Starting phenix.real_space_refine on Sat Jul 4 15:08:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o0l_49992/07_2026/9o0l_49992.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o0l_49992/07_2026/9o0l_49992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o0l_49992/07_2026/9o0l_49992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o0l_49992/07_2026/9o0l_49992.map" model { file = "/net/cci-nas-00/data/ceres_data/9o0l_49992/07_2026/9o0l_49992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o0l_49992/07_2026/9o0l_49992.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 1.117 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 Mn 16 7.51 5 S 126 5.16 5 C 13293 2.51 5 N 3620 2.21 5 O 3983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21038 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1136 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 133, 1126 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 132} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 133, 1126 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 132} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1122 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1110 Classifications: {'peptide': 131} Link IDs: {'TRANS': 130} Chain: "D" Number of atoms: 2368 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 292, 2359 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 280} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 292, 2359 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 280} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 2406 Chain: "E" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "F" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "I" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "J" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 154 " occ=0.35 ... (18 atoms not shown) pdb=" NE2BHIS A 154 " occ=0.65 residue: pdb=" N AGLU D 9 " occ=0.32 ... (16 atoms not shown) pdb=" OE2BGLU D 9 " occ=0.68 Time building chain proxies: 5.05, per 1000 atoms: 0.24 Number of scatterers: 21038 At special positions: 0 Unit cell: (119.184, 116.701, 216.021, 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) Mn 16 24.99 S 126 16.00 O 3983 8.00 N 3620 7.00 C 13293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 926.9 milliseconds 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4838 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 26 sheets defined 47.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 91 through 223 removed outlier: 3.901A pdb=" N ARG A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 222 removed outlier: 3.569A pdb=" N GLN B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 200 " --> pdb=" O ARG B 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 20 Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.730A pdb=" N LYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 Processing helix chain 'D' and resid 92 through 107 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.552A pdb=" N THR D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 Processing helix chain 'D' and resid 140 through 151 removed outlier: 3.902A pdb=" N LYS D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 181 removed outlier: 4.125A pdb=" N ILE D 180 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 181' Processing helix chain 'D' and resid 193 through 199 Processing helix chain 'D' and resid 221 through 233 removed outlier: 3.514A pdb=" N SER D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'E' and resid 5 through 18 Processing helix chain 'E' and resid 24 through 42 removed outlier: 4.545A pdb=" N GLU E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 73 Processing helix chain 'E' and resid 92 through 107 removed outlier: 3.624A pdb=" N THR E 96 " --> pdb=" O TYR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.832A pdb=" N GLY E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 138 Processing helix chain 'E' and resid 140 through 150 Processing helix chain 'E' and resid 176 through 183 removed outlier: 4.218A pdb=" N ILE E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 Processing helix chain 'E' and resid 221 through 233 removed outlier: 3.710A pdb=" N SER E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'F' and resid 5 through 18 Processing helix chain 'F' and resid 24 through 41 removed outlier: 4.698A pdb=" N GLU F 37 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 73 Processing helix chain 'F' and resid 93 through 107 Processing helix chain 'F' and resid 121 through 127 removed outlier: 3.685A pdb=" N GLN F 125 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 137 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 176 through 181 removed outlier: 3.999A pdb=" N ILE F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 199 removed outlier: 3.855A pdb=" N LEU F 199 " --> pdb=" O CYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 232 Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 24 through 41 removed outlier: 4.704A pdb=" N GLU G 37 " --> pdb=" O GLU G 33 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 73 Processing helix chain 'G' and resid 93 through 107 Processing helix chain 'G' and resid 120 through 125 removed outlier: 3.875A pdb=" N THR G 124 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 120 through 125' Processing helix chain 'G' and resid 128 through 138 Processing helix chain 'G' and resid 140 through 151 Processing helix chain 'G' and resid 176 through 181 removed outlier: 4.008A pdb=" N ILE G 180 " --> pdb=" O THR G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 200 removed outlier: 3.540A pdb=" N LEU G 199 " --> pdb=" O MET G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 233 Processing helix chain 'G' and resid 264 through 268 Processing helix chain 'I' and resid 5 through 19 removed outlier: 3.531A pdb=" N GLU I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 40 removed outlier: 3.995A pdb=" N GLU I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 73 Processing helix chain 'I' and resid 92 through 107 removed outlier: 3.808A pdb=" N THR I 96 " --> pdb=" O TYR I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 127 Processing helix chain 'I' and resid 128 through 138 Processing helix chain 'I' and resid 140 through 151 removed outlier: 3.521A pdb=" N LYS I 144 " --> pdb=" O ALA I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 181 Processing helix chain 'I' and resid 193 through 198 Processing helix chain 'I' and resid 221 through 233 removed outlier: 3.651A pdb=" N SER I 225 " --> pdb=" O GLY I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 268 Processing helix chain 'J' and resid 5 through 19 Processing helix chain 'J' and resid 24 through 41 removed outlier: 4.123A pdb=" N GLU J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 73 Processing helix chain 'J' and resid 92 through 107 removed outlier: 3.717A pdb=" N THR J 96 " --> pdb=" O TYR J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 127 removed outlier: 3.556A pdb=" N THR J 124 " --> pdb=" O SER J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 138 Processing helix chain 'J' and resid 141 through 151 Processing helix chain 'J' and resid 176 through 182 removed outlier: 3.551A pdb=" N ILE J 180 " --> pdb=" O THR J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 200 removed outlier: 3.768A pdb=" N LEU J 198 " --> pdb=" O PRO J 194 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 199 " --> pdb=" O MET J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 233 removed outlier: 3.522A pdb=" N SER J 225 " --> pdb=" O GLY J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 268 removed outlier: 3.699A pdb=" N ARG J 268 " --> pdb=" O TYR J 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 19 removed outlier: 3.570A pdb=" N GLU K 19 " --> pdb=" O GLU K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 42 removed outlier: 4.714A pdb=" N GLU K 37 " --> pdb=" O GLU K 33 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 73 Processing helix chain 'K' and resid 92 through 107 Processing helix chain 'K' and resid 122 through 128 removed outlier: 3.710A pdb=" N VAL K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY K 128 " --> pdb=" O THR K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 138 Processing helix chain 'K' and resid 141 through 151 removed outlier: 3.567A pdb=" N TYR K 145 " --> pdb=" O ASN K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 181 removed outlier: 3.739A pdb=" N ILE K 180 " --> pdb=" O THR K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 200 removed outlier: 3.656A pdb=" N LEU K 199 " --> pdb=" O MET K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 233 Processing helix chain 'K' and resid 264 through 268 Processing helix chain 'L' and resid 5 through 19 Processing helix chain 'L' and resid 24 through 41 removed outlier: 4.240A pdb=" N GLU L 37 " --> pdb=" O GLU L 33 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 73 Processing helix chain 'L' and resid 92 through 107 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'L' and resid 140 through 151 removed outlier: 3.512A pdb=" N LYS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 181 removed outlier: 3.587A pdb=" N ILE L 180 " --> pdb=" O THR L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 198 Processing helix chain 'L' and resid 221 through 233 removed outlier: 3.620A pdb=" N SER L 225 " --> pdb=" O GLY L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'D' and resid 45 through 48 removed outlier: 3.616A pdb=" N GLN D 46 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE D 164 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL D 237 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE D 259 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG D 239 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 111 through 113 removed outlier: 6.827A pdb=" N TYR D 80 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 202 through 203 removed outlier: 3.613A pdb=" N PHE D 220 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 48 removed outlier: 3.932A pdb=" N GLN E 46 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE E 164 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.794A pdb=" N THR E 53 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR E 80 " --> pdb=" O THR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 210 through 211 removed outlier: 3.550A pdb=" N THR E 219 " --> pdb=" O GLY E 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 273 through 275 Processing sheet with id=AA8, first strand: chain 'F' and resid 46 through 48 removed outlier: 6.243A pdb=" N GLN F 46 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE F 164 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 111 through 113 removed outlier: 6.386A pdb=" N TYR F 80 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR F 53 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 45 through 48 removed outlier: 3.989A pdb=" N GLN G 46 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE G 164 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 111 through 113 removed outlier: 3.582A pdb=" N THR G 112 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR G 53 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.933A pdb=" N ASP G 202 " --> pdb=" O PHE G 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 47 through 48 removed outlier: 6.082A pdb=" N PHE I 164 " --> pdb=" O SER I 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 111 through 113 removed outlier: 3.679A pdb=" N THR I 112 " --> pdb=" O TYR I 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 209 through 211 Processing sheet with id=AB7, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.281A pdb=" N GLN J 46 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE J 164 " --> pdb=" O SER J 238 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 111 through 113 removed outlier: 6.462A pdb=" N THR J 53 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 202 through 203 removed outlier: 3.768A pdb=" N ASP J 202 " --> pdb=" O TYR J 218 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE J 220 " --> pdb=" O ASP J 202 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 219 " --> pdb=" O GLY J 210 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 45 through 48 removed outlier: 5.988A pdb=" N GLN K 46 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE K 164 " --> pdb=" O SER K 238 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 80 through 81 removed outlier: 7.416A pdb=" N TYR K 80 " --> pdb=" O THR K 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.763A pdb=" N ASP K 202 " --> pdb=" O PHE K 220 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 273 through 277 Processing sheet with id=AC5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.165A pdb=" N GLN L 46 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 111 through 113 removed outlier: 6.352A pdb=" N THR L 53 " --> pdb=" O LEU L 81 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 202 through 203 removed outlier: 3.876A pdb=" N ASP L 202 " --> pdb=" O TYR L 218 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE L 220 " --> pdb=" O ASP L 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 237 through 239 1004 hydrogen bonds defined for protein. 2831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3600 1.30 - 1.43: 5735 1.43 - 1.56: 11974 1.56 - 1.70: 16 1.70 - 1.83: 172 Bond restraints: 21497 Sorted by residual: bond pdb=" CA TYR D 86 " pdb=" C TYR D 86 " ideal model delta sigma weight residual 1.524 1.427 0.097 1.29e-02 6.01e+03 5.71e+01 bond pdb=" C VAL D 87 " pdb=" O VAL D 87 " ideal model delta sigma weight residual 1.236 1.165 0.072 1.19e-02 7.06e+03 3.62e+01 bond pdb=" CG PRO F 213 " pdb=" CD PRO F 213 " ideal model delta sigma weight residual 1.503 1.337 0.166 3.40e-02 8.65e+02 2.38e+01 bond pdb=" C VAL D 87 " pdb=" N ASP D 88 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.23e-02 6.61e+03 1.86e+01 bond pdb=" N PRO F 213 " pdb=" CD PRO F 213 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.57e+01 ... (remaining 21492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 28842 4.74 - 9.49: 223 9.49 - 14.23: 36 14.23 - 18.98: 5 18.98 - 23.72: 2 Bond angle restraints: 29108 Sorted by residual: angle pdb=" CA PRO F 213 " pdb=" N PRO F 213 " pdb=" CD PRO F 213 " ideal model delta sigma weight residual 112.00 94.99 17.01 1.40e+00 5.10e-01 1.48e+02 angle pdb=" CA PRO J 194 " pdb=" N PRO J 194 " pdb=" CD PRO J 194 " ideal model delta sigma weight residual 112.00 95.95 16.05 1.40e+00 5.10e-01 1.31e+02 angle pdb=" CA PRO G 291 " pdb=" N PRO G 291 " pdb=" CD PRO G 291 " ideal model delta sigma weight residual 112.00 99.71 12.29 1.40e+00 5.10e-01 7.70e+01 angle pdb=" CA PRO G 213 " pdb=" N PRO G 213 " pdb=" CD PRO G 213 " ideal model delta sigma weight residual 112.00 99.80 12.20 1.40e+00 5.10e-01 7.60e+01 angle pdb=" N PRO F 213 " pdb=" CD PRO F 213 " pdb=" CG PRO F 213 " ideal model delta sigma weight residual 103.20 92.20 11.00 1.50e+00 4.44e-01 5.37e+01 ... (remaining 29103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 10820 17.87 - 35.75: 1533 35.75 - 53.62: 373 53.62 - 71.49: 45 71.49 - 89.37: 21 Dihedral angle restraints: 12792 sinusoidal: 5245 harmonic: 7547 Sorted by residual: dihedral pdb=" CA TYR K 86 " pdb=" C TYR K 86 " pdb=" N VAL K 87 " pdb=" CA VAL K 87 " ideal model delta harmonic sigma weight residual -180.00 -149.24 -30.76 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA TYR E 86 " pdb=" C TYR E 86 " pdb=" N VAL E 87 " pdb=" CA VAL E 87 " ideal model delta harmonic sigma weight residual -180.00 -149.46 -30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA TYR L 86 " pdb=" C TYR L 86 " pdb=" N VAL L 87 " pdb=" CA VAL L 87 " ideal model delta harmonic sigma weight residual 180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 12789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2787 0.088 - 0.175: 306 0.175 - 0.262: 19 0.262 - 0.350: 6 0.350 - 0.437: 5 Chirality restraints: 3123 Sorted by residual: chirality pdb=" CG LEU F 31 " pdb=" CB LEU F 31 " pdb=" CD1 LEU F 31 " pdb=" CD2 LEU F 31 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CB THR F 98 " pdb=" CA THR F 98 " pdb=" OG1 THR F 98 " pdb=" CG2 THR F 98 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CG LEU A 217 " pdb=" CB LEU A 217 " pdb=" CD1 LEU A 217 " pdb=" CD2 LEU A 217 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 3120 not shown) Planarity restraints: 3807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 193 " -0.125 5.00e-02 4.00e+02 1.74e-01 4.87e+01 pdb=" N PRO J 194 " 0.301 5.00e-02 4.00e+02 pdb=" CA PRO J 194 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO J 194 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 212 " 0.107 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO G 213 " -0.264 5.00e-02 4.00e+02 pdb=" CA PRO G 213 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO G 213 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 13 " -0.035 2.00e-02 2.50e+03 3.52e-02 3.09e+01 pdb=" CG TRP D 13 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP D 13 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP D 13 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 13 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP D 13 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 13 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 13 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 13 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 13 " -0.011 2.00e-02 2.50e+03 ... (remaining 3804 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 52 2.29 - 2.95: 9056 2.95 - 3.60: 31453 3.60 - 4.25: 48375 4.25 - 4.90: 82663 Nonbonded interactions: 171599 Sorted by model distance: nonbonded pdb="MN MN K 401 " pdb="MN MN K 402 " model vdw 1.642 3.080 nonbonded pdb="MN MN J 401 " pdb="MN MN J 402 " model vdw 1.743 3.080 nonbonded pdb=" OD2 ASP E 85 " pdb="MN MN E 402 " model vdw 2.105 3.060 nonbonded pdb=" OD1 ASN E 117 " pdb="MN MN E 402 " model vdw 2.128 3.060 nonbonded pdb=" OD2 ASP L 85 " pdb="MN MN L 402 " model vdw 2.128 3.060 ... (remaining 171594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 93 through 153 or resid 155 through 223)) selection = (chain 'B' and (resid 93 through 153 or resid 155 through 223)) } ncs_group { reference = (chain 'D' and (resid 4 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 294 or resid 401 through 402)) selection = (chain 'E' and (resid 4 through 8 or resid 10 through 402)) selection = (chain 'F' and (resid 4 through 8 or resid 10 through 402)) selection = (chain 'G' and (resid 4 through 8 or resid 10 through 402)) selection = (chain 'I' and (resid 4 through 8 or resid 10 through 402)) selection = (chain 'J' and (resid 4 through 8 or resid 10 through 402)) selection = (chain 'K' and (resid 4 through 8 or resid 10 through 402)) selection = (chain 'L' and (resid 4 through 8 or resid 10 through 402)) } 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=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.790 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.006 0.166 21497 Z= 0.258 Angle : 1.122 23.723 29108 Z= 0.602 Chirality : 0.057 0.437 3123 Planarity : 0.008 0.176 3807 Dihedral : 17.115 89.365 7954 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.35 % Allowed : 28.61 % Favored : 71.04 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.15), residues: 2579 helix: -0.17 (0.14), residues: 1164 sheet: -2.03 (0.22), residues: 516 loop : -2.02 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 106 TYR 0.044 0.002 TYR J 137 PHE 0.066 0.003 PHE K 62 TRP 0.089 0.003 TRP D 13 HIS 0.012 0.002 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.26 (21497) covalent geometry : angle 1.12215 / 0.60 (29108) hydrogen bonds : bond 0.13401 / 9.04 ( 1004) hydrogen bonds : angle 6.44583 / 4.61 ( 2831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 335 time to evaluate : 0.778 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: A 188 LYS cc_start: 0.7742 (tmtt) cc_final: 0.7163 (ttmt) REVERT: B 196 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7813 (ptm-80) REVERT: B 217 LEU cc_start: 0.9170 (mm) cc_final: 0.8727 (mm) REVERT: D 66 MET cc_start: 0.7502 (mmt) cc_final: 0.7145 (mmm) REVERT: D 86 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: E 41 LYS cc_start: 0.8106 (tptp) cc_final: 0.7492 (mtmm) REVERT: F 83 MET cc_start: 0.5592 (mmt) cc_final: 0.5188 (mmt) REVERT: F 129 PHE cc_start: 0.8074 (t80) cc_final: 0.7744 (t80) REVERT: F 236 LEU cc_start: 0.7068 (pp) cc_final: 0.6775 (mt) REVERT: G 66 MET cc_start: 0.8254 (mtm) cc_final: 0.6751 (tpt) REVERT: G 76 PRO cc_start: 0.5710 (Cg_endo) cc_final: 0.5472 (Cg_exo) REVERT: I 246 GLU cc_start: 0.7210 (tp30) cc_final: 0.6932 (tm-30) REVERT: L 36 LYS cc_start: 0.7301 (mmmm) cc_final: 0.6731 (tppt) REVERT: L 179 HIS cc_start: 0.6702 (m90) cc_final: 0.6348 (m170) outliers start: 8 outliers final: 3 residues processed: 340 average time/residue: 0.1746 time to fit residues: 87.8521 Evaluate side-chains 308 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 304 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain I residue 257 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.1980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN B 189 GLN E 118 HIS F 191 HIS F 229 ASN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 HIS ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 GLN J 230 HIS K 141 ASN ** K 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.174416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.140763 restraints weight = 63563.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141735 restraints weight = 34717.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.142961 restraints weight = 30153.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.144383 restraints weight = 20059.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146917 restraints weight = 17013.613| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21497 Z= 0.247 Angle : 0.731 11.663 29108 Z= 0.385 Chirality : 0.047 0.186 3123 Planarity : 0.005 0.090 3807 Dihedral : 5.080 45.956 2867 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.32 % Allowed : 24.55 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.16), residues: 2579 helix: 0.74 (0.15), residues: 1169 sheet: -2.14 (0.26), residues: 384 loop : -2.14 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 239 TYR 0.040 0.002 TYR J 145 PHE 0.026 0.002 PHE F 150 TRP 0.022 0.002 TRP A 218 HIS 0.009 0.002 HIS J 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (21497) covalent geometry : angle 0.73083 / 0.38 (29108) hydrogen bonds : bond 0.05175 / 3.42 ( 1004) hydrogen bonds : angle 5.03548 / 3.54 ( 2831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 326 time to evaluate : 0.816 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: A 188 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7416 (ttmt) REVERT: B 151 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7837 (tp40) REVERT: B 217 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8898 (mm) REVERT: E 283 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7926 (mptt) REVERT: F 66 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7542 (mpp) REVERT: F 246 GLU cc_start: 0.7903 (mp0) cc_final: 0.7678 (tp30) REVERT: G 277 GLU cc_start: 0.5931 (tp30) cc_final: 0.5679 (tp30) REVERT: I 70 ARG cc_start: 0.7632 (ttp-110) cc_final: 0.7296 (ttp80) REVERT: I 246 GLU cc_start: 0.7343 (tp30) cc_final: 0.6856 (tp30) REVERT: J 224 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8176 (mp) REVERT: L 248 TYR cc_start: 0.8107 (p90) cc_final: 0.7564 (p90) outliers start: 99 outliers final: 56 residues processed: 397 average time/residue: 0.1677 time to fit residues: 100.8711 Evaluate side-chains 351 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 292 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 191 HIS Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 164 PHE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 224 ILE Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 141 ASN Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 256 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 6 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 235 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 40 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 252 HIS ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN ** K 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.176508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135619 restraints weight = 74431.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.142297 restraints weight = 33389.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.142687 restraints weight = 18337.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143869 restraints weight = 16810.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143874 restraints weight = 14448.958| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3903 r_free = 0.3903 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3903 r_free = 0.3903 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21497 Z= 0.149 Angle : 0.638 12.661 29108 Z= 0.331 Chirality : 0.043 0.220 3123 Planarity : 0.004 0.062 3807 Dihedral : 4.669 42.050 2864 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.62 % Allowed : 25.25 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2579 helix: 1.19 (0.15), residues: 1180 sheet: -2.15 (0.25), residues: 402 loop : -1.96 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.037 0.001 TYR J 145 PHE 0.020 0.001 PHE F 150 TRP 0.017 0.001 TRP A 218 HIS 0.013 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (21497) covalent geometry : angle 0.63845 / 0.33 (29108) hydrogen bonds : bond 0.04566 / 3.04 ( 1004) hydrogen bonds : angle 4.70552 / 3.32 ( 2831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 322 time to evaluate : 0.831 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: A 188 LYS cc_start: 0.7946 (tmtt) cc_final: 0.7458 (ttmt) REVERT: A 195 LEU cc_start: 0.7663 (tt) cc_final: 0.6778 (pp) REVERT: B 217 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8981 (mm) REVERT: F 245 MET cc_start: 0.8365 (tpp) cc_final: 0.7913 (tpp) REVERT: G 21 LYS cc_start: 0.6660 (mttm) cc_final: 0.6449 (mttm) REVERT: I 37 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: I 70 ARG cc_start: 0.7552 (ttp-110) cc_final: 0.7228 (ttp80) REVERT: I 246 GLU cc_start: 0.7402 (tp30) cc_final: 0.7187 (tp30) REVERT: J 21 LYS cc_start: 0.8363 (pptt) cc_final: 0.8134 (pptt) REVERT: J 114 LEU cc_start: 0.8759 (mm) cc_final: 0.8439 (mp) REVERT: J 276 MET cc_start: 0.6618 (mtp) cc_final: 0.6372 (mtp) REVERT: L 67 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: L 248 TYR cc_start: 0.8039 (p90) cc_final: 0.7617 (p90) outliers start: 83 outliers final: 54 residues processed: 381 average time/residue: 0.1661 time to fit residues: 95.7149 Evaluate side-chains 360 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 303 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 164 PHE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 141 ASN Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 120 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 249 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 61 GLN E 232 ASN F 191 HIS G 191 HIS ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 HIS ** K 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.177793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.143937 restraints weight = 61964.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146145 restraints weight = 32321.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.146706 restraints weight = 28140.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148488 restraints weight = 18225.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149427 restraints weight = 14967.874| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21497 Z= 0.137 Angle : 0.618 13.388 29108 Z= 0.317 Chirality : 0.043 0.238 3123 Planarity : 0.004 0.057 3807 Dihedral : 4.470 38.947 2864 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.19 % Allowed : 25.25 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2579 helix: 1.44 (0.15), residues: 1180 sheet: -2.09 (0.27), residues: 354 loop : -1.97 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 206 TYR 0.031 0.001 TYR J 145 PHE 0.012 0.001 PHE F 260 TRP 0.017 0.001 TRP A 218 HIS 0.006 0.001 HIS I 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (21497) covalent geometry : angle 0.61751 / 0.32 (29108) hydrogen bonds : bond 0.04335 / 2.89 ( 1004) hydrogen bonds : angle 4.51510 / 3.19 ( 2831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 332 time to evaluate : 0.851 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: A 147 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7118 (ptp-170) REVERT: A 188 LYS cc_start: 0.8001 (tmtt) cc_final: 0.7433 (ttmt) REVERT: A 195 LEU cc_start: 0.7584 (tt) cc_final: 0.6743 (pp) REVERT: A 218 TRP cc_start: 0.6323 (t-100) cc_final: 0.5684 (t-100) REVERT: B 217 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8846 (mm) REVERT: E 283 LYS cc_start: 0.8119 (mptt) cc_final: 0.7723 (mptt) REVERT: F 69 PHE cc_start: 0.4919 (OUTLIER) cc_final: 0.3776 (m-10) REVERT: F 95 GLU cc_start: 0.7870 (pm20) cc_final: 0.7623 (pp20) REVERT: G 66 MET cc_start: 0.7203 (mtm) cc_final: 0.6886 (tpt) REVERT: I 9 GLU cc_start: 0.7119 (pt0) cc_final: 0.6883 (pt0) REVERT: I 37 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: I 70 ARG cc_start: 0.7582 (ttp-110) cc_final: 0.7256 (ttp80) REVERT: I 246 GLU cc_start: 0.7469 (tp30) cc_final: 0.6562 (tp30) REVERT: J 34 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7554 (tppt) REVERT: J 114 LEU cc_start: 0.8765 (mm) cc_final: 0.8445 (mp) REVERT: J 276 MET cc_start: 0.6601 (mtp) cc_final: 0.6355 (mtp) REVERT: K 170 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8342 (mm) REVERT: L 67 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: L 179 HIS cc_start: 0.6903 (m90) cc_final: 0.6465 (m170) REVERT: L 248 TYR cc_start: 0.8038 (p90) cc_final: 0.7667 (p90) REVERT: L 253 ASP cc_start: 0.7481 (p0) cc_final: 0.7165 (p0) REVERT: L 290 ASP cc_start: 0.8084 (m-30) cc_final: 0.7522 (m-30) outliers start: 96 outliers final: 68 residues processed: 397 average time/residue: 0.1611 time to fit residues: 96.5530 Evaluate side-chains 371 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 297 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 232 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 133 CYS Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 135 ARG Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 141 ASN Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 226 GLU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain K residue 256 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 111 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 146 optimal weight: 0.0050 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN E 232 ASN E 255 ASN F 288 GLN I 59 HIS ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN ** K 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.175528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142328 restraints weight = 68832.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.144420 restraints weight = 43342.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146223 restraints weight = 29506.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.147430 restraints weight = 18697.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.150248 restraints weight = 16367.791| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21497 Z= 0.171 Angle : 0.650 15.321 29108 Z= 0.334 Chirality : 0.044 0.259 3123 Planarity : 0.004 0.056 3807 Dihedral : 4.469 30.683 2862 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.80 % Allowed : 24.95 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2579 helix: 1.45 (0.15), residues: 1186 sheet: -2.15 (0.26), residues: 382 loop : -1.90 (0.17), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 89 TYR 0.034 0.001 TYR J 145 PHE 0.015 0.001 PHE L 164 TRP 0.015 0.001 TRP A 218 HIS 0.007 0.001 HIS I 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (21497) covalent geometry : angle 0.64988 / 0.33 (29108) hydrogen bonds : bond 0.04514 / 3.00 ( 1004) hydrogen bonds : angle 4.56523 / 3.24 ( 2831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 310 time to evaluate : 0.834 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: A 147 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7021 (ptp-170) REVERT: A 175 MET cc_start: 0.7110 (ptm) cc_final: 0.6883 (ptm) REVERT: A 195 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.6791 (pp) REVERT: A 218 TRP cc_start: 0.6395 (t-100) cc_final: 0.5714 (t-100) REVERT: B 217 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8898 (mm) REVERT: D 66 MET cc_start: 0.7600 (mmt) cc_final: 0.7393 (mmm) REVERT: D 197 ASP cc_start: 0.7048 (m-30) cc_final: 0.6622 (m-30) REVERT: E 115 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7427 (ttm170) REVERT: F 69 PHE cc_start: 0.4826 (OUTLIER) cc_final: 0.3645 (m-10) REVERT: F 245 MET cc_start: 0.8249 (tpp) cc_final: 0.7844 (tpp) REVERT: G 282 LEU cc_start: 0.6665 (tp) cc_final: 0.6064 (tp) REVERT: I 9 GLU cc_start: 0.7039 (pt0) cc_final: 0.6818 (pt0) REVERT: I 37 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6885 (pm20) REVERT: I 222 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: I 246 GLU cc_start: 0.7484 (tp30) cc_final: 0.6763 (tp30) REVERT: J 114 LEU cc_start: 0.8852 (mm) cc_final: 0.8498 (mp) REVERT: J 276 MET cc_start: 0.6607 (mtp) cc_final: 0.6351 (mtp) REVERT: K 170 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8364 (mm) REVERT: L 67 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: L 248 TYR cc_start: 0.8193 (p90) cc_final: 0.7879 (p90) REVERT: L 290 ASP cc_start: 0.8095 (m-30) cc_final: 0.7534 (m-30) outliers start: 110 outliers final: 79 residues processed: 392 average time/residue: 0.1671 time to fit residues: 98.3550 Evaluate side-chains 372 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 226 GLU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain K residue 256 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 6 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 55 CYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 75 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 249 optimal weight: 0.1980 chunk 160 optimal weight: 0.9990 chunk 218 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN F 229 ASN F 255 ASN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.172885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.141209 restraints weight = 48777.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.142464 restraints weight = 41387.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143652 restraints weight = 33906.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145341 restraints weight = 19796.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146196 restraints weight = 16128.919| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (16 function evaluations) r_final: 0.3918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21497 Z= 0.136 Angle : 0.623 13.474 29108 Z= 0.319 Chirality : 0.042 0.253 3123 Planarity : 0.003 0.056 3807 Dihedral : 4.328 29.868 2862 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.92 % Allowed : 26.43 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2579 helix: 1.64 (0.15), residues: 1174 sheet: -2.10 (0.27), residues: 346 loop : -1.87 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 89 TYR 0.032 0.001 TYR J 145 PHE 0.013 0.001 PHE F 260 TRP 0.014 0.001 TRP A 218 HIS 0.006 0.001 HIS I 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21497) covalent geometry : angle 0.62252 / 0.32 (29108) hydrogen bonds : bond 0.04275 / 2.85 ( 1004) hydrogen bonds : angle 4.41485 / 3.12 ( 2831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 315 time to evaluate : 0.848 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: A 95 ARG cc_start: 0.7373 (tpp80) cc_final: 0.7126 (ttm170) REVERT: A 147 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7103 (ptp-170) REVERT: A 175 MET cc_start: 0.7214 (ptm) cc_final: 0.6951 (ptm) REVERT: A 188 LYS cc_start: 0.7959 (tmtt) cc_final: 0.7059 (ttmt) REVERT: A 195 LEU cc_start: 0.7749 (tt) cc_final: 0.6922 (pp) REVERT: A 218 TRP cc_start: 0.6141 (t-100) cc_final: 0.5568 (t-100) REVERT: B 217 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8819 (mm) REVERT: D 66 MET cc_start: 0.7571 (mmt) cc_final: 0.7363 (mmm) REVERT: D 197 ASP cc_start: 0.7031 (m-30) cc_final: 0.6594 (m-30) REVERT: F 69 PHE cc_start: 0.5348 (OUTLIER) cc_final: 0.3939 (m-10) REVERT: F 109 GLU cc_start: 0.5597 (tp30) cc_final: 0.5182 (tm-30) REVERT: F 245 MET cc_start: 0.7963 (tpp) cc_final: 0.7619 (tpp) REVERT: I 9 GLU cc_start: 0.6959 (pt0) cc_final: 0.6753 (pt0) REVERT: I 37 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: I 66 MET cc_start: 0.7370 (mmm) cc_final: 0.7155 (mmm) REVERT: I 70 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7137 (ttp80) REVERT: I 222 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: I 246 GLU cc_start: 0.7366 (tp30) cc_final: 0.7152 (tp30) REVERT: J 34 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7469 (tppt) REVERT: J 114 LEU cc_start: 0.8783 (mm) cc_final: 0.8409 (mp) REVERT: K 139 ASN cc_start: 0.7592 (p0) cc_final: 0.7066 (p0) REVERT: K 170 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8337 (mm) REVERT: L 67 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: L 179 HIS cc_start: 0.6916 (m90) cc_final: 0.6532 (m170) REVERT: L 248 TYR cc_start: 0.8152 (p90) cc_final: 0.7879 (p90) REVERT: L 290 ASP cc_start: 0.8155 (m-30) cc_final: 0.7606 (m-30) outliers start: 90 outliers final: 63 residues processed: 382 average time/residue: 0.1718 time to fit residues: 97.9963 Evaluate side-chains 355 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 285 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 133 CYS Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 226 GLU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 6 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 55 CYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 156 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 196 optimal weight: 0.0770 chunk 249 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN F 255 ASN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 230 HIS K 264 ASN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.178835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.144025 restraints weight = 56481.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.144299 restraints weight = 28289.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145891 restraints weight = 22827.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.146610 restraints weight = 17333.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.147008 restraints weight = 16299.033| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21497 Z= 0.132 Angle : 0.635 15.361 29108 Z= 0.324 Chirality : 0.042 0.275 3123 Planarity : 0.004 0.057 3807 Dihedral : 4.256 29.668 2862 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.10 % Allowed : 26.38 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2579 helix: 1.70 (0.16), residues: 1174 sheet: -2.11 (0.28), residues: 336 loop : -1.80 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 89 TYR 0.030 0.001 TYR J 145 PHE 0.014 0.001 PHE E 228 TRP 0.018 0.001 TRP E 13 HIS 0.007 0.001 HIS K 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (21497) covalent geometry : angle 0.63467 / 0.32 (29108) hydrogen bonds : bond 0.04235 / 2.84 ( 1004) hydrogen bonds : angle 4.38194 / 3.09 ( 2831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 308 time to evaluate : 0.849 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: A 147 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7074 (ptp-170) REVERT: A 188 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7207 (ttmt) REVERT: A 195 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7046 (pp) REVERT: A 218 TRP cc_start: 0.6642 (t-100) cc_final: 0.5875 (t-100) REVERT: B 168 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: B 217 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8959 (mm) REVERT: D 66 MET cc_start: 0.7597 (mmt) cc_final: 0.7289 (mmm) REVERT: D 197 ASP cc_start: 0.7070 (m-30) cc_final: 0.6713 (m-30) REVERT: E 41 LYS cc_start: 0.7958 (tptp) cc_final: 0.7434 (mttt) REVERT: F 69 PHE cc_start: 0.5229 (OUTLIER) cc_final: 0.3949 (m-10) REVERT: F 109 GLU cc_start: 0.6459 (tp30) cc_final: 0.5524 (tm-30) REVERT: F 245 MET cc_start: 0.8247 (tpp) cc_final: 0.7922 (tpp) REVERT: G 25 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6076 (pm20) REVERT: G 66 MET cc_start: 0.7382 (mtm) cc_final: 0.6875 (tpt) REVERT: G 267 TYR cc_start: 0.6923 (m-10) cc_final: 0.6586 (m-10) REVERT: I 9 GLU cc_start: 0.7018 (pt0) cc_final: 0.6782 (pt0) REVERT: I 37 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: I 66 MET cc_start: 0.7374 (mmm) cc_final: 0.7143 (mmm) REVERT: I 70 ARG cc_start: 0.7472 (ttp-110) cc_final: 0.7199 (ttp80) REVERT: I 151 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6716 (m-30) REVERT: I 222 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: J 34 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7498 (tppt) REVERT: J 114 LEU cc_start: 0.8767 (mm) cc_final: 0.8407 (mp) REVERT: K 139 ASN cc_start: 0.7634 (p0) cc_final: 0.7340 (p0) REVERT: K 145 TYR cc_start: 0.7620 (m-80) cc_final: 0.7315 (m-80) REVERT: K 170 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8290 (mm) REVERT: L 67 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: L 290 ASP cc_start: 0.8131 (m-30) cc_final: 0.7590 (m-30) outliers start: 94 outliers final: 73 residues processed: 379 average time/residue: 0.1735 time to fit residues: 98.6922 Evaluate side-chains 376 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 292 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 133 CYS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 226 GLU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain K residue 256 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 264 ASN Chi-restraints excluded: chain L residue 6 PHE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 55 CYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 108 ARG Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 190 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 201 optimal weight: 0.0270 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 204 optimal weight: 0.2980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.180171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.145794 restraints weight = 65562.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.147795 restraints weight = 34217.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148943 restraints weight = 27950.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.151357 restraints weight = 18713.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.153134 restraints weight = 15155.763| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21497 Z= 0.122 Angle : 0.633 15.793 29108 Z= 0.322 Chirality : 0.042 0.298 3123 Planarity : 0.003 0.058 3807 Dihedral : 4.196 28.959 2862 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.71 % Allowed : 26.91 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2579 helix: 1.74 (0.16), residues: 1180 sheet: -2.05 (0.28), residues: 336 loop : -1.77 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 89 TYR 0.037 0.001 TYR J 145 PHE 0.015 0.001 PHE F 260 TRP 0.017 0.001 TRP E 13 HIS 0.006 0.001 HIS I 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (21497) covalent geometry : angle 0.63288 / 0.32 (29108) hydrogen bonds : bond 0.04145 / 2.78 ( 1004) hydrogen bonds : angle 4.32177 / 3.05 ( 2831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 314 time to evaluate : 0.864 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: A 92 ARG cc_start: 0.7849 (mmp80) cc_final: 0.7550 (mmp80) REVERT: A 147 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7020 (ptp-170) REVERT: A 188 LYS cc_start: 0.8003 (tmtt) cc_final: 0.7207 (ttmt) REVERT: A 195 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7011 (pp) REVERT: B 168 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: B 217 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8915 (mm) REVERT: D 66 MET cc_start: 0.7552 (mmt) cc_final: 0.7248 (mmm) REVERT: D 86 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7864 (p90) REVERT: D 197 ASP cc_start: 0.7114 (m-30) cc_final: 0.6733 (m-30) REVERT: E 41 LYS cc_start: 0.7893 (tptp) cc_final: 0.7417 (mttt) REVERT: F 69 PHE cc_start: 0.5194 (OUTLIER) cc_final: 0.3915 (m-10) REVERT: F 245 MET cc_start: 0.8106 (tpp) cc_final: 0.7811 (tpp) REVERT: G 25 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6024 (pm20) REVERT: G 66 MET cc_start: 0.7221 (mtm) cc_final: 0.6860 (tpt) REVERT: G 267 TYR cc_start: 0.6971 (m-10) cc_final: 0.6553 (m-10) REVERT: I 37 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: I 66 MET cc_start: 0.7351 (mmm) cc_final: 0.7127 (mmm) REVERT: I 70 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7222 (ttp80) REVERT: I 151 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6663 (m-30) REVERT: I 222 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: I 246 GLU cc_start: 0.7430 (tp30) cc_final: 0.6888 (tp30) REVERT: J 34 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7443 (tppt) REVERT: J 114 LEU cc_start: 0.8739 (mm) cc_final: 0.8405 (mp) REVERT: K 42 GLU cc_start: 0.5204 (tt0) cc_final: 0.4941 (tt0) REVERT: K 139 ASN cc_start: 0.7553 (p0) cc_final: 0.7322 (p0) REVERT: K 170 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8278 (mm) REVERT: L 67 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: L 179 HIS cc_start: 0.6732 (m90) cc_final: 0.6324 (m170) REVERT: L 290 ASP cc_start: 0.8122 (m-30) cc_final: 0.7604 (m-30) outliers start: 85 outliers final: 65 residues processed: 375 average time/residue: 0.1705 time to fit residues: 95.8223 Evaluate side-chains 369 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 133 CYS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 226 GLU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain K residue 256 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 6 PHE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 55 CYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 108 ARG Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 65 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 242 optimal weight: 0.6980 chunk 220 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN E 232 ASN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 GLN J 191 HIS ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.178021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137973 restraints weight = 81701.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.142708 restraints weight = 34416.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146231 restraints weight = 20049.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146709 restraints weight = 16367.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.146621 restraints weight = 13800.465| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21497 Z= 0.146 Angle : 0.665 16.113 29108 Z= 0.336 Chirality : 0.043 0.380 3123 Planarity : 0.004 0.058 3807 Dihedral : 4.303 29.464 2862 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.92 % Allowed : 26.86 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2579 helix: 1.62 (0.15), residues: 1181 sheet: -2.01 (0.27), residues: 346 loop : -1.74 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 239 TYR 0.036 0.001 TYR J 145 PHE 0.013 0.001 PHE E 228 TRP 0.024 0.001 TRP A 218 HIS 0.007 0.001 HIS I 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (21497) covalent geometry : angle 0.66534 / 0.34 (29108) hydrogen bonds : bond 0.04311 / 2.88 ( 1004) hydrogen bonds : angle 4.39804 / 3.11 ( 2831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 297 time to evaluate : 0.678 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: A 147 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7203 (ptp-110) REVERT: A 188 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7269 (ttmt) REVERT: A 195 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7118 (pp) REVERT: B 168 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: B 217 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8963 (mm) REVERT: D 66 MET cc_start: 0.7495 (mmt) cc_final: 0.7151 (mmm) REVERT: D 86 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7702 (p90) REVERT: D 197 ASP cc_start: 0.7052 (m-30) cc_final: 0.6589 (m-30) REVERT: E 41 LYS cc_start: 0.7959 (tptp) cc_final: 0.7447 (mttt) REVERT: F 69 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.3745 (m-10) REVERT: F 109 GLU cc_start: 0.6208 (tp30) cc_final: 0.5435 (tm-30) REVERT: F 245 MET cc_start: 0.8035 (tpp) cc_final: 0.7725 (tpp) REVERT: G 25 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6146 (pm20) REVERT: G 66 MET cc_start: 0.7222 (mtm) cc_final: 0.6951 (tpt) REVERT: G 243 LEU cc_start: 0.7904 (tp) cc_final: 0.7672 (tp) REVERT: I 37 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: I 70 ARG cc_start: 0.7555 (ttp-110) cc_final: 0.7248 (ttp80) REVERT: I 151 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6719 (m-30) REVERT: I 222 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: I 246 GLU cc_start: 0.7523 (tp30) cc_final: 0.6933 (tp30) REVERT: J 34 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7482 (tppt) REVERT: J 114 LEU cc_start: 0.8851 (mm) cc_final: 0.8482 (mp) REVERT: K 42 GLU cc_start: 0.5503 (tt0) cc_final: 0.5242 (tt0) REVERT: K 139 ASN cc_start: 0.7478 (p0) cc_final: 0.7212 (p0) REVERT: K 170 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8303 (mm) REVERT: L 67 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: L 248 TYR cc_start: 0.7992 (p90) cc_final: 0.7455 (p90) REVERT: L 290 ASP cc_start: 0.8097 (m-30) cc_final: 0.7511 (m-30) outliers start: 90 outliers final: 69 residues processed: 362 average time/residue: 0.1722 time to fit residues: 93.2124 Evaluate side-chains 366 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 285 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 133 CYS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 226 GLU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 256 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 6 PHE Chi-restraints excluded: chain L residue 55 CYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 108 ARG Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 178 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130163 restraints weight = 69606.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133799 restraints weight = 30737.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137089 restraints weight = 19704.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137318 restraints weight = 16250.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137597 restraints weight = 13696.343| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21497 Z= 0.131 Angle : 0.667 16.264 29108 Z= 0.337 Chirality : 0.043 0.356 3123 Planarity : 0.004 0.058 3807 Dihedral : 4.281 29.055 2862 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.71 % Allowed : 27.00 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2579 helix: 1.65 (0.15), residues: 1181 sheet: -2.04 (0.28), residues: 336 loop : -1.71 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 239 TYR 0.036 0.001 TYR J 145 PHE 0.016 0.001 PHE F 260 TRP 0.036 0.001 TRP E 13 HIS 0.007 0.001 HIS I 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21497) covalent geometry : angle 0.66667 / 0.34 (29108) hydrogen bonds : bond 0.04220 / 2.83 ( 1004) hydrogen bonds : angle 4.36440 / 3.09 ( 2831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 297 time to evaluate : 1.022 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: A 147 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7112 (ptp-170) REVERT: A 188 LYS cc_start: 0.7958 (tmtt) cc_final: 0.7185 (ttmt) REVERT: A 195 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7176 (pp) REVERT: B 168 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: B 217 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8986 (mm) REVERT: D 66 MET cc_start: 0.7617 (mmt) cc_final: 0.7180 (mmm) REVERT: D 86 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7656 (p90) REVERT: D 197 ASP cc_start: 0.7338 (m-30) cc_final: 0.6799 (m-30) REVERT: E 41 LYS cc_start: 0.7992 (tptp) cc_final: 0.7440 (mttt) REVERT: F 69 PHE cc_start: 0.4755 (OUTLIER) cc_final: 0.3677 (m-10) REVERT: F 109 GLU cc_start: 0.6379 (tp30) cc_final: 0.5543 (tm-30) REVERT: F 245 MET cc_start: 0.8231 (tpp) cc_final: 0.7900 (tpp) REVERT: G 25 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6197 (pm20) REVERT: G 66 MET cc_start: 0.7300 (mtm) cc_final: 0.6861 (tpt) REVERT: I 37 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6733 (pm20) REVERT: I 70 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7362 (ttp80) REVERT: I 151 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6598 (m-30) REVERT: I 222 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: I 246 GLU cc_start: 0.7589 (tp30) cc_final: 0.6925 (tp30) REVERT: J 34 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7456 (tppt) REVERT: J 114 LEU cc_start: 0.8821 (mm) cc_final: 0.8489 (mp) REVERT: K 42 GLU cc_start: 0.5699 (tt0) cc_final: 0.5469 (tt0) REVERT: K 139 ASN cc_start: 0.7524 (p0) cc_final: 0.7290 (p0) REVERT: K 170 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8267 (mm) REVERT: L 67 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: L 248 TYR cc_start: 0.8012 (p90) cc_final: 0.7461 (p90) REVERT: L 290 ASP cc_start: 0.8244 (m-30) cc_final: 0.7656 (m-30) outliers start: 85 outliers final: 70 residues processed: 357 average time/residue: 0.1712 time to fit residues: 92.1122 Evaluate side-chains 371 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 289 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 289 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 133 CYS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain J residue 284 TYR Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 226 GLU Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain K residue 256 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 6 PHE Chi-restraints excluded: chain L residue 55 CYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 108 ARG Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 189 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.170082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130137 restraints weight = 66326.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134030 restraints weight = 29627.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137225 restraints weight = 18581.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137582 restraints weight = 15716.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137814 restraints weight = 12546.855| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21497 Z= 0.160 Angle : 0.799 59.199 29108 Z= 0.432 Chirality : 0.045 0.538 3123 Planarity : 0.004 0.058 3807 Dihedral : 4.287 28.999 2862 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.84 % Allowed : 26.73 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2579 helix: 1.65 (0.15), residues: 1181 sheet: -2.03 (0.28), residues: 336 loop : -1.71 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 206 TYR 0.034 0.001 TYR J 145 PHE 0.017 0.001 PHE F 129 TRP 0.029 0.001 TRP E 13 HIS 0.007 0.001 HIS I 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (21497) covalent geometry : angle 0.79868 / 0.43 (29108) hydrogen bonds : bond 0.04248 / 2.85 ( 1004) hydrogen bonds : angle 4.36770 / 3.09 ( 2831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.34 seconds wall clock time: 72 minutes 18.25 seconds (4338.25 seconds total)