 0.5847 (p90) REVERT: D 269 VAL cc_start: 0.7997 (m) cc_final: 0.7790 (m) REVERT: E 12 HIS cc_start: 0.7605 (t70) cc_final: 0.6242 (t70) REVERT: E 16 HIS cc_start: 0.7010 (m-70) cc_final: 0.6784 (m170) REVERT: E 101 VAL cc_start: 0.8891 (t) cc_final: 0.8606 (m) REVERT: E 150 GLN cc_start: 0.7567 (mm110) cc_final: 0.6945 (mm110) REVERT: E 159 THR cc_start: 0.8240 (m) cc_final: 0.7495 (p) REVERT: E 178 LEU cc_start: 0.8807 (mt) cc_final: 0.8594 (mt) REVERT: E 201 PHE cc_start: 0.7640 (t80) cc_final: 0.7321 (t80) REVERT: E 205 LYS cc_start: 0.8716 (mttt) cc_final: 0.8381 (mmtp) REVERT: E 206 GLU cc_start: 0.8169 (pt0) cc_final: 0.6940 (pp20) REVERT: F 65 VAL cc_start: 0.6822 (t) cc_final: 0.6432 (p) REVERT: F 77 VAL cc_start: 0.6754 (m) cc_final: 0.6422 (m) REVERT: F 82 ASN cc_start: 0.8128 (m110) cc_final: 0.7831 (m-40) REVERT: F 104 MET cc_start: 0.7459 (ptm) cc_final: 0.7255 (ppp) REVERT: F 105 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8489 (mttm) REVERT: F 154 GLU cc_start: 0.7371 (mp0) cc_final: 0.7163 (mp0) REVERT: F 164 LEU cc_start: 0.8248 (mt) cc_final: 0.8028 (mt) REVERT: F 183 ILE cc_start: 0.6329 (mt) cc_final: 0.5955 (mt) REVERT: F 198 MET cc_start: 0.7732 (ppp) cc_final: 0.7227 (ppp) REVERT: F 199 ASP cc_start: 0.7846 (m-30) cc_final: 0.7395 (m-30) REVERT: F 202 ILE cc_start: 0.8329 (mt) cc_final: 0.8103 (mt) REVERT: F 204 ASN cc_start: 0.8295 (p0) cc_final: 0.8027 (p0) REVERT: F 206 GLU cc_start: 0.7946 (pp20) cc_final: 0.7659 (pp20) REVERT: F 209 ARG cc_start: 0.7547 (ppt170) cc_final: 0.7326 (ttp80) REVERT: F 210 ILE cc_start: 0.8354 (pt) cc_final: 0.8024 (pt) REVERT: F 230 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7986 (mmmm) REVERT: F 242 GLN cc_start: 0.6629 (tt0) cc_final: 0.6419 (pp30) REVERT: F 243 VAL cc_start: 0.8333 (t) cc_final: 0.7421 (p) REVERT: F 244 LEU cc_start: 0.7937 (tt) cc_final: 0.7543 (tt) REVERT: F 256 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7561 (ttm110) REVERT: G 25 GLU cc_start: 0.6688 (pm20) cc_final: 0.6486 (pm20) REVERT: G 48 MET cc_start: -0.0386 (ppp) cc_final: -0.1330 (ppp) REVERT: G 85 LEU cc_start: 0.7086 (tp) cc_final: 0.6875 (tp) REVERT: G 132 MET cc_start: 0.7576 (tmm) cc_final: 0.7105 (tmm) REVERT: G 157 HIS cc_start: 0.7796 (m90) cc_final: 0.7467 (m90) REVERT: G 183 ILE cc_start: 0.6826 (mt) cc_final: 0.6594 (mt) REVERT: G 199 ASP cc_start: 0.8374 (m-30) cc_final: 0.8082 (m-30) REVERT: G 201 PHE cc_start: 0.7873 (t80) cc_final: 0.7583 (t80) REVERT: G 202 ILE cc_start: 0.8542 (mt) cc_final: 0.8054 (mt) REVERT: G 205 LYS cc_start: 0.8681 (mtmm) cc_final: 0.7828 (mtmm) REVERT: G 209 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7621 (ttp80) REVERT: G 210 ILE cc_start: 0.8406 (pt) cc_final: 0.7377 (pt) REVERT: H 62 HIS cc_start: 0.7065 (t-90) cc_final: 0.6268 (t-170) REVERT: H 78 TRP cc_start: 0.4188 (m-10) cc_final: 0.3883 (m-10) REVERT: H 109 MET cc_start: 0.7376 (mtm) cc_final: 0.6898 (ptp) REVERT: H 168 ILE cc_start: 0.8430 (pt) cc_final: 0.8228 (mt) REVERT: I 60 ILE cc_start: 0.8646 (mt) cc_final: 0.8158 (mm) REVERT: I 66 ASP cc_start: 0.7787 (t0) cc_final: 0.7496 (t70) REVERT: I 79 VAL cc_start: 0.7926 (t) cc_final: 0.7285 (p) REVERT: I 81 THR cc_start: 0.8551 (p) cc_final: 0.8214 (t) REVERT: I 86 ILE cc_start: 0.8438 (pt) cc_final: 0.8073 (mp) REVERT: I 92 LYS cc_start: 0.8985 (mtmm) cc_final: 0.8414 (mtpp) REVERT: I 97 GLN cc_start: 0.8084 (pm20) cc_final: 0.7570 (pm20) REVERT: I 98 GLU cc_start: 0.8008 (mp0) cc_final: 0.7743 (mp0) REVERT: I 102 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8072 (mm-40) REVERT: I 105 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8223 (mtmm) REVERT: I 113 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7537 (mmmm) REVERT: I 146 ASN cc_start: 0.7821 (m110) cc_final: 0.7583 (m-40) REVERT: I 152 LEU cc_start: 0.7366 (pt) cc_final: 0.6349 (mp) REVERT: I 155 ARG cc_start: 0.8303 (tpt90) cc_final: 0.7286 (mmm160) REVERT: I 158 GLN cc_start: 0.8725 (tt0) cc_final: 0.8296 (tt0) REVERT: I 160 LEU cc_start: 0.8517 (tt) cc_final: 0.8011 (tt) REVERT: I 162 ASN cc_start: 0.8684 (t0) cc_final: 0.8377 (m-40) REVERT: I 163 THR cc_start: 0.8442 (m) cc_final: 0.8083 (p) REVERT: I 164 LEU cc_start: 0.8587 (mt) cc_final: 0.8160 (mt) REVERT: I 183 ILE cc_start: 0.8813 (mt) cc_final: 0.8351 (mm) REVERT: I 184 THR cc_start: 0.8491 (m) cc_final: 0.8238 (p) REVERT: I 198 MET cc_start: 0.8352 (ttm) cc_final: 0.8047 (tpp) REVERT: I 203 PHE cc_start: 0.8202 (t80) cc_final: 0.7748 (t80) REVERT: I 208 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8025 (tm-30) REVERT: I 254 LYS cc_start: 0.8665 (ttmm) cc_final: 0.7988 (tptt) REVERT: I 260 ARG cc_start: 0.6644 (ptm160) cc_final: 0.6057 (ptm160) REVERT: I 264 ILE cc_start: 0.7304 (mm) cc_final: 0.7028 (mm) REVERT: J 40 CYS cc_start: 0.6979 (t) cc_final: 0.6774 (p) REVERT: J 63 TRP cc_start: 0.7639 (m100) cc_final: 0.6372 (m100) REVERT: J 65 VAL cc_start: 0.8822 (t) cc_final: 0.8586 (t) REVERT: J 86 ILE cc_start: 0.8910 (pt) cc_final: 0.8408 (mm) REVERT: J 87 TYR cc_start: 0.8160 (t80) cc_final: 0.7874 (t80) REVERT: J 89 GLU cc_start: 0.7531 (tt0) cc_final: 0.7263 (tt0) REVERT: J 92 LYS cc_start: 0.8827 (tptp) cc_final: 0.8437 (tptp) REVERT: J 100 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7356 (mtt-85) REVERT: J 103 THR cc_start: 0.8542 (t) cc_final: 0.8272 (t) REVERT: J 104 MET cc_start: 0.8186 (mmp) cc_final: 0.7834 (mmp) REVERT: J 105 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8789 (mtpt) REVERT: J 131 LEU cc_start: 0.8469 (tt) cc_final: 0.8191 (tt) REVERT: J 132 MET cc_start: 0.8450 (mmp) cc_final: 0.7699 (mmp) REVERT: J 139 HIS cc_start: 0.8221 (t70) cc_final: 0.7859 (t70) REVERT: J 150 GLN cc_start: 0.7419 (pt0) cc_final: 0.7058 (pt0) REVERT: J 160 LEU cc_start: 0.8667 (tt) cc_final: 0.8419 (tt) REVERT: J 182 LEU cc_start: 0.8146 (mt) cc_final: 0.7875 (mt) REVERT: J 189 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6712 (mtm110) REVERT: J 204 ASN cc_start: 0.6984 (m110) cc_final: 0.6780 (m110) REVERT: J 205 LYS cc_start: 0.8374 (tptp) cc_final: 0.7601 (tptp) REVERT: J 208 GLN cc_start: 0.7754 (pt0) cc_final: 0.7093 (pt0) REVERT: K 10 GLU cc_start: 0.7709 (pp20) cc_final: 0.7169 (tm-30) REVERT: K 15 TRP cc_start: 0.8467 (m100) cc_final: 0.7884 (m100) REVERT: K 30 ARG cc_start: 0.7683 (ttt180) cc_final: 0.7130 (ttt180) REVERT: K 34 GLU cc_start: 0.8317 (pt0) cc_final: 0.7953 (pt0) REVERT: L 226 TYR cc_start: 0.6194 (p90) cc_final: 0.5535 (p90) REVERT: L 266 ASN cc_start: 0.8614 (m-40) cc_final: 0.8179 (m-40) REVERT: L 269 VAL cc_start: 0.7818 (m) cc_final: 0.7485 (m) REVERT: M 7 LEU cc_start: 0.8223 (tt) cc_final: 0.7423 (tt) REVERT: M 11 GLU cc_start: 0.7933 (mp0) cc_final: 0.7713 (mp0) REVERT: M 14 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8229 (mtpt) REVERT: M 18 ASP cc_start: 0.7022 (t70) cc_final: 0.6771 (t70) REVERT: M 25 GLU cc_start: 0.8309 (tt0) cc_final: 0.7932 (tt0) REVERT: M 36 ILE cc_start: 0.8572 (mt) cc_final: 0.8329 (mt) REVERT: M 87 TYR cc_start: 0.5855 (t80) cc_final: 0.5525 (t80) REVERT: M 89 GLU cc_start: 0.5534 (pm20) cc_final: 0.4171 (mp0) REVERT: M 109 MET cc_start: 0.8528 (tmm) cc_final: 0.7837 (ttt) REVERT: M 159 THR cc_start: 0.8295 (m) cc_final: 0.7378 (p) REVERT: M 178 LEU cc_start: 0.8720 (mt) cc_final: 0.8159 (mt) REVERT: M 205 LYS cc_start: 0.8913 (mttm) cc_final: 0.8698 (mtpp) REVERT: M 207 GLN cc_start: 0.7888 (mm110) cc_final: 0.7662 (mm110) REVERT: M 220 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7269 (mmtm) REVERT: N 104 MET cc_start: 0.7954 (ptm) cc_final: 0.7560 (ppp) REVERT: N 183 ILE cc_start: 0.6782 (mt) cc_final: 0.6414 (mt) REVERT: N 198 MET cc_start: 0.7505 (ppp) cc_final: 0.7128 (ppp) REVERT: N 207 GLN cc_start: 0.8200 (mp10) cc_final: 0.7739 (mp10) REVERT: N 210 ILE cc_start: 0.8348 (pt) cc_final: 0.7852 (pt) REVERT: N 213 GLN cc_start: 0.8712 (mt0) cc_final: 0.8300 (mt0) REVERT: N 230 LYS cc_start: 0.8367 (mttt) cc_final: 0.7956 (tptp) REVERT: N 233 HIS cc_start: 0.7585 (m-70) cc_final: 0.7350 (m-70) REVERT: N 243 VAL cc_start: 0.8126 (t) cc_final: 0.7725 (p) REVERT: N 256 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7445 (ttm110) REVERT: N 270 LYS cc_start: 0.8002 (mptt) cc_final: 0.7595 (mptt) REVERT: O 22 LEU cc_start: 0.8105 (mm) cc_final: 0.7349 (mm) REVERT: O 23 HIS cc_start: 0.6380 (t70) cc_final: 0.5687 (t70) REVERT: O 25 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6069 (tp30) REVERT: O 48 MET cc_start: -0.1861 (ppp) cc_final: -0.2120 (ppp) REVERT: O 132 MET cc_start: 0.7542 (tmm) cc_final: 0.6903 (tmm) REVERT: O 175 GLU cc_start: 0.8129 (pm20) cc_final: 0.7867 (pm20) REVERT: P 62 HIS cc_start: 0.7240 (t70) cc_final: 0.6589 (t70) REVERT: P 85 LEU cc_start: 0.8146 (tp) cc_final: 0.7849 (tp) REVERT: P 115 LEU cc_start: 0.3908 (tp) cc_final: 0.3436 (tp) REVERT: P 168 ILE cc_start: 0.8511 (pt) cc_final: 0.8243 (mt) outliers start: 2 outliers final: 1 residues processed: 1188 average time/residue: 0.4871 time to fit residues: 887.9173 Evaluate side-chains 1115 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1113 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 2.9990 chunk 337 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 375 optimal weight: 0.0870 chunk 311 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 197 optimal weight: 0.0980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN G 211 GLN H 157 HIS H 238 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34119 Z= 0.184 Angle : 0.652 12.946 46515 Z= 0.342 Chirality : 0.047 0.240 5006 Planarity : 0.005 0.132 5714 Dihedral : 14.645 174.083 5007 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer: Outliers : 0.06 % Allowed : 1.92 % Favored : 98.02 % 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: 0.04 (0.13), residues: 3851 helix: 1.29 (0.12), residues: 1877 sheet: -0.48 (0.17), residues: 861 loop : -1.67 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 106 HIS 0.008 0.001 HIS O 62 PHE 0.030 0.002 PHE K 26 TYR 0.030 0.001 TYR F 225 ARG 0.009 0.001 ARG K 222 *********************** 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 1195 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1193 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7622 (pp20) cc_final: 0.7039 (tm-30) REVERT: A 48 MET cc_start: 0.6088 (mmm) cc_final: 0.5876 (mmm) REVERT: A 66 ASP cc_start: 0.7688 (t0) cc_final: 0.7346 (t70) REVERT: A 79 VAL cc_start: 0.7930 (t) cc_final: 0.7342 (p) REVERT: A 92 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8512 (mtpp) REVERT: A 97 GLN cc_start: 0.7753 (pm20) cc_final: 0.7213 (pm20) REVERT: A 100 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7601 (mtm110) REVERT: A 104 MET cc_start: 0.8503 (ttm) cc_final: 0.7713 (ttm) REVERT: A 113 LYS cc_start: 0.7949 (mmmm) cc_final: 0.7701 (mmmm) REVERT: A 118 ASP cc_start: 0.7748 (p0) cc_final: 0.7465 (p0) REVERT: A 132 MET cc_start: 0.7729 (mmm) cc_final: 0.7312 (mmm) REVERT: A 152 LEU cc_start: 0.7406 (pt) cc_final: 0.6430 (mp) REVERT: A 155 ARG cc_start: 0.8321 (tpt90) cc_final: 0.7199 (tpp-160) REVERT: A 160 LEU cc_start: 0.8468 (tt) cc_final: 0.8260 (tt) REVERT: A 161 LYS cc_start: 0.8613 (tptt) cc_final: 0.8390 (tptt) REVERT: A 175 GLU cc_start: 0.8719 (pm20) cc_final: 0.8444 (pm20) REVERT: A 184 THR cc_start: 0.8583 (m) cc_final: 0.8293 (p) REVERT: A 190 LYS cc_start: 0.7562 (mtmm) cc_final: 0.7094 (mtpp) REVERT: A 201 PHE cc_start: 0.8443 (t80) cc_final: 0.8094 (t80) REVERT: A 203 PHE cc_start: 0.8266 (t80) cc_final: 0.7832 (t80) REVERT: A 254 LYS cc_start: 0.8328 (pptt) cc_final: 0.7902 (pptt) REVERT: B 40 CYS cc_start: 0.7398 (t) cc_final: 0.7126 (p) REVERT: B 63 TRP cc_start: 0.8176 (m100) cc_final: 0.6280 (m100) REVERT: B 64 GLN cc_start: 0.6650 (mm110) cc_final: 0.6232 (mm110) REVERT: B 86 ILE cc_start: 0.8790 (pt) cc_final: 0.8374 (mm) REVERT: B 89 GLU cc_start: 0.7376 (tt0) cc_final: 0.6993 (tt0) REVERT: B 92 LYS cc_start: 0.8525 (tppp) cc_final: 0.8199 (tppp) REVERT: B 98 GLU cc_start: 0.7931 (pm20) cc_final: 0.7454 (pm20) REVERT: B 101 VAL cc_start: 0.8829 (t) cc_final: 0.8580 (t) REVERT: B 102 GLN cc_start: 0.8239 (mp-120) cc_final: 0.7722 (mm-40) REVERT: B 103 THR cc_start: 0.8797 (p) cc_final: 0.8508 (p) REVERT: B 104 MET cc_start: 0.8163 (mmp) cc_final: 0.7942 (mmp) REVERT: B 105 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8607 (mtpp) REVERT: B 106 TRP cc_start: 0.8183 (t60) cc_final: 0.7923 (t60) REVERT: B 129 GLN cc_start: 0.8357 (pt0) cc_final: 0.7997 (pt0) REVERT: B 131 LEU cc_start: 0.8689 (tt) cc_final: 0.8258 (tt) REVERT: B 132 MET cc_start: 0.8338 (mmp) cc_final: 0.7627 (mmp) REVERT: B 139 HIS cc_start: 0.8181 (t70) cc_final: 0.7755 (t70) REVERT: B 198 MET cc_start: 0.7887 (tpt) cc_final: 0.7427 (tpp) REVERT: B 204 ASN cc_start: 0.7035 (p0) cc_final: 0.6633 (p0) REVERT: B 207 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7530 (mm-40) REVERT: B 208 GLN cc_start: 0.7712 (pt0) cc_final: 0.7213 (pt0) REVERT: C 11 GLU cc_start: 0.7410 (tp30) cc_final: 0.6101 (tp30) REVERT: C 28 ILE cc_start: 0.7929 (tp) cc_final: 0.7642 (tp) REVERT: C 30 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7797 (ttt180) REVERT: C 36 ILE cc_start: 0.8787 (mm) cc_final: 0.8581 (mm) REVERT: C 132 MET cc_start: 0.7720 (ppp) cc_final: 0.7020 (ppp) REVERT: C 157 HIS cc_start: 0.7040 (m90) cc_final: 0.6656 (m-70) REVERT: C 208 GLN cc_start: 0.8307 (mt0) cc_final: 0.8017 (mt0) REVERT: C 209 ARG cc_start: 0.8051 (ptt90) cc_final: 0.7680 (ptt90) REVERT: C 262 LEU cc_start: 0.6577 (mt) cc_final: 0.6329 (mt) REVERT: D 218 GLN cc_start: 0.8160 (mm110) cc_final: 0.7795 (mm110) REVERT: D 223 PHE cc_start: 0.5523 (p90) cc_final: 0.5224 (p90) REVERT: D 226 TYR cc_start: 0.6451 (p90) cc_final: 0.5824 (p90) REVERT: D 269 VAL cc_start: 0.8066 (m) cc_final: 0.7816 (m) REVERT: E 7 LEU cc_start: 0.7806 (tt) cc_final: 0.7428 (tt) REVERT: E 12 HIS cc_start: 0.7608 (t70) cc_final: 0.6149 (t70) REVERT: E 16 HIS cc_start: 0.7050 (m-70) cc_final: 0.6829 (m170) REVERT: E 101 VAL cc_start: 0.9013 (t) cc_final: 0.8764 (t) REVERT: E 150 GLN cc_start: 0.7546 (mm110) cc_final: 0.6925 (mm110) REVERT: E 159 THR cc_start: 0.8221 (m) cc_final: 0.7469 (p) REVERT: E 178 LEU cc_start: 0.8776 (mt) cc_final: 0.8565 (mt) REVERT: E 201 PHE cc_start: 0.7669 (t80) cc_final: 0.7275 (t80) REVERT: E 205 LYS cc_start: 0.8727 (mttt) cc_final: 0.8472 (mmtp) REVERT: E 206 GLU cc_start: 0.8054 (pt0) cc_final: 0.6814 (pp20) REVERT: F 65 VAL cc_start: 0.6382 (t) cc_final: 0.6116 (p) REVERT: F 82 ASN cc_start: 0.8155 (m110) cc_final: 0.7845 (m-40) REVERT: F 86 ILE cc_start: 0.7975 (pt) cc_final: 0.7171 (tp) REVERT: F 89 GLU cc_start: 0.4645 (tp30) cc_final: 0.4418 (tp30) REVERT: F 102 GLN cc_start: 0.8308 (mp10) cc_final: 0.7937 (mp10) REVERT: F 104 MET cc_start: 0.7529 (ptm) cc_final: 0.7199 (ppp) REVERT: F 105 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8610 (mttt) REVERT: F 154 GLU cc_start: 0.7729 (mp0) cc_final: 0.7129 (mp0) REVERT: F 164 LEU cc_start: 0.8264 (mt) cc_final: 0.8054 (mt) REVERT: F 183 ILE cc_start: 0.6389 (mt) cc_final: 0.6033 (mt) REVERT: F 198 MET cc_start: 0.7857 (ppp) cc_final: 0.7350 (ppp) REVERT: F 199 ASP cc_start: 0.7915 (m-30) cc_final: 0.7471 (m-30) REVERT: F 204 ASN cc_start: 0.8272 (p0) cc_final: 0.7941 (p0) REVERT: F 209 ARG cc_start: 0.7564 (ppt170) cc_final: 0.7338 (ttp80) REVERT: F 210 ILE cc_start: 0.8428 (pt) cc_final: 0.8151 (pt) REVERT: F 230 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7967 (mmmm) REVERT: F 242 GLN cc_start: 0.6666 (tt0) cc_final: 0.6408 (pp30) REVERT: F 243 VAL cc_start: 0.8338 (t) cc_final: 0.7473 (p) REVERT: F 244 LEU cc_start: 0.7915 (tt) cc_final: 0.7590 (tt) REVERT: F 256 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7519 (ttm110) REVERT: G 48 MET cc_start: -0.0411 (ppp) cc_final: -0.1304 (ppp) REVERT: G 62 HIS cc_start: 0.4958 (p90) cc_final: 0.4752 (p-80) REVERT: G 132 MET cc_start: 0.7617 (tmm) cc_final: 0.7089 (tmm) REVERT: G 157 HIS cc_start: 0.7826 (m90) cc_final: 0.7366 (m90) REVERT: G 183 ILE cc_start: 0.7189 (mt) cc_final: 0.6951 (mt) REVERT: G 199 ASP cc_start: 0.8427 (m-30) cc_final: 0.8050 (m-30) REVERT: G 201 PHE cc_start: 0.7874 (t80) cc_final: 0.7517 (t80) REVERT: G 202 ILE cc_start: 0.8523 (mt) cc_final: 0.8054 (mt) REVERT: G 205 LYS cc_start: 0.8623 (mtmm) cc_final: 0.7589 (mtmm) REVERT: G 209 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7676 (ttp80) REVERT: G 210 ILE cc_start: 0.8477 (pt) cc_final: 0.7369 (pt) REVERT: H 62 HIS cc_start: 0.7091 (t-170) cc_final: 0.6308 (t-170) REVERT: H 85 LEU cc_start: 0.8100 (tp) cc_final: 0.7766 (tp) REVERT: H 109 MET cc_start: 0.7379 (mtm) cc_final: 0.6914 (ptp) REVERT: H 202 ILE cc_start: 0.8666 (mm) cc_final: 0.8213 (mm) REVERT: H 207 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7148 (mm-40) REVERT: I 60 ILE cc_start: 0.8617 (mt) cc_final: 0.8191 (mm) REVERT: I 66 ASP cc_start: 0.7806 (t0) cc_final: 0.7556 (t0) REVERT: I 79 VAL cc_start: 0.7938 (t) cc_final: 0.7258 (p) REVERT: I 81 THR cc_start: 0.8609 (p) cc_final: 0.8260 (t) REVERT: I 86 ILE cc_start: 0.8427 (pt) cc_final: 0.8003 (mm) REVERT: I 92 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8401 (mtpp) REVERT: I 97 GLN cc_start: 0.8136 (pm20) cc_final: 0.7538 (pm20) REVERT: I 98 GLU cc_start: 0.7999 (mp0) cc_final: 0.7664 (mp0) REVERT: I 101 VAL cc_start: 0.9311 (t) cc_final: 0.9107 (t) REVERT: I 102 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8082 (mm-40) REVERT: I 105 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8203 (mtmm) REVERT: I 113 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7556 (mmmm) REVERT: I 118 ASP cc_start: 0.7682 (p0) cc_final: 0.7392 (p0) REVERT: I 145 TRP cc_start: 0.8219 (m-90) cc_final: 0.8001 (m-90) REVERT: I 146 ASN cc_start: 0.7794 (m110) cc_final: 0.7294 (m-40) REVERT: I 152 LEU cc_start: 0.7314 (pt) cc_final: 0.6384 (mp) REVERT: I 155 ARG cc_start: 0.8277 (tpt90) cc_final: 0.7308 (mmm160) REVERT: I 158 GLN cc_start: 0.8711 (tt0) cc_final: 0.8243 (tt0) REVERT: I 160 LEU cc_start: 0.8492 (tt) cc_final: 0.8018 (tt) REVERT: I 162 ASN cc_start: 0.8629 (t0) cc_final: 0.8410 (m-40) REVERT: I 163 THR cc_start: 0.8452 (m) cc_final: 0.8050 (p) REVERT: I 164 LEU cc_start: 0.8657 (mt) cc_final: 0.8257 (mt) REVERT: I 183 ILE cc_start: 0.8855 (mt) cc_final: 0.8387 (mm) REVERT: I 201 PHE cc_start: 0.8579 (t80) cc_final: 0.8376 (t80) REVERT: I 203 PHE cc_start: 0.8152 (t80) cc_final: 0.7706 (t80) REVERT: I 254 LYS cc_start: 0.8745 (ttmm) cc_final: 0.7976 (tptt) REVERT: I 260 ARG cc_start: 0.6629 (ptm160) cc_final: 0.6084 (ptm160) REVERT: I 261 TYR cc_start: 0.6849 (m-10) cc_final: 0.6357 (m-10) REVERT: I 264 ILE cc_start: 0.7121 (mm) cc_final: 0.6858 (mm) REVERT: J 63 TRP cc_start: 0.7759 (m100) cc_final: 0.6208 (m100) REVERT: J 65 VAL cc_start: 0.8827 (t) cc_final: 0.8575 (t) REVERT: J 76 LEU cc_start: 0.7971 (mm) cc_final: 0.7769 (mm) REVERT: J 86 ILE cc_start: 0.8912 (pt) cc_final: 0.8357 (mm) REVERT: J 101 VAL cc_start: 0.8863 (t) cc_final: 0.8545 (t) REVERT: J 102 GLN cc_start: 0.8192 (mp-120) cc_final: 0.7920 (mm-40) REVERT: J 103 THR cc_start: 0.8573 (t) cc_final: 0.8272 (t) REVERT: J 104 MET cc_start: 0.8157 (mmp) cc_final: 0.7782 (mmp) REVERT: J 105 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8786 (mtpt) REVERT: J 131 LEU cc_start: 0.8410 (tt) cc_final: 0.8164 (tt) REVERT: J 132 MET cc_start: 0.8427 (mmp) cc_final: 0.7662 (mmp) REVERT: J 139 HIS cc_start: 0.8183 (t70) cc_final: 0.7847 (t70) REVERT: J 160 LEU cc_start: 0.8680 (tt) cc_final: 0.8361 (tt) REVERT: J 161 LYS cc_start: 0.8671 (ptpt) cc_final: 0.8434 (pttm) REVERT: J 182 LEU cc_start: 0.8173 (mt) cc_final: 0.7922 (mt) REVERT: J 189 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.6393 (mtm180) REVERT: J 204 ASN cc_start: 0.7171 (m110) cc_final: 0.6939 (m110) REVERT: J 205 LYS cc_start: 0.8400 (tptp) cc_final: 0.7748 (tptp) REVERT: J 207 GLN cc_start: 0.7659 (mm110) cc_final: 0.7373 (mm-40) REVERT: J 208 GLN cc_start: 0.7738 (pt0) cc_final: 0.7181 (pt0) REVERT: K 22 LEU cc_start: 0.7920 (mm) cc_final: 0.7477 (mm) REVERT: K 34 GLU cc_start: 0.8291 (pt0) cc_final: 0.7762 (pp20) REVERT: K 39 GLN cc_start: 0.7469 (tp40) cc_final: 0.6765 (tp40) REVERT: K 132 MET cc_start: 0.6448 (ppp) cc_final: 0.5683 (ppp) REVERT: K 157 HIS cc_start: 0.7805 (m-70) cc_final: 0.7520 (m-70) REVERT: L 209 ARG cc_start: 0.8353 (mmp-170) cc_final: 0.7950 (mmp80) REVERT: L 226 TYR cc_start: 0.6322 (p90) cc_final: 0.5642 (p90) REVERT: L 266 ASN cc_start: 0.8658 (m-40) cc_final: 0.8184 (m-40) REVERT: L 269 VAL cc_start: 0.7762 (m) cc_final: 0.7389 (m) REVERT: M 14 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8247 (mtpt) REVERT: M 16 HIS cc_start: 0.6907 (m170) cc_final: 0.6628 (m170) REVERT: M 18 ASP cc_start: 0.7024 (t70) cc_final: 0.6787 (t70) REVERT: M 25 GLU cc_start: 0.8324 (tt0) cc_final: 0.7940 (tt0) REVERT: M 103 THR cc_start: 0.8643 (p) cc_final: 0.8412 (p) REVERT: M 133 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8440 (mmtt) REVERT: M 155 ARG cc_start: 0.8499 (ptp90) cc_final: 0.8034 (ptt-90) REVERT: M 159 THR cc_start: 0.8254 (m) cc_final: 0.7532 (p) REVERT: M 178 LEU cc_start: 0.8709 (mt) cc_final: 0.8042 (mt) REVERT: M 207 GLN cc_start: 0.7870 (mm110) cc_final: 0.7578 (mm110) REVERT: M 209 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7957 (ttp80) REVERT: M 220 LYS cc_start: 0.7567 (mmtt) cc_final: 0.7292 (mmtt) REVERT: N 104 MET cc_start: 0.7802 (ptm) cc_final: 0.7374 (ppp) REVERT: N 183 ILE cc_start: 0.6819 (mt) cc_final: 0.6406 (mt) REVERT: N 198 MET cc_start: 0.7576 (ppp) cc_final: 0.7187 (ppp) REVERT: N 210 ILE cc_start: 0.8415 (pt) cc_final: 0.7908 (pt) REVERT: N 213 GLN cc_start: 0.8642 (mt0) cc_final: 0.8195 (mt0) REVERT: N 230 LYS cc_start: 0.8392 (mttt) cc_final: 0.8049 (tptp) REVERT: N 233 HIS cc_start: 0.7597 (m-70) cc_final: 0.7346 (m-70) REVERT: N 243 VAL cc_start: 0.8135 (t) cc_final: 0.7348 (m) REVERT: N 256 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7438 (ttm110) REVERT: N 267 LYS cc_start: 0.8967 (ptmt) cc_final: 0.8282 (mmtm) REVERT: N 270 LYS cc_start: 0.7984 (mptt) cc_final: 0.7360 (mmtp) REVERT: O 23 HIS cc_start: 0.6741 (t70) cc_final: 0.6395 (t70) REVERT: O 48 MET cc_start: -0.1888 (ppp) cc_final: -0.2112 (ppp) REVERT: O 62 HIS cc_start: 0.4939 (p90) cc_final: 0.4703 (p-80) REVERT: O 115 LEU cc_start: 0.8180 (tp) cc_final: 0.7965 (tp) REVERT: O 132 MET cc_start: 0.7482 (tmm) cc_final: 0.6849 (tmm) REVERT: O 157 HIS cc_start: 0.7897 (m90) cc_final: 0.7689 (m90) REVERT: O 175 GLU cc_start: 0.7982 (pm20) cc_final: 0.7529 (mm-30) REVERT: O 193 LEU cc_start: 0.8321 (mm) cc_final: 0.8020 (mm) REVERT: O 204 ASN cc_start: 0.8800 (p0) cc_final: 0.8203 (p0) REVERT: P 62 HIS cc_start: 0.7237 (t70) cc_final: 0.6527 (t70) REVERT: P 85 LEU cc_start: 0.8182 (tp) cc_final: 0.7856 (tp) REVERT: P 115 LEU cc_start: 0.4030 (tp) cc_final: 0.3674 (tp) REVERT: P 168 ILE cc_start: 0.8547 (pt) cc_final: 0.8302 (mt) REVERT: P 201 PHE cc_start: 0.6551 (t80) cc_final: 0.6247 (t80) REVERT: P 248 ASP cc_start: 0.7596 (p0) cc_final: 0.7370 (p0) outliers start: 2 outliers final: 1 residues processed: 1193 average time/residue: 0.4731 time to fit residues: 876.9302 Evaluate side-chains 1111 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1110 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 213 optimal weight: 0.9980 chunk 274 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 316 optimal weight: 0.6980 chunk 209 optimal weight: 0.3980 chunk 373 optimal weight: 0.8980 chunk 234 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN C 186 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN G 211 GLN H 148 GLN H 157 HIS H 204 ASN H 242 GLN ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN L 186 ASN M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 218 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 GLN O 208 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34119 Z= 0.204 Angle : 0.686 12.995 46515 Z= 0.362 Chirality : 0.048 0.243 5006 Planarity : 0.005 0.072 5714 Dihedral : 14.669 174.371 5007 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.13), residues: 3851 helix: 1.20 (0.12), residues: 1871 sheet: -0.49 (0.18), residues: 813 loop : -1.76 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP F 78 HIS 0.010 0.001 HIS B 157 PHE 0.027 0.002 PHE J 174 TYR 0.048 0.002 TYR C 87 ARG 0.013 0.001 ARG M 100 *********************** 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 1191 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1191 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7690 (pp20) cc_final: 0.7059 (tm-30) REVERT: A 48 MET cc_start: 0.6172 (mmm) cc_final: 0.5962 (mmm) REVERT: A 66 ASP cc_start: 0.7715 (t0) cc_final: 0.7319 (t70) REVERT: A 79 VAL cc_start: 0.7950 (t) cc_final: 0.7615 (p) REVERT: A 80 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6552 (tm-30) REVERT: A 81 THR cc_start: 0.8656 (p) cc_final: 0.8264 (t) REVERT: A 86 ILE cc_start: 0.8526 (pt) cc_final: 0.7943 (mp) REVERT: A 92 LYS cc_start: 0.8999 (mtmm) cc_final: 0.8528 (mtpp) REVERT: A 97 GLN cc_start: 0.7808 (pm20) cc_final: 0.7458 (pm20) REVERT: A 98 GLU cc_start: 0.7993 (mp0) cc_final: 0.7780 (mp0) REVERT: A 104 MET cc_start: 0.8531 (ttm) cc_final: 0.7759 (ttm) REVERT: A 113 LYS cc_start: 0.7940 (mmmm) cc_final: 0.7675 (mmmm) REVERT: A 132 MET cc_start: 0.7729 (mmm) cc_final: 0.7313 (mmm) REVERT: A 152 LEU cc_start: 0.7004 (pt) cc_final: 0.5473 (tt) REVERT: A 155 ARG cc_start: 0.8301 (tpt90) cc_final: 0.7284 (mmm160) REVERT: A 158 GLN cc_start: 0.8678 (tt0) cc_final: 0.8257 (tt0) REVERT: A 160 LEU cc_start: 0.8456 (tt) cc_final: 0.8197 (tt) REVERT: A 164 LEU cc_start: 0.8246 (mt) cc_final: 0.8002 (mt) REVERT: A 190 LYS cc_start: 0.7637 (mtmm) cc_final: 0.6998 (mtpt) REVERT: A 201 PHE cc_start: 0.8574 (t80) cc_final: 0.8185 (t80) REVERT: A 203 PHE cc_start: 0.8284 (t80) cc_final: 0.7805 (t80) REVERT: A 254 LYS cc_start: 0.8237 (pptt) cc_final: 0.7918 (pptt) REVERT: A 262 LEU cc_start: 0.8128 (tt) cc_final: 0.7919 (tp) REVERT: B 40 CYS cc_start: 0.7370 (t) cc_final: 0.7138 (p) REVERT: B 63 TRP cc_start: 0.8129 (m100) cc_final: 0.6230 (m100) REVERT: B 64 GLN cc_start: 0.6595 (mm110) cc_final: 0.6260 (mm110) REVERT: B 86 ILE cc_start: 0.8764 (pt) cc_final: 0.8305 (mm) REVERT: B 89 GLU cc_start: 0.7551 (tt0) cc_final: 0.6944 (tt0) REVERT: B 92 LYS cc_start: 0.8599 (tppp) cc_final: 0.8290 (tppp) REVERT: B 98 GLU cc_start: 0.7900 (pm20) cc_final: 0.7669 (pm20) REVERT: B 103 THR cc_start: 0.8847 (p) cc_final: 0.8550 (p) REVERT: B 104 MET cc_start: 0.8290 (mmp) cc_final: 0.7912 (mmp) REVERT: B 106 TRP cc_start: 0.8161 (t60) cc_final: 0.7859 (t60) REVERT: B 129 GLN cc_start: 0.8410 (pt0) cc_final: 0.8056 (pt0) REVERT: B 131 LEU cc_start: 0.8725 (tt) cc_final: 0.8203 (tt) REVERT: B 132 MET cc_start: 0.8354 (mmp) cc_final: 0.7551 (mmp) REVERT: B 139 HIS cc_start: 0.8220 (t70) cc_final: 0.7764 (t70) REVERT: B 178 LEU cc_start: 0.9050 (mm) cc_final: 0.8730 (mm) REVERT: B 188 LYS cc_start: 0.7342 (mmtp) cc_final: 0.7001 (mmtp) REVERT: B 198 MET cc_start: 0.7883 (tpt) cc_final: 0.7505 (tpp) REVERT: B 204 ASN cc_start: 0.6959 (p0) cc_final: 0.6424 (p0) REVERT: B 207 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7530 (mm-40) REVERT: B 208 GLN cc_start: 0.7762 (pt0) cc_final: 0.7242 (pt0) REVERT: C 7 LEU cc_start: 0.8207 (tt) cc_final: 0.7654 (tt) REVERT: C 15 TRP cc_start: 0.8445 (m100) cc_final: 0.8048 (m100) REVERT: C 30 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7658 (ttt180) REVERT: C 36 ILE cc_start: 0.8797 (mm) cc_final: 0.8595 (mm) REVERT: C 38 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6966 (tm-30) REVERT: C 132 MET cc_start: 0.7808 (ppp) cc_final: 0.7131 (ppp) REVERT: C 157 HIS cc_start: 0.7062 (m90) cc_final: 0.6711 (m-70) REVERT: C 186 ASN cc_start: 0.6967 (m-40) cc_final: 0.6634 (m110) REVERT: C 208 GLN cc_start: 0.8270 (mt0) cc_final: 0.7983 (mt0) REVERT: C 209 ARG cc_start: 0.8306 (ptt90) cc_final: 0.7636 (ptt90) REVERT: C 262 LEU cc_start: 0.6612 (mt) cc_final: 0.6323 (mt) REVERT: C 270 LYS cc_start: 0.7981 (pptt) cc_final: 0.7658 (pptt) REVERT: D 209 ARG cc_start: 0.8498 (tpm170) cc_final: 0.8096 (mmp80) REVERT: D 218 GLN cc_start: 0.8191 (mm110) cc_final: 0.7892 (mm110) REVERT: D 226 TYR cc_start: 0.6580 (p90) cc_final: 0.5857 (p90) REVERT: D 269 VAL cc_start: 0.8013 (m) cc_final: 0.7763 (m) REVERT: E 7 LEU cc_start: 0.8173 (tt) cc_final: 0.7225 (tt) REVERT: E 11 GLU cc_start: 0.8138 (mp0) cc_final: 0.7717 (mp0) REVERT: E 12 HIS cc_start: 0.7638 (t70) cc_final: 0.6100 (t70) REVERT: E 16 HIS cc_start: 0.7138 (m-70) cc_final: 0.6912 (m170) REVERT: E 18 ASP cc_start: 0.7150 (t70) cc_final: 0.6806 (t70) REVERT: E 101 VAL cc_start: 0.8997 (t) cc_final: 0.8730 (t) REVERT: E 159 THR cc_start: 0.8216 (m) cc_final: 0.7478 (p) REVERT: E 178 LEU cc_start: 0.8784 (mt) cc_final: 0.8561 (mt) REVERT: F 65 VAL cc_start: 0.6202 (t) cc_final: 0.5853 (p) REVERT: F 89 GLU cc_start: 0.4898 (tp30) cc_final: 0.4584 (tp30) REVERT: F 104 MET cc_start: 0.7592 (ptm) cc_final: 0.7197 (ppp) REVERT: F 105 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8478 (mtmm) REVERT: F 183 ILE cc_start: 0.6228 (mt) cc_final: 0.5888 (mt) REVERT: F 198 MET cc_start: 0.7992 (ppp) cc_final: 0.7476 (ppp) REVERT: F 199 ASP cc_start: 0.7903 (m-30) cc_final: 0.7694 (m-30) REVERT: F 230 LYS cc_start: 0.8479 (mmmt) cc_final: 0.7985 (mmmm) REVERT: F 242 GLN cc_start: 0.6731 (tt0) cc_final: 0.6324 (pp30) REVERT: F 243 VAL cc_start: 0.8362 (t) cc_final: 0.7650 (p) REVERT: F 244 LEU cc_start: 0.7986 (tt) cc_final: 0.7668 (tt) REVERT: F 256 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7548 (ttm110) REVERT: G 48 MET cc_start: -0.0391 (ppp) cc_final: -0.1302 (ppp) REVERT: G 104 MET cc_start: 0.7344 (pmm) cc_final: 0.7103 (pmm) REVERT: G 132 MET cc_start: 0.7626 (tmm) cc_final: 0.7056 (tmm) REVERT: G 157 HIS cc_start: 0.7983 (m90) cc_final: 0.7522 (m90) REVERT: G 183 ILE cc_start: 0.6927 (mt) cc_final: 0.6695 (mt) REVERT: G 201 PHE cc_start: 0.7839 (t80) cc_final: 0.7550 (t80) REVERT: G 202 ILE cc_start: 0.8535 (mt) cc_final: 0.8058 (mt) REVERT: G 205 LYS cc_start: 0.8672 (mtmm) cc_final: 0.7510 (mtmm) REVERT: G 209 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7638 (ttp80) REVERT: G 210 ILE cc_start: 0.8505 (pt) cc_final: 0.7516 (pt) REVERT: H 62 HIS cc_start: 0.7102 (t-170) cc_final: 0.6249 (t-170) REVERT: H 109 MET cc_start: 0.7348 (mtm) cc_final: 0.6889 (ptp) REVERT: H 202 ILE cc_start: 0.8646 (mm) cc_final: 0.8299 (mm) REVERT: H 207 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7200 (mm-40) REVERT: H 267 LYS cc_start: 0.7484 (ptmm) cc_final: 0.7240 (ptmm) REVERT: I 60 ILE cc_start: 0.8644 (mt) cc_final: 0.8204 (mm) REVERT: I 66 ASP cc_start: 0.7916 (t0) cc_final: 0.7590 (t0) REVERT: I 79 VAL cc_start: 0.7973 (t) cc_final: 0.7275 (p) REVERT: I 81 THR cc_start: 0.8663 (p) cc_final: 0.8314 (t) REVERT: I 86 ILE cc_start: 0.8440 (pt) cc_final: 0.8019 (mm) REVERT: I 92 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8431 (mtpp) REVERT: I 97 GLN cc_start: 0.8156 (pm20) cc_final: 0.7537 (pm20) REVERT: I 98 GLU cc_start: 0.7988 (mp0) cc_final: 0.7632 (mp0) REVERT: I 102 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8112 (mm-40) REVERT: I 105 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8178 (mtmm) REVERT: I 113 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7537 (mmmm) REVERT: I 118 ASP cc_start: 0.7704 (p0) cc_final: 0.7479 (p0) REVERT: I 152 LEU cc_start: 0.7395 (pt) cc_final: 0.6469 (mp) REVERT: I 155 ARG cc_start: 0.8256 (tpt90) cc_final: 0.7281 (mmm160) REVERT: I 158 GLN cc_start: 0.8692 (tt0) cc_final: 0.8164 (tt0) REVERT: I 160 LEU cc_start: 0.8508 (tt) cc_final: 0.8063 (tt) REVERT: I 163 THR cc_start: 0.8304 (m) cc_final: 0.7814 (p) REVERT: I 164 LEU cc_start: 0.8595 (mt) cc_final: 0.8374 (mt) REVERT: I 183 ILE cc_start: 0.8894 (mt) cc_final: 0.8383 (mm) REVERT: I 190 LYS cc_start: 0.8015 (mptt) cc_final: 0.7684 (mptt) REVERT: I 198 MET cc_start: 0.8414 (ttm) cc_final: 0.8161 (tpp) REVERT: I 201 PHE cc_start: 0.8684 (t80) cc_final: 0.8448 (t80) REVERT: I 203 PHE cc_start: 0.8161 (t80) cc_final: 0.7711 (t80) REVERT: I 238 GLN cc_start: 0.5497 (mt0) cc_final: 0.5065 (mt0) REVERT: I 264 ILE cc_start: 0.7033 (mm) cc_final: 0.6790 (mm) REVERT: J 62 HIS cc_start: 0.6989 (t70) cc_final: 0.6469 (t70) REVERT: J 63 TRP cc_start: 0.7675 (m100) cc_final: 0.6190 (m100) REVERT: J 86 ILE cc_start: 0.8895 (pt) cc_final: 0.8387 (mm) REVERT: J 100 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7436 (mtt-85) REVERT: J 101 VAL cc_start: 0.8840 (t) cc_final: 0.8526 (t) REVERT: J 102 GLN cc_start: 0.8379 (mp-120) cc_final: 0.8107 (mm-40) REVERT: J 103 THR cc_start: 0.8564 (t) cc_final: 0.8253 (t) REVERT: J 104 MET cc_start: 0.8177 (mmp) cc_final: 0.7840 (mmp) REVERT: J 131 LEU cc_start: 0.8424 (tt) cc_final: 0.8176 (tt) REVERT: J 132 MET cc_start: 0.8436 (mmp) cc_final: 0.7646 (mmp) REVERT: J 139 HIS cc_start: 0.8186 (t70) cc_final: 0.7890 (t70) REVERT: J 160 LEU cc_start: 0.8654 (tt) cc_final: 0.8388 (tt) REVERT: J 161 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8419 (pttp) REVERT: J 178 LEU cc_start: 0.9075 (mm) cc_final: 0.8865 (mm) REVERT: J 182 LEU cc_start: 0.8215 (mt) cc_final: 0.7912 (mt) REVERT: J 189 ARG cc_start: 0.7321 (ttp-110) cc_final: 0.6411 (mtm180) REVERT: J 205 LYS cc_start: 0.8436 (tptp) cc_final: 0.7661 (tptp) REVERT: J 208 GLN cc_start: 0.7740 (pt0) cc_final: 0.7026 (pt0) REVERT: K 34 GLU cc_start: 0.8308 (pt0) cc_final: 0.7793 (pp20) REVERT: K 39 GLN cc_start: 0.7445 (tp40) cc_final: 0.6761 (tp40) REVERT: K 132 MET cc_start: 0.6684 (ppp) cc_final: 0.6278 (ppp) REVERT: K 157 HIS cc_start: 0.7420 (m-70) cc_final: 0.7198 (m90) REVERT: L 209 ARG cc_start: 0.8356 (mmp-170) cc_final: 0.8022 (mmp-170) REVERT: L 226 TYR cc_start: 0.6484 (p90) cc_final: 0.5720 (p90) REVERT: L 266 ASN cc_start: 0.8697 (m-40) cc_final: 0.8215 (m-40) REVERT: L 269 VAL cc_start: 0.7749 (m) cc_final: 0.7371 (m) REVERT: M 7 LEU cc_start: 0.8213 (tt) cc_final: 0.7406 (tt) REVERT: M 14 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8158 (mtpt) REVERT: M 16 HIS cc_start: 0.6898 (m170) cc_final: 0.6642 (m170) REVERT: M 18 ASP cc_start: 0.7055 (t70) cc_final: 0.6798 (t70) REVERT: M 25 GLU cc_start: 0.8340 (tt0) cc_final: 0.7924 (tt0) REVERT: M 103 THR cc_start: 0.8661 (p) cc_final: 0.8454 (p) REVERT: M 133 LYS cc_start: 0.8566 (ptpp) cc_final: 0.8317 (mmtt) REVERT: M 155 ARG cc_start: 0.8542 (ptp90) cc_final: 0.8034 (ptt-90) REVERT: M 159 THR cc_start: 0.8256 (m) cc_final: 0.7492 (p) REVERT: M 178 LEU cc_start: 0.8739 (mt) cc_final: 0.8129 (mt) REVERT: M 207 GLN cc_start: 0.7928 (mm110) cc_final: 0.7567 (mm110) REVERT: M 220 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7285 (mmtm) REVERT: N 104 MET cc_start: 0.7778 (ptm) cc_final: 0.7391 (ppp) REVERT: N 183 ILE cc_start: 0.6870 (mt) cc_final: 0.6532 (mt) REVERT: N 198 MET cc_start: 0.7619 (ppp) cc_final: 0.7214 (ppp) REVERT: N 210 ILE cc_start: 0.8403 (pt) cc_final: 0.7920 (pt) REVERT: N 213 GLN cc_start: 0.8672 (mt0) cc_final: 0.8216 (mt0) REVERT: N 230 LYS cc_start: 0.8413 (mttt) cc_final: 0.8088 (tptp) REVERT: N 233 HIS cc_start: 0.7661 (m-70) cc_final: 0.7412 (m-70) REVERT: N 243 VAL cc_start: 0.8138 (t) cc_final: 0.7403 (m) REVERT: N 256 ARG cc_start: 0.7938 (ttm110) cc_final: 0.7453 (ttm110) REVERT: N 270 LYS cc_start: 0.7932 (mptt) cc_final: 0.7306 (mmtp) REVERT: O 23 HIS cc_start: 0.6728 (t70) cc_final: 0.5994 (t70) REVERT: O 48 MET cc_start: -0.2091 (ppp) cc_final: -0.2398 (ppp) REVERT: O 109 MET cc_start: 0.6808 (tpp) cc_final: 0.6415 (tpt) REVERT: O 132 MET cc_start: 0.7499 (tmm) cc_final: 0.6797 (tmm) REVERT: P 62 HIS cc_start: 0.7299 (t70) cc_final: 0.6567 (t70) REVERT: P 85 LEU cc_start: 0.8247 (tp) cc_final: 0.7849 (tp) REVERT: P 115 LEU cc_start: 0.3992 (tp) cc_final: 0.3750 (tp) REVERT: P 168 ILE cc_start: 0.8516 (pt) cc_final: 0.8245 (mt) REVERT: P 201 PHE cc_start: 0.6755 (t80) cc_final: 0.6226 (t80) outliers start: 0 outliers final: 0 residues processed: 1191 average time/residue: 0.4706 time to fit residues: 870.7083 Evaluate side-chains 1110 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1110 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 237 optimal weight: 0.0970 chunk 254 optimal weight: 4.9990 chunk 184 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN G 211 GLN H 157 HIS I 207 GLN ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 GLN P 233 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34119 Z= 0.206 Angle : 0.703 14.585 46515 Z= 0.369 Chirality : 0.048 0.259 5006 Planarity : 0.004 0.064 5714 Dihedral : 14.685 174.736 5007 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.54 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -0.16 (0.13), residues: 3851 helix: 1.09 (0.12), residues: 1885 sheet: -0.45 (0.17), residues: 853 loop : -1.84 (0.16), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 78 HIS 0.010 0.001 HIS P 157 PHE 0.035 0.002 PHE C 26 TYR 0.034 0.002 TYR C 87 ARG 0.008 0.001 ARG G 189 *********************** 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 1191 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1191 time to evaluate : 3.536 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 15 TRP cc_start: 0.6969 (m100) cc_final: 0.6423 (m100) REVERT: A 30 ARG cc_start: 0.7135 (mtp-110) cc_final: 0.6913 (mtm-85) REVERT: A 45 GLU cc_start: 0.7710 (pp20) cc_final: 0.7324 (pp20) REVERT: A 66 ASP cc_start: 0.7699 (t0) cc_final: 0.7292 (t70) REVERT: A 79 VAL cc_start: 0.7910 (t) cc_final: 0.7573 (p) REVERT: A 80 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6350 (tm-30) REVERT: A 81 THR cc_start: 0.8707 (p) cc_final: 0.8426 (t) REVERT: A 92 LYS cc_start: 0.9024 (mtmm) cc_final: 0.8541 (mtpp) REVERT: A 97 GLN cc_start: 0.7783 (pm20) cc_final: 0.7354 (pm20) REVERT: A 98 GLU cc_start: 0.8007 (mp0) cc_final: 0.7751 (mp0) REVERT: A 104 MET cc_start: 0.8565 (ttm) cc_final: 0.7694 (ttm) REVERT: A 105 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8742 (mtpp) REVERT: A 113 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7739 (mmmm) REVERT: A 118 ASP cc_start: 0.7851 (p0) cc_final: 0.7514 (p0) REVERT: A 132 MET cc_start: 0.7724 (mmm) cc_final: 0.7379 (mmm) REVERT: A 152 LEU cc_start: 0.7029 (pt) cc_final: 0.5639 (tt) REVERT: A 155 ARG cc_start: 0.8312 (tpt90) cc_final: 0.7260 (mmm160) REVERT: A 158 GLN cc_start: 0.8704 (tt0) cc_final: 0.8246 (tt0) REVERT: A 160 LEU cc_start: 0.8479 (tt) cc_final: 0.8246 (tt) REVERT: A 164 LEU cc_start: 0.8250 (mt) cc_final: 0.8018 (mt) REVERT: A 190 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7254 (mtpt) REVERT: A 201 PHE cc_start: 0.8623 (t80) cc_final: 0.8288 (t80) REVERT: A 203 PHE cc_start: 0.8299 (t80) cc_final: 0.7852 (t80) REVERT: A 223 PHE cc_start: 0.6868 (m-80) cc_final: 0.6358 (m-10) REVERT: A 244 LEU cc_start: 0.8333 (mp) cc_final: 0.8096 (mp) REVERT: A 254 LYS cc_start: 0.8263 (pptt) cc_final: 0.7845 (pptt) REVERT: B 40 CYS cc_start: 0.7371 (t) cc_final: 0.7097 (p) REVERT: B 63 TRP cc_start: 0.8175 (m100) cc_final: 0.6308 (m100) REVERT: B 64 GLN cc_start: 0.6651 (mm110) cc_final: 0.6202 (mm110) REVERT: B 70 TYR cc_start: 0.8195 (t80) cc_final: 0.7359 (t80) REVERT: B 86 ILE cc_start: 0.8799 (pt) cc_final: 0.8417 (mm) REVERT: B 89 GLU cc_start: 0.7473 (tt0) cc_final: 0.6876 (tt0) REVERT: B 92 LYS cc_start: 0.8653 (tppp) cc_final: 0.8356 (tppp) REVERT: B 101 VAL cc_start: 0.8868 (t) cc_final: 0.8420 (t) REVERT: B 102 GLN cc_start: 0.8236 (mp-120) cc_final: 0.7622 (mm-40) REVERT: B 104 MET cc_start: 0.8223 (mmp) cc_final: 0.7836 (mmp) REVERT: B 105 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8642 (mtpp) REVERT: B 129 GLN cc_start: 0.8435 (pt0) cc_final: 0.8084 (pt0) REVERT: B 131 LEU cc_start: 0.8709 (tt) cc_final: 0.8236 (tt) REVERT: B 132 MET cc_start: 0.8370 (mmp) cc_final: 0.7495 (mmp) REVERT: B 139 HIS cc_start: 0.8258 (t70) cc_final: 0.7772 (t70) REVERT: B 165 GLU cc_start: 0.7599 (tp30) cc_final: 0.7274 (tp30) REVERT: B 186 ASN cc_start: 0.7953 (m-40) cc_final: 0.7695 (m-40) REVERT: B 188 LYS cc_start: 0.7245 (mmtp) cc_final: 0.6682 (mmtp) REVERT: B 198 MET cc_start: 0.7884 (tpt) cc_final: 0.7500 (tpp) REVERT: B 204 ASN cc_start: 0.6987 (p0) cc_final: 0.6424 (p0) REVERT: B 205 LYS cc_start: 0.8309 (tptp) cc_final: 0.7959 (tppp) REVERT: B 207 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7536 (mm-40) REVERT: B 208 GLN cc_start: 0.7792 (pt0) cc_final: 0.7250 (pt0) REVERT: C 7 LEU cc_start: 0.8172 (tt) cc_final: 0.7708 (tt) REVERT: C 11 GLU cc_start: 0.7874 (tp30) cc_final: 0.7178 (tp30) REVERT: C 22 LEU cc_start: 0.8016 (mm) cc_final: 0.7567 (mm) REVERT: C 28 ILE cc_start: 0.7855 (tp) cc_final: 0.7605 (tp) REVERT: C 30 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7755 (ttt180) REVERT: C 38 GLN cc_start: 0.7330 (tm-30) cc_final: 0.6991 (tm-30) REVERT: C 132 MET cc_start: 0.7823 (ppp) cc_final: 0.7399 (ppp) REVERT: C 157 HIS cc_start: 0.7097 (m90) cc_final: 0.6784 (m-70) REVERT: C 186 ASN cc_start: 0.6793 (m-40) cc_final: 0.6464 (m110) REVERT: C 255 ASP cc_start: 0.7293 (m-30) cc_final: 0.6660 (t0) REVERT: D 205 LYS cc_start: 0.8459 (mmpt) cc_final: 0.8118 (mmpt) REVERT: D 209 ARG cc_start: 0.8469 (tpm170) cc_final: 0.8122 (mmp80) REVERT: D 218 GLN cc_start: 0.8203 (mm110) cc_final: 0.7805 (mm110) REVERT: D 223 PHE cc_start: 0.5410 (p90) cc_final: 0.5108 (p90) REVERT: D 226 TYR cc_start: 0.6562 (p90) cc_final: 0.5909 (p90) REVERT: D 262 LEU cc_start: 0.8305 (mm) cc_final: 0.8074 (mm) REVERT: D 269 VAL cc_start: 0.8053 (m) cc_final: 0.7717 (m) REVERT: E 7 LEU cc_start: 0.8402 (tt) cc_final: 0.7619 (tt) REVERT: E 12 HIS cc_start: 0.7641 (t70) cc_final: 0.6142 (t70) REVERT: E 15 TRP cc_start: 0.7778 (m-10) cc_final: 0.7365 (m-10) REVERT: E 16 HIS cc_start: 0.7166 (m-70) cc_final: 0.6920 (m170) REVERT: E 18 ASP cc_start: 0.7166 (t70) cc_final: 0.6862 (t70) REVERT: E 150 GLN cc_start: 0.7680 (mm110) cc_final: 0.7360 (mm110) REVERT: E 159 THR cc_start: 0.8206 (m) cc_final: 0.7422 (p) REVERT: E 178 LEU cc_start: 0.8814 (mt) cc_final: 0.8564 (mt) REVERT: E 200 ILE cc_start: 0.8342 (mp) cc_final: 0.8077 (mp) REVERT: E 201 PHE cc_start: 0.7871 (t80) cc_final: 0.7404 (t80) REVERT: F 21 SER cc_start: 0.7513 (m) cc_final: 0.7272 (m) REVERT: F 65 VAL cc_start: 0.6153 (t) cc_final: 0.5919 (p) REVERT: F 82 ASN cc_start: 0.8105 (m110) cc_final: 0.7730 (m-40) REVERT: F 102 GLN cc_start: 0.8438 (mp-120) cc_final: 0.8211 (mp10) REVERT: F 104 MET cc_start: 0.7350 (ptm) cc_final: 0.7060 (ppp) REVERT: F 105 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8467 (mttm) REVERT: F 164 LEU cc_start: 0.8252 (mt) cc_final: 0.8043 (mt) REVERT: F 183 ILE cc_start: 0.6050 (mt) cc_final: 0.5772 (mt) REVERT: F 198 MET cc_start: 0.7978 (ppp) cc_final: 0.7447 (ppp) REVERT: F 202 ILE cc_start: 0.8376 (mt) cc_final: 0.7929 (mt) REVERT: F 230 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7859 (mmmm) REVERT: F 242 GLN cc_start: 0.6793 (tt0) cc_final: 0.6423 (pp30) REVERT: F 243 VAL cc_start: 0.8366 (t) cc_final: 0.7677 (p) REVERT: F 256 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7590 (ttm110) REVERT: F 262 LEU cc_start: 0.7531 (mt) cc_final: 0.7308 (mt) REVERT: G 48 MET cc_start: -0.0358 (ppp) cc_final: -0.1317 (ppp) REVERT: G 115 LEU cc_start: 0.8347 (tp) cc_final: 0.8138 (tp) REVERT: G 132 MET cc_start: 0.7597 (tmm) cc_final: 0.6996 (tmm) REVERT: G 157 HIS cc_start: 0.8017 (m90) cc_final: 0.7532 (m90) REVERT: G 175 GLU cc_start: 0.8160 (pm20) cc_final: 0.7800 (pm20) REVERT: G 183 ILE cc_start: 0.6833 (mt) cc_final: 0.6607 (mt) REVERT: G 201 PHE cc_start: 0.7834 (t80) cc_final: 0.7564 (t80) REVERT: G 205 LYS cc_start: 0.8714 (mtmm) cc_final: 0.7680 (mtmm) REVERT: G 209 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7713 (ttp80) REVERT: G 210 ILE cc_start: 0.8544 (pt) cc_final: 0.7554 (pt) REVERT: H 62 HIS cc_start: 0.7112 (t-170) cc_final: 0.6248 (t-170) REVERT: H 104 MET cc_start: 0.8224 (mpp) cc_final: 0.7716 (mpp) REVERT: H 109 MET cc_start: 0.7437 (mtm) cc_final: 0.6839 (ptp) REVERT: H 207 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7178 (mm-40) REVERT: I 60 ILE cc_start: 0.8545 (mt) cc_final: 0.8174 (mm) REVERT: I 66 ASP cc_start: 0.7968 (t0) cc_final: 0.7655 (t0) REVERT: I 79 VAL cc_start: 0.7976 (t) cc_final: 0.7383 (p) REVERT: I 81 THR cc_start: 0.8691 (p) cc_final: 0.8320 (t) REVERT: I 86 ILE cc_start: 0.8447 (pt) cc_final: 0.8021 (mm) REVERT: I 92 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8408 (mtpp) REVERT: I 97 GLN cc_start: 0.8180 (pm20) cc_final: 0.7457 (pm20) REVERT: I 98 GLU cc_start: 0.7977 (mp0) cc_final: 0.7566 (mp0) REVERT: I 102 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8090 (mm-40) REVERT: I 105 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8177 (mtmm) REVERT: I 113 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7557 (mmmm) REVERT: I 118 ASP cc_start: 0.7812 (p0) cc_final: 0.7550 (p0) REVERT: I 152 LEU cc_start: 0.7392 (pt) cc_final: 0.6439 (mp) REVERT: I 155 ARG cc_start: 0.8256 (tpt90) cc_final: 0.7240 (mmm160) REVERT: I 158 GLN cc_start: 0.8683 (tt0) cc_final: 0.8163 (tt0) REVERT: I 160 LEU cc_start: 0.8538 (tt) cc_final: 0.8082 (tt) REVERT: I 163 THR cc_start: 0.8158 (m) cc_final: 0.7645 (p) REVERT: I 164 LEU cc_start: 0.8586 (mt) cc_final: 0.8379 (mt) REVERT: I 183 ILE cc_start: 0.8825 (mt) cc_final: 0.8398 (mm) REVERT: I 201 PHE cc_start: 0.8703 (t80) cc_final: 0.8413 (t80) REVERT: I 203 PHE cc_start: 0.8166 (t80) cc_final: 0.7708 (t80) REVERT: I 254 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8311 (tptt) REVERT: I 260 ARG cc_start: 0.6658 (ptm160) cc_final: 0.6150 (ptm160) REVERT: I 261 TYR cc_start: 0.6899 (m-10) cc_final: 0.6496 (m-10) REVERT: J 40 CYS cc_start: 0.6840 (t) cc_final: 0.6584 (p) REVERT: J 63 TRP cc_start: 0.7628 (m100) cc_final: 0.5831 (m100) REVERT: J 64 GLN cc_start: 0.7233 (tp40) cc_final: 0.6868 (tp40) REVERT: J 65 VAL cc_start: 0.8861 (t) cc_final: 0.8590 (t) REVERT: J 86 ILE cc_start: 0.8919 (pt) cc_final: 0.8339 (mm) REVERT: J 101 VAL cc_start: 0.8875 (t) cc_final: 0.8493 (t) REVERT: J 102 GLN cc_start: 0.8455 (mp-120) cc_final: 0.8074 (mm-40) REVERT: J 103 THR cc_start: 0.8670 (t) cc_final: 0.8300 (t) REVERT: J 104 MET cc_start: 0.8248 (mmp) cc_final: 0.7852 (mmp) REVERT: J 105 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8779 (mtpp) REVERT: J 131 LEU cc_start: 0.8460 (tt) cc_final: 0.8222 (tt) REVERT: J 132 MET cc_start: 0.8515 (mmp) cc_final: 0.7663 (mmp) REVERT: J 139 HIS cc_start: 0.8270 (t70) cc_final: 0.7986 (t70) REVERT: J 160 LEU cc_start: 0.8632 (tt) cc_final: 0.8367 (tt) REVERT: J 161 LYS cc_start: 0.8690 (ptpt) cc_final: 0.8420 (pttp) REVERT: J 178 LEU cc_start: 0.9208 (mm) cc_final: 0.8969 (mm) REVERT: J 182 LEU cc_start: 0.8209 (mt) cc_final: 0.7980 (mt) REVERT: J 201 PHE cc_start: 0.8983 (t80) cc_final: 0.8633 (t80) REVERT: J 204 ASN cc_start: 0.7133 (m110) cc_final: 0.6681 (p0) REVERT: J 205 LYS cc_start: 0.8507 (tptp) cc_final: 0.7670 (tptp) REVERT: J 208 GLN cc_start: 0.7835 (pt0) cc_final: 0.7132 (pt0) REVERT: K 38 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7102 (tm-30) REVERT: K 39 GLN cc_start: 0.7356 (tp40) cc_final: 0.6964 (tp40) REVERT: K 132 MET cc_start: 0.6686 (ppp) cc_final: 0.6340 (ppp) REVERT: K 209 ARG cc_start: 0.8323 (ptt90) cc_final: 0.8013 (ptt90) REVERT: K 244 LEU cc_start: 0.8102 (mm) cc_final: 0.7295 (mm) REVERT: L 209 ARG cc_start: 0.8183 (mmp-170) cc_final: 0.7917 (mmm160) REVERT: L 226 TYR cc_start: 0.6590 (p90) cc_final: 0.5805 (p90) REVERT: L 269 VAL cc_start: 0.7705 (m) cc_final: 0.7368 (m) REVERT: M 16 HIS cc_start: 0.6904 (m170) cc_final: 0.6597 (m170) REVERT: M 18 ASP cc_start: 0.7016 (t70) cc_final: 0.6681 (t70) REVERT: M 25 GLU cc_start: 0.8290 (tt0) cc_final: 0.7914 (tt0) REVERT: M 100 ARG cc_start: 0.8223 (ptp-170) cc_final: 0.7550 (ptt-90) REVERT: M 155 ARG cc_start: 0.8550 (ptp90) cc_final: 0.8052 (ptt-90) REVERT: M 159 THR cc_start: 0.8247 (m) cc_final: 0.7535 (p) REVERT: M 178 LEU cc_start: 0.8757 (mt) cc_final: 0.8093 (mt) REVERT: M 205 LYS cc_start: 0.8993 (mttm) cc_final: 0.8503 (mttt) REVERT: M 207 GLN cc_start: 0.8011 (mm110) cc_final: 0.7693 (mm110) REVERT: M 209 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7963 (ttp80) REVERT: N 104 MET cc_start: 0.7817 (ptm) cc_final: 0.7382 (ppp) REVERT: N 161 LYS cc_start: 0.8488 (ptpp) cc_final: 0.8257 (ptpp) REVERT: N 183 ILE cc_start: 0.6997 (mt) cc_final: 0.6632 (mt) REVERT: N 198 MET cc_start: 0.7664 (ppp) cc_final: 0.7230 (ppp) REVERT: N 202 ILE cc_start: 0.8137 (mt) cc_final: 0.7841 (mt) REVERT: N 210 ILE cc_start: 0.8428 (pt) cc_final: 0.7790 (pt) REVERT: N 213 GLN cc_start: 0.8700 (mt0) cc_final: 0.8203 (mt0) REVERT: N 233 HIS cc_start: 0.7720 (m-70) cc_final: 0.7453 (m-70) REVERT: N 243 VAL cc_start: 0.8156 (t) cc_final: 0.7454 (m) REVERT: N 253 VAL cc_start: 0.8241 (p) cc_final: 0.7996 (m) REVERT: N 256 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7472 (ttm110) REVERT: N 267 LYS cc_start: 0.8846 (ptpt) cc_final: 0.8468 (pttt) REVERT: N 270 LYS cc_start: 0.7911 (mptt) cc_final: 0.7312 (mmtp) REVERT: O 23 HIS cc_start: 0.6691 (t70) cc_final: 0.6028 (t70) REVERT: O 48 MET cc_start: -0.2077 (ppp) cc_final: -0.2410 (ppp) REVERT: O 115 LEU cc_start: 0.8141 (tp) cc_final: 0.7924 (tp) REVERT: O 152 LEU cc_start: 0.8277 (tp) cc_final: 0.7812 (tp) REVERT: O 203 PHE cc_start: 0.7600 (t80) cc_final: 0.7246 (t80) REVERT: P 62 HIS cc_start: 0.7286 (t70) cc_final: 0.6551 (t70) REVERT: P 85 LEU cc_start: 0.8318 (tp) cc_final: 0.7962 (tp) REVERT: P 115 LEU cc_start: 0.4076 (tp) cc_final: 0.3831 (tp) REVERT: P 168 ILE cc_start: 0.8442 (pt) cc_final: 0.8168 (mt) REVERT: P 199 ASP cc_start: 0.6952 (m-30) cc_final: 0.6588 (m-30) REVERT: P 201 PHE cc_start: 0.6735 (t80) cc_final: 0.6301 (t80) REVERT: P 238 GLN cc_start: 0.5877 (mp10) cc_final: 0.5476 (mp10) outliers start: 0 outliers final: 0 residues processed: 1191 average time/residue: 0.4658 time to fit residues: 863.3397 Evaluate side-chains 1107 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1107 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 0.6980 chunk 358 optimal weight: 0.0270 chunk 326 optimal weight: 4.9990 chunk 348 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 273 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 329 optimal weight: 0.6980 chunk 347 optimal weight: 0.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 HIS G 208 GLN G 211 GLN H 62 HIS H 157 HIS H 204 ASN I 146 ASN J 13 ASN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34119 Z= 0.253 Angle : 0.740 13.228 46515 Z= 0.396 Chirality : 0.050 0.265 5006 Planarity : 0.005 0.074 5714 Dihedral : 14.763 176.829 5007 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.81 % 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: -0.33 (0.13), residues: 3851 helix: 0.96 (0.12), residues: 1877 sheet: -0.54 (0.17), residues: 853 loop : -1.89 (0.16), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP J 106 HIS 0.019 0.002 HIS O 157 PHE 0.047 0.002 PHE E 201 TYR 0.026 0.002 TYR C 87 ARG 0.009 0.001 ARG L 256 *********************** 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 1211 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1211 time to evaluate : 3.478 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 66 ASP cc_start: 0.7959 (t0) cc_final: 0.7694 (t0) REVERT: A 79 VAL cc_start: 0.8210 (t) cc_final: 0.7796 (p) REVERT: A 92 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8489 (mtpp) REVERT: A 104 MET cc_start: 0.8510 (ttm) cc_final: 0.7731 (ttm) REVERT: A 105 LYS cc_start: 0.8997 (mtpp) cc_final: 0.8745 (mtpp) REVERT: A 113 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7693 (mmmm) REVERT: A 116 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6948 (tm-30) REVERT: A 118 ASP cc_start: 0.7867 (p0) cc_final: 0.7609 (p0) REVERT: A 132 MET cc_start: 0.7660 (mmm) cc_final: 0.7389 (mmm) REVERT: A 155 ARG cc_start: 0.8329 (tpt90) cc_final: 0.7358 (tpp-160) REVERT: A 160 LEU cc_start: 0.8539 (tt) cc_final: 0.8300 (tt) REVERT: A 164 LEU cc_start: 0.8416 (mt) cc_final: 0.8147 (mt) REVERT: A 183 ILE cc_start: 0.9163 (tt) cc_final: 0.8848 (pt) REVERT: A 190 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7446 (mtpp) REVERT: A 203 PHE cc_start: 0.8293 (t80) cc_final: 0.7900 (t80) REVERT: A 254 LYS cc_start: 0.8125 (pptt) cc_final: 0.7763 (pptt) REVERT: B 40 CYS cc_start: 0.7514 (t) cc_final: 0.7177 (p) REVERT: B 63 TRP cc_start: 0.8190 (m100) cc_final: 0.6814 (m100) REVERT: B 64 GLN cc_start: 0.6626 (mm110) cc_final: 0.5807 (mm110) REVERT: B 86 ILE cc_start: 0.8789 (pt) cc_final: 0.8454 (mm) REVERT: B 87 TYR cc_start: 0.8007 (t80) cc_final: 0.7427 (t80) REVERT: B 89 GLU cc_start: 0.7612 (tt0) cc_final: 0.6718 (tt0) REVERT: B 92 LYS cc_start: 0.8708 (tppp) cc_final: 0.8489 (tppp) REVERT: B 101 VAL cc_start: 0.8856 (t) cc_final: 0.8503 (t) REVERT: B 102 GLN cc_start: 0.8439 (mp-120) cc_final: 0.7924 (mm-40) REVERT: B 103 THR cc_start: 0.8949 (p) cc_final: 0.8470 (p) REVERT: B 104 MET cc_start: 0.8235 (mmp) cc_final: 0.7919 (mmp) REVERT: B 105 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8650 (mtpp) REVERT: B 116 GLN cc_start: 0.6481 (tm-30) cc_final: 0.5957 (tm-30) REVERT: B 126 GLU cc_start: 0.9202 (pm20) cc_final: 0.8909 (pm20) REVERT: B 129 GLN cc_start: 0.8462 (pt0) cc_final: 0.8103 (pt0) REVERT: B 131 LEU cc_start: 0.8735 (tt) cc_final: 0.8311 (tt) REVERT: B 132 MET cc_start: 0.8459 (mmp) cc_final: 0.7545 (mmp) REVERT: B 139 HIS cc_start: 0.8326 (t70) cc_final: 0.7857 (t70) REVERT: B 198 MET cc_start: 0.7942 (tpt) cc_final: 0.7550 (tpp) REVERT: B 205 LYS cc_start: 0.8404 (tptp) cc_final: 0.8079 (tppp) REVERT: B 207 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7566 (mm-40) REVERT: B 208 GLN cc_start: 0.7836 (pt0) cc_final: 0.7248 (pt0) REVERT: C 7 LEU cc_start: 0.8194 (tt) cc_final: 0.7716 (tt) REVERT: C 15 TRP cc_start: 0.8566 (m100) cc_final: 0.8234 (m100) REVERT: C 28 ILE cc_start: 0.8005 (tp) cc_final: 0.7796 (tp) REVERT: C 30 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7797 (ttt180) REVERT: C 131 LEU cc_start: 0.6658 (mm) cc_final: 0.6457 (mt) REVERT: C 132 MET cc_start: 0.7853 (ppp) cc_final: 0.7415 (ppp) REVERT: C 157 HIS cc_start: 0.7210 (m90) cc_final: 0.6990 (m90) REVERT: C 186 ASN cc_start: 0.6968 (m-40) cc_final: 0.6524 (m110) REVERT: C 198 MET cc_start: 0.7618 (tpt) cc_final: 0.7111 (tpt) REVERT: C 202 ILE cc_start: 0.7721 (mt) cc_final: 0.7149 (mt) REVERT: C 208 GLN cc_start: 0.8606 (mt0) cc_final: 0.8043 (mt0) REVERT: C 209 ARG cc_start: 0.8470 (ptt90) cc_final: 0.8096 (ptt90) REVERT: C 233 HIS cc_start: 0.5556 (p90) cc_final: 0.5249 (p90) REVERT: C 244 LEU cc_start: 0.8288 (mm) cc_final: 0.7702 (mm) REVERT: D 205 LYS cc_start: 0.8478 (mmpt) cc_final: 0.8051 (mmpt) REVERT: D 209 ARG cc_start: 0.8557 (tpm170) cc_final: 0.8242 (mmm160) REVERT: D 218 GLN cc_start: 0.8176 (mm110) cc_final: 0.7854 (mm110) REVERT: D 226 TYR cc_start: 0.6887 (p90) cc_final: 0.6183 (p90) REVERT: D 248 ASP cc_start: 0.7656 (p0) cc_final: 0.7292 (p0) REVERT: D 262 LEU cc_start: 0.8500 (mm) cc_final: 0.8296 (mm) REVERT: D 266 ASN cc_start: 0.8612 (m110) cc_final: 0.8168 (m110) REVERT: E 7 LEU cc_start: 0.8133 (tt) cc_final: 0.7566 (tt) REVERT: E 15 TRP cc_start: 0.7877 (m-10) cc_final: 0.7389 (m-10) REVERT: E 16 HIS cc_start: 0.7220 (m-70) cc_final: 0.6927 (m170) REVERT: E 25 GLU cc_start: 0.8181 (tt0) cc_final: 0.7821 (tt0) REVERT: E 109 MET cc_start: 0.8522 (tmm) cc_final: 0.8283 (tmm) REVERT: E 150 GLN cc_start: 0.7759 (mm110) cc_final: 0.7526 (mm110) REVERT: E 159 THR cc_start: 0.8064 (m) cc_final: 0.7327 (p) REVERT: E 178 LEU cc_start: 0.8827 (mt) cc_final: 0.8200 (mt) REVERT: E 206 GLU cc_start: 0.8046 (pt0) cc_final: 0.7681 (pt0) REVERT: F 65 VAL cc_start: 0.7185 (t) cc_final: 0.6910 (p) REVERT: F 82 ASN cc_start: 0.8103 (m110) cc_final: 0.7842 (m110) REVERT: F 104 MET cc_start: 0.7388 (ptm) cc_final: 0.7052 (ppp) REVERT: F 164 LEU cc_start: 0.8323 (mt) cc_final: 0.7937 (mt) REVERT: F 202 ILE cc_start: 0.8547 (mt) cc_final: 0.8340 (mt) REVERT: F 206 GLU cc_start: 0.8117 (pp20) cc_final: 0.6508 (pp20) REVERT: F 212 GLN cc_start: 0.8345 (pp30) cc_final: 0.8066 (pp30) REVERT: F 230 LYS cc_start: 0.8499 (mmmt) cc_final: 0.7920 (mmmm) REVERT: F 233 HIS cc_start: 0.7696 (m90) cc_final: 0.7472 (m90) REVERT: F 242 GLN cc_start: 0.7170 (tt0) cc_final: 0.6568 (pp30) REVERT: F 243 VAL cc_start: 0.8343 (t) cc_final: 0.7744 (p) REVERT: F 267 LYS cc_start: 0.8829 (ptmt) cc_final: 0.8617 (pttt) REVERT: G 48 MET cc_start: -0.0376 (ppp) cc_final: -0.1310 (ppp) REVERT: G 107 TYR cc_start: 0.7255 (t80) cc_final: 0.6582 (t80) REVERT: G 115 LEU cc_start: 0.8290 (tp) cc_final: 0.8066 (tp) REVERT: G 132 MET cc_start: 0.7636 (tmm) cc_final: 0.6958 (tmm) REVERT: G 152 LEU cc_start: 0.8395 (tp) cc_final: 0.7923 (tp) REVERT: G 157 HIS cc_start: 0.8200 (m90) cc_final: 0.7644 (m90) REVERT: G 168 ILE cc_start: 0.7151 (mt) cc_final: 0.6907 (pt) REVERT: G 175 GLU cc_start: 0.8171 (pm20) cc_final: 0.7594 (pm20) REVERT: G 183 ILE cc_start: 0.7283 (mt) cc_final: 0.7025 (mt) REVERT: G 205 LYS cc_start: 0.8985 (mtmm) cc_final: 0.8698 (mttp) REVERT: G 209 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7763 (ttp80) REVERT: G 210 ILE cc_start: 0.8728 (pt) cc_final: 0.7754 (pt) REVERT: H 62 HIS cc_start: 0.7469 (t70) cc_final: 0.6553 (t70) REVERT: H 85 LEU cc_start: 0.8228 (tp) cc_final: 0.7950 (tp) REVERT: H 104 MET cc_start: 0.8185 (mpp) cc_final: 0.7675 (mpp) REVERT: H 109 MET cc_start: 0.7580 (mtm) cc_final: 0.7092 (ptp) REVERT: H 170 MET cc_start: 0.7837 (mtt) cc_final: 0.7418 (mpp) REVERT: H 199 ASP cc_start: 0.7088 (m-30) cc_final: 0.6692 (m-30) REVERT: H 205 LYS cc_start: 0.7997 (mttt) cc_final: 0.7582 (mptt) REVERT: I 60 ILE cc_start: 0.8583 (mt) cc_final: 0.8111 (mm) REVERT: I 62 HIS cc_start: 0.7787 (t70) cc_final: 0.7548 (t-170) REVERT: I 64 GLN cc_start: 0.6814 (pm20) cc_final: 0.6372 (pm20) REVERT: I 66 ASP cc_start: 0.8167 (t0) cc_final: 0.7778 (t70) REVERT: I 79 VAL cc_start: 0.8020 (t) cc_final: 0.7710 (m) REVERT: I 81 THR cc_start: 0.8768 (p) cc_final: 0.8360 (t) REVERT: I 86 ILE cc_start: 0.8445 (pt) cc_final: 0.8230 (tp) REVERT: I 87 TYR cc_start: 0.8077 (t80) cc_final: 0.6297 (t80) REVERT: I 92 LYS cc_start: 0.9038 (mtmm) cc_final: 0.8412 (mtpp) REVERT: I 97 GLN cc_start: 0.8221 (pm20) cc_final: 0.7423 (pm20) REVERT: I 98 GLU cc_start: 0.7945 (mp0) cc_final: 0.7709 (mp0) REVERT: I 102 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8126 (mm-40) REVERT: I 104 MET cc_start: 0.8332 (ttm) cc_final: 0.7355 (ttm) REVERT: I 105 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8123 (mtmm) REVERT: I 113 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7641 (mmmm) REVERT: I 152 LEU cc_start: 0.7273 (pt) cc_final: 0.6266 (mp) REVERT: I 155 ARG cc_start: 0.8238 (tpt90) cc_final: 0.7289 (tpp-160) REVERT: I 160 LEU cc_start: 0.8562 (tt) cc_final: 0.8131 (tt) REVERT: I 163 THR cc_start: 0.8480 (m) cc_final: 0.8049 (p) REVERT: I 164 LEU cc_start: 0.8692 (mt) cc_final: 0.8395 (mt) REVERT: I 190 LYS cc_start: 0.8351 (mptt) cc_final: 0.8033 (mptt) REVERT: I 201 PHE cc_start: 0.8653 (t80) cc_final: 0.8307 (t80) REVERT: I 203 PHE cc_start: 0.8179 (t80) cc_final: 0.7921 (t80) REVERT: I 204 ASN cc_start: 0.8751 (m-40) cc_final: 0.8476 (m-40) REVERT: I 207 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7349 (tp40) REVERT: J 62 HIS cc_start: 0.6860 (t70) cc_final: 0.6532 (t70) REVERT: J 63 TRP cc_start: 0.7517 (m100) cc_final: 0.6182 (m100) REVERT: J 76 LEU cc_start: 0.8116 (mm) cc_final: 0.7893 (mm) REVERT: J 86 ILE cc_start: 0.8926 (pt) cc_final: 0.8504 (mm) REVERT: J 101 VAL cc_start: 0.8833 (t) cc_final: 0.8553 (t) REVERT: J 102 GLN cc_start: 0.8374 (mp-120) cc_final: 0.8011 (mm-40) REVERT: J 103 THR cc_start: 0.8639 (t) cc_final: 0.8333 (p) REVERT: J 104 MET cc_start: 0.8278 (mmp) cc_final: 0.7932 (mmp) REVERT: J 132 MET cc_start: 0.8495 (mmp) cc_final: 0.7609 (mmp) REVERT: J 139 HIS cc_start: 0.8426 (t70) cc_final: 0.7828 (t-90) REVERT: J 160 LEU cc_start: 0.8694 (tt) cc_final: 0.8363 (tt) REVERT: J 161 LYS cc_start: 0.8752 (ptpt) cc_final: 0.8202 (pttm) REVERT: J 178 LEU cc_start: 0.9197 (mm) cc_final: 0.8978 (mm) REVERT: J 182 LEU cc_start: 0.8150 (mt) cc_final: 0.7908 (mt) REVERT: J 189 ARG cc_start: 0.7519 (ttp-110) cc_final: 0.6860 (mtm110) REVERT: J 201 PHE cc_start: 0.9050 (t80) cc_final: 0.8670 (t80) REVERT: J 204 ASN cc_start: 0.7367 (m110) cc_final: 0.7065 (p0) REVERT: J 205 LYS cc_start: 0.8552 (tptp) cc_final: 0.7865 (tptp) REVERT: J 208 GLN cc_start: 0.7927 (pt0) cc_final: 0.7375 (pt0) REVERT: K 7 LEU cc_start: 0.8132 (tt) cc_final: 0.7865 (tt) REVERT: K 38 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7184 (tm-30) REVERT: K 39 GLN cc_start: 0.7340 (tp40) cc_final: 0.6997 (tp40) REVERT: K 132 MET cc_start: 0.6830 (ppp) cc_final: 0.6413 (ppp) REVERT: K 208 GLN cc_start: 0.8203 (pp30) cc_final: 0.7475 (pp30) REVERT: K 209 ARG cc_start: 0.8369 (ptt90) cc_final: 0.7953 (ptt90) REVERT: K 212 GLN cc_start: 0.7609 (mp10) cc_final: 0.7375 (mp10) REVERT: L 209 ARG cc_start: 0.8045 (mmp-170) cc_final: 0.7738 (mmp-170) REVERT: L 226 TYR cc_start: 0.6795 (p90) cc_final: 0.5971 (p90) REVERT: L 269 VAL cc_start: 0.7734 (m) cc_final: 0.7364 (m) REVERT: M 7 LEU cc_start: 0.8161 (tt) cc_final: 0.6917 (tt) REVERT: M 10 GLU cc_start: 0.7830 (pp20) cc_final: 0.7309 (pp20) REVERT: M 11 GLU cc_start: 0.8012 (pm20) cc_final: 0.7380 (pm20) REVERT: M 15 TRP cc_start: 0.7683 (m-10) cc_final: 0.7303 (m-10) REVERT: M 16 HIS cc_start: 0.6850 (m170) cc_final: 0.5411 (m170) REVERT: M 18 ASP cc_start: 0.7189 (t70) cc_final: 0.6931 (t70) REVERT: M 25 GLU cc_start: 0.8366 (tt0) cc_final: 0.8054 (tt0) REVERT: M 155 ARG cc_start: 0.8564 (ptp90) cc_final: 0.8082 (ptt-90) REVERT: M 159 THR cc_start: 0.8253 (m) cc_final: 0.7489 (p) REVERT: M 178 LEU cc_start: 0.8790 (mt) cc_final: 0.8200 (mt) REVERT: M 205 LYS cc_start: 0.8898 (mttm) cc_final: 0.8556 (mmtt) REVERT: M 207 GLN cc_start: 0.8067 (mm110) cc_final: 0.7825 (mm110) REVERT: N 102 GLN cc_start: 0.8503 (mp10) cc_final: 0.7919 (mp-120) REVERT: N 104 MET cc_start: 0.7723 (ptm) cc_final: 0.7329 (ppp) REVERT: N 105 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8931 (mttt) REVERT: N 161 LYS cc_start: 0.8576 (ptpp) cc_final: 0.8215 (ptpp) REVERT: N 183 ILE cc_start: 0.7008 (mt) cc_final: 0.6636 (mt) REVERT: N 197 PRO cc_start: 0.7810 (Cg_exo) cc_final: 0.7571 (Cg_endo) REVERT: N 198 MET cc_start: 0.7697 (ppp) cc_final: 0.6969 (ppp) REVERT: N 199 ASP cc_start: 0.7971 (m-30) cc_final: 0.7349 (m-30) REVERT: N 202 ILE cc_start: 0.8269 (mt) cc_final: 0.7731 (mt) REVERT: N 204 ASN cc_start: 0.8214 (p0) cc_final: 0.7683 (p0) REVERT: N 206 GLU cc_start: 0.7806 (pp20) cc_final: 0.6462 (pp20) REVERT: N 210 ILE cc_start: 0.8457 (pt) cc_final: 0.8029 (pt) REVERT: N 213 GLN cc_start: 0.8787 (mt0) cc_final: 0.8413 (mt0) REVERT: N 221 ILE cc_start: 0.8852 (mp) cc_final: 0.8563 (mp) REVERT: N 224 CYS cc_start: 0.7692 (p) cc_final: 0.7235 (p) REVERT: N 233 HIS cc_start: 0.7730 (m-70) cc_final: 0.7439 (m-70) REVERT: N 243 VAL cc_start: 0.8218 (t) cc_final: 0.7666 (p) REVERT: N 253 VAL cc_start: 0.8425 (p) cc_final: 0.8169 (m) REVERT: N 256 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7483 (ttm110) REVERT: N 262 LEU cc_start: 0.7959 (mt) cc_final: 0.7635 (mt) REVERT: N 267 LYS cc_start: 0.8993 (ptpt) cc_final: 0.8484 (pttt) REVERT: N 270 LYS cc_start: 0.7924 (mptt) cc_final: 0.7251 (mmtp) REVERT: O 48 MET cc_start: -0.2113 (ppp) cc_final: -0.2407 (ppp) REVERT: O 115 LEU cc_start: 0.7943 (tp) cc_final: 0.7614 (tp) REVERT: O 152 LEU cc_start: 0.8311 (tp) cc_final: 0.7827 (tp) REVERT: O 156 THR cc_start: 0.8721 (m) cc_final: 0.8387 (m) REVERT: O 161 LYS cc_start: 0.8404 (ptpp) cc_final: 0.8062 (pttt) REVERT: O 203 PHE cc_start: 0.7594 (t80) cc_final: 0.7218 (t80) REVERT: P 62 HIS cc_start: 0.7554 (t70) cc_final: 0.6708 (t70) REVERT: P 85 LEU cc_start: 0.8378 (tp) cc_final: 0.7977 (tp) REVERT: P 100 ARG cc_start: 0.5606 (mtt90) cc_final: 0.4923 (mtm-85) REVERT: P 115 LEU cc_start: 0.4612 (tp) cc_final: 0.4211 (tp) REVERT: P 168 ILE cc_start: 0.8420 (pt) cc_final: 0.8190 (mt) REVERT: P 199 ASP cc_start: 0.6941 (m-30) cc_final: 0.6581 (m-30) REVERT: P 201 PHE cc_start: 0.6792 (t80) cc_final: 0.6502 (t80) REVERT: P 202 ILE cc_start: 0.8810 (mt) cc_final: 0.8418 (mt) outliers start: 0 outliers final: 0 residues processed: 1211 average time/residue: 0.4679 time to fit residues: 883.9398 Evaluate side-chains 1118 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1118 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 0.6980 chunk 368 optimal weight: 0.0870 chunk 224 optimal weight: 0.4980 chunk 174 optimal weight: 1.9990 chunk 256 optimal weight: 0.7980 chunk 386 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 307 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 188 optimal weight: 0.0770 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN B 23 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 157 HIS ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 HIS ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34119 Z= 0.218 Angle : 0.759 12.905 46515 Z= 0.403 Chirality : 0.052 0.585 5006 Planarity : 0.005 0.097 5714 Dihedral : 14.743 176.227 5007 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.86 % Favored : 94.99 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % 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: 0.87 (0.12), residues: 1883 sheet: -0.56 (0.18), residues: 825 loop : -1.84 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP O 106 HIS 0.036 0.002 HIS M 16 PHE 0.074 0.002 PHE H 201 TYR 0.042 0.002 TYR F 134 ARG 0.017 0.001 ARG N 209 ********************** 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 1197 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1196 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7623 (pp20) cc_final: 0.7368 (pp20) REVERT: A 66 ASP cc_start: 0.7875 (t0) cc_final: 0.7459 (t70) REVERT: A 79 VAL cc_start: 0.8128 (t) cc_final: 0.7593 (p) REVERT: A 92 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8496 (mtpp) REVERT: A 97 GLN cc_start: 0.7498 (pm20) cc_final: 0.7055 (pm20) REVERT: A 98 GLU cc_start: 0.7800 (mp0) cc_final: 0.7537 (mp0) REVERT: A 104 MET cc_start: 0.8594 (ttm) cc_final: 0.7525 (ttm) REVERT: A 105 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8672 (mtpp) REVERT: A 113 LYS cc_start: 0.7934 (mmmm) cc_final: 0.7695 (mmmm) REVERT: A 132 MET cc_start: 0.7579 (mmm) cc_final: 0.7222 (mmm) REVERT: A 135 LEU cc_start: 0.9044 (mt) cc_final: 0.8766 (mt) REVERT: A 152 LEU cc_start: 0.7302 (pt) cc_final: 0.6288 (mp) REVERT: A 155 ARG cc_start: 0.8297 (tpt90) cc_final: 0.7306 (tpp-160) REVERT: A 160 LEU cc_start: 0.8506 (tt) cc_final: 0.8258 (tt) REVERT: A 164 LEU cc_start: 0.8398 (mt) cc_final: 0.8156 (mt) REVERT: A 190 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7566 (mtpt) REVERT: A 203 PHE cc_start: 0.8224 (t80) cc_final: 0.7838 (t80) REVERT: A 254 LYS cc_start: 0.8079 (pptt) cc_final: 0.7757 (pptt) REVERT: B 40 CYS cc_start: 0.7160 (t) cc_final: 0.6902 (p) REVERT: B 63 TRP cc_start: 0.8201 (m100) cc_final: 0.6518 (m100) REVERT: B 64 GLN cc_start: 0.6733 (mm110) cc_final: 0.5818 (mm110) REVERT: B 86 ILE cc_start: 0.8804 (pt) cc_final: 0.8474 (mm) REVERT: B 87 TYR cc_start: 0.7844 (t80) cc_final: 0.7592 (t80) REVERT: B 89 GLU cc_start: 0.7570 (tt0) cc_final: 0.6886 (tt0) REVERT: B 98 GLU cc_start: 0.8181 (pm20) cc_final: 0.7838 (pm20) REVERT: B 101 VAL cc_start: 0.8855 (t) cc_final: 0.8443 (t) REVERT: B 102 GLN cc_start: 0.8292 (mp-120) cc_final: 0.7720 (mm-40) REVERT: B 103 THR cc_start: 0.8921 (p) cc_final: 0.8425 (p) REVERT: B 104 MET cc_start: 0.8249 (mmp) cc_final: 0.7851 (mmp) REVERT: B 116 GLN cc_start: 0.6591 (tm-30) cc_final: 0.6018 (tm-30) REVERT: B 129 GLN cc_start: 0.8429 (pt0) cc_final: 0.8065 (pt0) REVERT: B 131 LEU cc_start: 0.8647 (tt) cc_final: 0.8193 (tt) REVERT: B 132 MET cc_start: 0.8407 (mmp) cc_final: 0.7520 (mmp) REVERT: B 139 HIS cc_start: 0.8265 (t70) cc_final: 0.7867 (t70) REVERT: B 178 LEU cc_start: 0.9023 (mm) cc_final: 0.8788 (mm) REVERT: B 198 MET cc_start: 0.7979 (tpt) cc_final: 0.7557 (tpp) REVERT: B 204 ASN cc_start: 0.7225 (p0) cc_final: 0.6733 (p0) REVERT: B 205 LYS cc_start: 0.8410 (tptp) cc_final: 0.7999 (tppp) REVERT: B 207 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7483 (mm-40) REVERT: B 208 GLN cc_start: 0.7723 (pt0) cc_final: 0.7199 (pt0) REVERT: C 7 LEU cc_start: 0.8196 (tt) cc_final: 0.7693 (tt) REVERT: C 28 ILE cc_start: 0.7907 (tp) cc_final: 0.7630 (tp) REVERT: C 30 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7563 (ttt180) REVERT: C 132 MET cc_start: 0.7882 (ppp) cc_final: 0.7434 (ppp) REVERT: C 157 HIS cc_start: 0.7104 (m90) cc_final: 0.6717 (m-70) REVERT: C 186 ASN cc_start: 0.6674 (m-40) cc_final: 0.6421 (m110) REVERT: C 198 MET cc_start: 0.7581 (tpt) cc_final: 0.7098 (tpt) REVERT: C 202 ILE cc_start: 0.7667 (mt) cc_final: 0.6988 (mt) REVERT: C 204 ASN cc_start: 0.8186 (p0) cc_final: 0.7908 (p0) REVERT: C 208 GLN cc_start: 0.8358 (mt0) cc_final: 0.7973 (mt0) REVERT: C 209 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8139 (ptt90) REVERT: C 233 HIS cc_start: 0.5463 (p90) cc_final: 0.5158 (p90) REVERT: D 205 LYS cc_start: 0.8345 (mmpt) cc_final: 0.8033 (mmpt) REVERT: D 209 ARG cc_start: 0.8547 (tpm170) cc_final: 0.8305 (mmm160) REVERT: D 218 GLN cc_start: 0.8144 (mm110) cc_final: 0.7812 (mm110) REVERT: D 226 TYR cc_start: 0.6894 (p90) cc_final: 0.6253 (p90) REVERT: D 248 ASP cc_start: 0.7647 (p0) cc_final: 0.7261 (p0) REVERT: D 262 LEU cc_start: 0.8491 (mm) cc_final: 0.8264 (mm) REVERT: D 266 ASN cc_start: 0.8491 (m110) cc_final: 0.8069 (m110) REVERT: E 7 LEU cc_start: 0.8222 (tt) cc_final: 0.6930 (tt) REVERT: E 10 GLU cc_start: 0.7971 (pp20) cc_final: 0.7346 (pp20) REVERT: E 11 GLU cc_start: 0.7798 (pm20) cc_final: 0.7210 (pm20) REVERT: E 18 ASP cc_start: 0.7204 (t70) cc_final: 0.6990 (t70) REVERT: E 25 GLU cc_start: 0.8107 (tt0) cc_final: 0.7800 (tt0) REVERT: E 109 MET cc_start: 0.8631 (tmm) cc_final: 0.7958 (tmm) REVERT: E 150 GLN cc_start: 0.7867 (mm110) cc_final: 0.7225 (mm110) REVERT: E 158 GLN cc_start: 0.6856 (tm-30) cc_final: 0.6593 (tm-30) REVERT: E 159 THR cc_start: 0.8028 (m) cc_final: 0.7191 (p) REVERT: E 178 LEU cc_start: 0.8769 (mt) cc_final: 0.8308 (mt) REVERT: E 205 LYS cc_start: 0.8458 (mtmm) cc_final: 0.7363 (ptpp) REVERT: E 206 GLU cc_start: 0.7993 (pt0) cc_final: 0.7518 (pt0) REVERT: E 220 LYS cc_start: 0.8260 (pptt) cc_final: 0.7739 (tmmt) REVERT: F 65 VAL cc_start: 0.7151 (t) cc_final: 0.6851 (p) REVERT: F 104 MET cc_start: 0.7313 (ptm) cc_final: 0.6957 (ppp) REVERT: F 199 ASP cc_start: 0.7669 (m-30) cc_final: 0.7253 (m-30) REVERT: F 202 ILE cc_start: 0.8342 (mt) cc_final: 0.7465 (mt) REVERT: F 205 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8323 (mtmt) REVERT: F 230 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7897 (mmmm) REVERT: F 233 HIS cc_start: 0.7652 (m90) cc_final: 0.7451 (m90) REVERT: F 243 VAL cc_start: 0.8262 (t) cc_final: 0.8018 (p) REVERT: G 48 MET cc_start: -0.0364 (ppp) cc_final: -0.1290 (ppp) REVERT: G 107 TYR cc_start: 0.7170 (t80) cc_final: 0.6512 (t80) REVERT: G 115 LEU cc_start: 0.8235 (tp) cc_final: 0.7944 (tp) REVERT: G 132 MET cc_start: 0.7589 (tmm) cc_final: 0.7335 (tmm) REVERT: G 152 LEU cc_start: 0.8386 (tp) cc_final: 0.7956 (tp) REVERT: G 157 HIS cc_start: 0.8115 (m90) cc_final: 0.7630 (m90) REVERT: G 168 ILE cc_start: 0.7085 (mt) cc_final: 0.6873 (pt) REVERT: G 175 GLU cc_start: 0.7985 (pm20) cc_final: 0.7675 (pm20) REVERT: G 183 ILE cc_start: 0.7252 (mt) cc_final: 0.7013 (mt) REVERT: G 201 PHE cc_start: 0.7844 (t80) cc_final: 0.7370 (t80) REVERT: G 202 ILE cc_start: 0.8595 (mt) cc_final: 0.8087 (mt) REVERT: G 205 LYS cc_start: 0.8866 (mtmm) cc_final: 0.7779 (mtmm) REVERT: G 210 ILE cc_start: 0.8428 (pt) cc_final: 0.8204 (pt) REVERT: H 62 HIS cc_start: 0.7291 (t70) cc_final: 0.6379 (t70) REVERT: H 85 LEU cc_start: 0.8174 (tp) cc_final: 0.7837 (tp) REVERT: H 109 MET cc_start: 0.7428 (mtm) cc_final: 0.7068 (ptp) REVERT: H 170 MET cc_start: 0.7698 (mtt) cc_final: 0.7227 (mpp) REVERT: H 199 ASP cc_start: 0.6950 (m-30) cc_final: 0.6545 (m-30) REVERT: H 201 PHE cc_start: 0.6880 (t80) cc_final: 0.6489 (t80) REVERT: H 238 GLN cc_start: 0.6456 (mp10) cc_final: 0.6255 (mp10) REVERT: I 60 ILE cc_start: 0.8562 (mt) cc_final: 0.8088 (mm) REVERT: I 66 ASP cc_start: 0.8084 (t0) cc_final: 0.7789 (t0) REVERT: I 79 VAL cc_start: 0.7932 (t) cc_final: 0.7461 (p) REVERT: I 81 THR cc_start: 0.8754 (p) cc_final: 0.8439 (t) REVERT: I 82 ASN cc_start: 0.8715 (t0) cc_final: 0.8506 (t0) REVERT: I 86 ILE cc_start: 0.8412 (pt) cc_final: 0.8073 (mm) REVERT: I 92 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8495 (mtpp) REVERT: I 97 GLN cc_start: 0.8169 (pm20) cc_final: 0.7711 (pm20) REVERT: I 100 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7634 (mtm110) REVERT: I 102 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8591 (mm-40) REVERT: I 104 MET cc_start: 0.8281 (ttm) cc_final: 0.7336 (ttm) REVERT: I 113 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7631 (mmmm) REVERT: I 118 ASP cc_start: 0.7784 (p0) cc_final: 0.7557 (p0) REVERT: I 152 LEU cc_start: 0.7151 (pt) cc_final: 0.5243 (tp) REVERT: I 155 ARG cc_start: 0.8236 (tpt90) cc_final: 0.7246 (mmm160) REVERT: I 158 GLN cc_start: 0.8927 (tt0) cc_final: 0.8134 (tt0) REVERT: I 160 LEU cc_start: 0.8505 (tt) cc_final: 0.8055 (tt) REVERT: I 163 THR cc_start: 0.8036 (m) cc_final: 0.7525 (p) REVERT: I 164 LEU cc_start: 0.8560 (mt) cc_final: 0.8331 (mt) REVERT: I 190 LYS cc_start: 0.8397 (mptt) cc_final: 0.8139 (mptt) REVERT: I 201 PHE cc_start: 0.8701 (t80) cc_final: 0.8443 (t80) REVERT: I 203 PHE cc_start: 0.8121 (t80) cc_final: 0.7622 (t80) REVERT: I 204 ASN cc_start: 0.8665 (m-40) cc_final: 0.8378 (m-40) REVERT: I 237 TRP cc_start: 0.6051 (m100) cc_final: 0.5758 (m100) REVERT: J 63 TRP cc_start: 0.7610 (m100) cc_final: 0.5846 (m100) REVERT: J 76 LEU cc_start: 0.8090 (mm) cc_final: 0.7848 (mm) REVERT: J 86 ILE cc_start: 0.8880 (pt) cc_final: 0.8413 (mm) REVERT: J 92 LYS cc_start: 0.8835 (tptm) cc_final: 0.8580 (tppt) REVERT: J 103 THR cc_start: 0.8551 (t) cc_final: 0.8060 (p) REVERT: J 104 MET cc_start: 0.8227 (mmp) cc_final: 0.7782 (mmp) REVERT: J 105 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8797 (mtpp) REVERT: J 131 LEU cc_start: 0.8580 (tt) cc_final: 0.8287 (tt) REVERT: J 132 MET cc_start: 0.8431 (mmp) cc_final: 0.7587 (mmp) REVERT: J 160 LEU cc_start: 0.8625 (tt) cc_final: 0.8269 (tt) REVERT: J 182 LEU cc_start: 0.8145 (mt) cc_final: 0.7938 (mt) REVERT: J 189 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.6831 (mtm110) REVERT: J 201 PHE cc_start: 0.8953 (t80) cc_final: 0.8640 (t80) REVERT: J 205 LYS cc_start: 0.8583 (tptp) cc_final: 0.7928 (tptp) REVERT: J 208 GLN cc_start: 0.7823 (pt0) cc_final: 0.7289 (pt0) REVERT: K 15 TRP cc_start: 0.8541 (m100) cc_final: 0.7959 (m-90) REVERT: K 39 GLN cc_start: 0.7326 (tp40) cc_final: 0.6776 (tp40) REVERT: K 132 MET cc_start: 0.7009 (ppp) cc_final: 0.6550 (ppp) REVERT: K 209 ARG cc_start: 0.8315 (ptt90) cc_final: 0.8109 (ptt90) REVERT: L 226 TYR cc_start: 0.6726 (p90) cc_final: 0.5960 (p90) REVERT: L 269 VAL cc_start: 0.7630 (m) cc_final: 0.7285 (m) REVERT: M 7 LEU cc_start: 0.8156 (tt) cc_final: 0.6993 (tt) REVERT: M 10 GLU cc_start: 0.7846 (pp20) cc_final: 0.7271 (pp20) REVERT: M 11 GLU cc_start: 0.8023 (pm20) cc_final: 0.7401 (pm20) REVERT: M 16 HIS cc_start: 0.5108 (m170) cc_final: 0.4887 (m-70) REVERT: M 25 GLU cc_start: 0.8302 (tt0) cc_final: 0.8064 (tt0) REVERT: M 100 ARG cc_start: 0.8087 (ptp-170) cc_final: 0.7881 (ptp-170) REVERT: M 154 GLU cc_start: 0.8335 (mp0) cc_final: 0.8101 (mp0) REVERT: M 155 ARG cc_start: 0.8479 (ptp90) cc_final: 0.8076 (ptp90) REVERT: M 159 THR cc_start: 0.8170 (m) cc_final: 0.7476 (p) REVERT: M 178 LEU cc_start: 0.8751 (mt) cc_final: 0.8342 (mt) REVERT: M 205 LYS cc_start: 0.8864 (mttm) cc_final: 0.8239 (mttt) REVERT: M 207 GLN cc_start: 0.7996 (mm110) cc_final: 0.7742 (mm110) REVERT: M 209 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7955 (ttp80) REVERT: N 10 GLU cc_start: 0.7023 (pp20) cc_final: 0.6711 (pp20) REVERT: N 102 GLN cc_start: 0.8480 (mp10) cc_final: 0.7882 (mp10) REVERT: N 104 MET cc_start: 0.7663 (ptm) cc_final: 0.7210 (ppp) REVERT: N 183 ILE cc_start: 0.7042 (mt) cc_final: 0.6656 (mt) REVERT: N 184 THR cc_start: 0.7866 (p) cc_final: 0.7615 (p) REVERT: N 198 MET cc_start: 0.7901 (ppp) cc_final: 0.7170 (ppp) REVERT: N 199 ASP cc_start: 0.7916 (m-30) cc_final: 0.7553 (m-30) REVERT: N 202 ILE cc_start: 0.8158 (mt) cc_final: 0.7604 (mt) REVERT: N 210 ILE cc_start: 0.8286 (pt) cc_final: 0.8038 (pt) REVERT: N 213 GLN cc_start: 0.8715 (mt0) cc_final: 0.8253 (mt0) REVERT: N 224 CYS cc_start: 0.7678 (p) cc_final: 0.7220 (p) REVERT: N 233 HIS cc_start: 0.7617 (m-70) cc_final: 0.7378 (m-70) REVERT: N 253 VAL cc_start: 0.8370 (p) cc_final: 0.8167 (m) REVERT: N 256 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7454 (ttm110) REVERT: N 262 LEU cc_start: 0.7891 (mt) cc_final: 0.7534 (mt) REVERT: N 267 LYS cc_start: 0.8963 (ptpt) cc_final: 0.8596 (pttt) REVERT: O 23 HIS cc_start: 0.6651 (t70) cc_final: 0.5992 (t70) REVERT: O 48 MET cc_start: -0.2101 (ppp) cc_final: -0.2403 (ppp) REVERT: O 85 LEU cc_start: 0.7373 (tp) cc_final: 0.6890 (tp) REVERT: O 115 LEU cc_start: 0.7980 (tp) cc_final: 0.7755 (tp) REVERT: O 152 LEU cc_start: 0.8424 (tp) cc_final: 0.7950 (tp) REVERT: O 161 LYS cc_start: 0.8296 (ptpp) cc_final: 0.8093 (pttt) REVERT: O 201 PHE cc_start: 0.7934 (t80) cc_final: 0.6951 (t80) REVERT: P 62 HIS cc_start: 0.7474 (t70) cc_final: 0.6675 (t70) REVERT: P 85 LEU cc_start: 0.8373 (tp) cc_final: 0.7927 (tp) REVERT: P 100 ARG cc_start: 0.5580 (mtt90) cc_final: 0.5000 (mtm-85) REVERT: P 115 LEU cc_start: 0.4458 (tp) cc_final: 0.4155 (tp) REVERT: P 199 ASP cc_start: 0.6765 (m-30) cc_final: 0.6315 (m-30) REVERT: P 201 PHE cc_start: 0.6872 (t80) cc_final: 0.6332 (t80) outliers start: 1 outliers final: 1 residues processed: 1196 average time/residue: 0.4731 time to fit residues: 880.5370 Evaluate side-chains 1106 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1105 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 1.9990 chunk 327 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 283 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 308 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 316 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN G 208 GLN H 157 HIS H 242 GLN ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 ASN ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS P 207 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.192812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.146693 restraints weight = 71563.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.152297 restraints weight = 44053.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.156184 restraints weight = 30525.604| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.6085 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= 0.224 Angle : 0.773 12.626 46515 Z= 0.412 Chirality : 0.052 0.801 5006 Planarity : 0.005 0.073 5714 Dihedral : 14.741 176.685 5007 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 0.03 % Allowed : 0.56 % Favored : 99.41 % Cbeta Deviations : 0.03 % 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: -0.45 (0.13), residues: 3851 helix: 0.81 (0.12), residues: 1876 sheet: -0.62 (0.18), residues: 840 loop : -1.81 (0.16), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP B 106 HIS 0.023 0.002 HIS M 16 PHE 0.057 0.002 PHE H 201 TYR 0.027 0.002 TYR B 70 ARG 0.017 0.001 ARG F 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12306.18 seconds wall clock time: 219 minutes 13.22 seconds (13153.22 seconds total)