Starting phenix.real_space_refine on Fri Feb 6 00:35:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o0l_49992/02_2026/9o0l_49992.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o0l_49992/02_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_49992/02_2026/9o0l_49992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o0l_49992/02_2026/9o0l_49992.map" model { file = "/net/cci-nas-00/data/ceres_data/9o0l_49992/02_2026/9o0l_49992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o0l_49992/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 5.70, per 1000 atoms: 0.27 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: 1.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.79 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: 3.91 Time building geometry restraints manager: 2.21 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 1.600 nonbonded pdb="MN MN J 401 " pdb="MN MN J 402 " model vdw 1.743 1.600 nonbonded pdb=" OD2 ASP E 85 " pdb="MN MN E 402 " model vdw 2.105 2.320 nonbonded pdb=" OD1 ASN E 117 " pdb="MN MN E 402 " model vdw 2.128 2.320 nonbonded pdb=" OD2 ASP L 85 " pdb="MN MN L 402 " model vdw 2.128 2.320 ... (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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.950 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 covalent geometry : bond 0.00574 (21497) covalent geometry : angle 1.12215 (29108) hydrogen bonds : bond 0.13401 ( 1004) hydrogen bonds : angle 6.44583 ( 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 : 0.863 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: 0.1751 time to fit residues: 87.8334 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 : 0.832 ------------------------------------------------------------------------------- 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: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN F 191 HIS G 252 HIS G 255 ASN J 122 GLN J 230 HIS K 141 ASN ** K 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.174611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.140905 restraints weight = 63669.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142523 restraints weight = 39264.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143999 restraints weight = 31208.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.145571 restraints weight = 20223.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.146455 restraints weight = 17132.434| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3960 r_free = 0.3960 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3960 r_free = 0.3960 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21497 Z= 0.245 Angle : 0.724 12.195 29108 Z= 0.381 Chirality : 0.046 0.209 3123 Planarity : 0.005 0.090 3807 Dihedral : 5.039 42.311 2867 Min Nonbonded Distance : 1.287 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.88 % Allowed : 24.73 % Favored : 71.39 % 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: -1.18 (0.16), residues: 2579 helix: 0.70 (0.15), residues: 1187 sheet: -2.10 (0.26), residues: 402 loop : -2.01 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 239 TYR 0.041 0.002 TYR J 145 PHE 0.026 0.002 PHE F 150 TRP 0.021 0.002 TRP A 218 HIS 0.009 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00576 (21497) covalent geometry : angle 0.72383 (29108) hydrogen bonds : bond 0.05110 ( 1004) hydrogen bonds : angle 5.04864 ( 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 418 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 329 time to evaluate : 0.885 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: 0.8066 (tmtt) cc_final: 0.7398 (ttmt) REVERT: B 217 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8865 (mm) REVERT: F 66 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7482 (mpp) REVERT: G 277 GLU cc_start: 0.5786 (tp30) cc_final: 0.5516 (tp30) REVERT: I 70 ARG cc_start: 0.7673 (ttp-110) cc_final: 0.7331 (ttp80) REVERT: I 246 GLU cc_start: 0.7275 (tp30) cc_final: 0.6646 (tp30) REVERT: J 114 LEU cc_start: 0.8773 (mm) cc_final: 0.8404 (mp) REVERT: J 146 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8327 (m-10) REVERT: J 224 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8146 (mp) REVERT: L 248 TYR cc_start: 0.8063 (p90) cc_final: 0.7555 (p90) outliers start: 89 outliers final: 54 residues processed: 393 average time/residue: 0.1630 time to fit residues: 96.4242 Evaluate side-chains 351 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 191 THR 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 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 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 133 CYS 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 65 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 146 PHE 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 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: 0.9980 chunk 139 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN D 61 GLN F 125 GLN F 229 ASN G 63 HIS ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.176999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.144264 restraints weight = 74340.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.145576 restraints weight = 50626.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.148263 restraints weight = 33136.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.149481 restraints weight = 20641.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.153401 restraints weight = 17303.777| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3988 r_free = 0.3988 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3988 r_free = 0.3988 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21497 Z= 0.149 Angle : 0.637 12.685 29108 Z= 0.330 Chirality : 0.043 0.214 3123 Planarity : 0.004 0.061 3807 Dihedral : 4.649 37.145 2864 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.92 % Allowed : 25.16 % Favored : 70.91 % 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: -0.80 (0.16), residues: 2579 helix: 1.20 (0.15), residues: 1180 sheet: -2.12 (0.25), residues: 402 loop : -1.94 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 206 TYR 0.037 0.001 TYR J 145 PHE 0.031 0.001 PHE F 150 TRP 0.018 0.001 TRP A 218 HIS 0.016 0.001 HIS F 191 Details of bonding type rmsd covalent geometry : bond 0.00347 (21497) covalent geometry : angle 0.63721 (29108) hydrogen bonds : bond 0.04535 ( 1004) hydrogen bonds : angle 4.68926 ( 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 417 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 327 time to evaluate : 0.627 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: 0.8048 (tmtt) cc_final: 0.7486 (ttmt) REVERT: A 195 LEU cc_start: 0.7565 (tt) cc_final: 0.6642 (pp) REVERT: B 217 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8835 (mm) REVERT: D 66 MET cc_start: 0.7481 (mmt) cc_final: 0.7264 (mmm) REVERT: E 46 GLN cc_start: 0.4130 (OUTLIER) cc_final: 0.3896 (tm-30) REVERT: F 245 MET cc_start: 0.7700 (tpp) cc_final: 0.7352 (tpp) REVERT: F 246 GLU cc_start: 0.7117 (tp30) cc_final: 0.6803 (tp30) REVERT: G 277 GLU cc_start: 0.5669 (tp30) cc_final: 0.5454 (tp30) REVERT: I 37 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: I 70 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7237 (ttp80) REVERT: I 246 GLU cc_start: 0.7393 (tp30) cc_final: 0.7142 (tp30) REVERT: J 114 LEU cc_start: 0.8753 (mm) cc_final: 0.8429 (mp) REVERT: J 276 MET cc_start: 0.6704 (mtp) cc_final: 0.6459 (mtp) REVERT: L 67 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: L 248 TYR cc_start: 0.8096 (p90) cc_final: 0.7640 (p90) outliers start: 90 outliers final: 55 residues processed: 394 average time/residue: 0.1552 time to fit residues: 91.6797 Evaluate side-chains 358 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 D residue 176 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 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 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 53 THR 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 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 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 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 242 GLN 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: 3.9990 chunk 169 optimal weight: 0.7980 chunk 128 optimal weight: 0.0050 chunk 88 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 249 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN F 191 HIS G 191 HIS ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.174622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.140750 restraints weight = 62023.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.142440 restraints weight = 32105.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143036 restraints weight = 29442.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.145509 restraints weight = 19020.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145932 restraints weight = 14791.185| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21497 Z= 0.183 Angle : 0.648 13.232 29108 Z= 0.336 Chirality : 0.044 0.204 3123 Planarity : 0.004 0.057 3807 Dihedral : 4.645 35.164 2864 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.54 % Allowed : 25.29 % Favored : 70.17 % 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: -0.76 (0.16), residues: 2579 helix: 1.31 (0.15), residues: 1180 sheet: -2.14 (0.25), residues: 402 loop : -2.03 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 108 TYR 0.030 0.001 TYR J 145 PHE 0.029 0.002 PHE F 150 TRP 0.018 0.001 TRP A 218 HIS 0.005 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00432 (21497) covalent geometry : angle 0.64785 (29108) hydrogen bonds : bond 0.04638 ( 1004) hydrogen bonds : angle 4.66698 ( 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 424 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 320 time to evaluate : 0.812 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: 0.7777 (OUTLIER) cc_final: 0.7179 (ptp-170) REVERT: A 188 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7514 (ttmt) REVERT: A 218 TRP cc_start: 0.6360 (t-100) cc_final: 0.5758 (t-100) REVERT: B 217 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8855 (mm) REVERT: D 279 ASP cc_start: 0.7194 (m-30) cc_final: 0.6987 (m-30) REVERT: E 46 GLN cc_start: 0.4253 (OUTLIER) cc_final: 0.3994 (tm130) REVERT: E 115 ARG cc_start: 0.7462 (ttm170) cc_final: 0.6896 (ttm170) REVERT: E 283 LYS cc_start: 0.8118 (mptt) cc_final: 0.7734 (mptt) REVERT: F 69 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.3675 (m-10) REVERT: I 9 GLU cc_start: 0.7114 (pt0) cc_final: 0.6896 (pt0) REVERT: I 37 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: I 70 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: I 246 GLU cc_start: 0.7394 (tp30) cc_final: 0.6615 (tp30) REVERT: J 34 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7535 (tppt) REVERT: J 114 LEU cc_start: 0.8829 (mm) cc_final: 0.8480 (mp) REVERT: J 276 MET cc_start: 0.6733 (mtp) cc_final: 0.6506 (mtp) REVERT: K 170 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8363 (mm) REVERT: L 67 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6897 (tt0) REVERT: L 248 TYR cc_start: 0.8175 (p90) cc_final: 0.7760 (p90) REVERT: L 253 ASP cc_start: 0.7490 (p0) cc_final: 0.7269 (p0) REVERT: L 290 ASP cc_start: 0.8061 (m-30) cc_final: 0.7476 (m-30) outliers start: 104 outliers final: 73 residues processed: 393 average time/residue: 0.1685 time to fit residues: 99.5787 Evaluate side-chains 368 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 288 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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 46 GLN Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 232 ASN 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 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 123 ILE 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 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 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 52 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 87 VAL 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 223 ASP Chi-restraints excluded: chain K residue 226 GLU 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 86 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 111 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN E 232 ASN F 255 ASN K 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.176225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142849 restraints weight = 68786.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145851 restraints weight = 39604.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.147011 restraints weight = 28494.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.148880 restraints weight = 17971.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150067 restraints weight = 15163.440| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2377 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= 0.139 Angle : 0.628 14.302 29108 Z= 0.322 Chirality : 0.043 0.268 3123 Planarity : 0.004 0.057 3807 Dihedral : 4.415 30.942 2862 Min Nonbonded Distance : 1.360 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.19 % Allowed : 25.82 % Favored : 70.00 % 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: 1.50 (0.15), residues: 1186 sheet: -2.11 (0.25), residues: 384 loop : -1.98 (0.17), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.035 0.001 TYR J 145 PHE 0.027 0.001 PHE F 150 TRP 0.015 0.001 TRP A 218 HIS 0.005 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00324 (21497) covalent geometry : angle 0.62848 (29108) hydrogen bonds : bond 0.04375 ( 1004) hydrogen bonds : angle 4.49354 ( 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 412 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 316 time to evaluate : 0.768 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: 0.7739 (OUTLIER) cc_final: 0.7046 (ptp-170) REVERT: A 195 LEU cc_start: 0.7569 (tt) cc_final: 0.6708 (pp) REVERT: A 218 TRP cc_start: 0.6311 (t-100) cc_final: 0.5662 (t-100) REVERT: B 217 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8858 (mm) REVERT: E 115 ARG cc_start: 0.7330 (ttm170) cc_final: 0.6777 (ttm170) REVERT: F 69 PHE cc_start: 0.5108 (OUTLIER) cc_final: 0.3779 (m-10) REVERT: F 245 MET cc_start: 0.8033 (tpp) cc_final: 0.7730 (tpp) REVERT: I 9 GLU cc_start: 0.7097 (pt0) cc_final: 0.6871 (pt0) REVERT: I 37 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: I 70 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.7230 (ttp80) REVERT: I 222 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: I 246 GLU cc_start: 0.7440 (tp30) cc_final: 0.7016 (tp30) REVERT: J 34 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7465 (tppt) REVERT: J 114 LEU cc_start: 0.8820 (mm) cc_final: 0.8478 (mp) REVERT: J 119 GLU cc_start: 0.7090 (mp0) cc_final: 0.6859 (mp0) REVERT: J 146 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8295 (m-10) REVERT: J 276 MET cc_start: 0.6613 (mtp) cc_final: 0.6377 (mtp) REVERT: K 170 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8312 (mm) REVERT: L 67 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6883 (tt0) REVERT: L 179 HIS cc_start: 0.6956 (m90) cc_final: 0.6551 (m170) REVERT: L 248 TYR cc_start: 0.8198 (p90) cc_final: 0.7889 (p90) REVERT: L 290 ASP cc_start: 0.8163 (m-30) cc_final: 0.7604 (m-30) outliers start: 96 outliers final: 65 residues processed: 389 average time/residue: 0.1737 time to fit residues: 100.9179 Evaluate side-chains 367 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 294 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 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 91 TYR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 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 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 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 61 GLN Chi-restraints excluded: chain I residue 71 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 222 GLN 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 146 PHE 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 58 VAL Chi-restraints excluded: chain K residue 71 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 48 VAL Chi-restraints excluded: chain L residue 55 CYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 86 TYR 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: 4.9990 chunk 246 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 42 optimal weight: 0.0040 chunk 222 optimal weight: 0.7980 chunk 249 optimal weight: 0.0770 chunk 160 optimal weight: 0.4980 chunk 218 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN E 255 ASN F 255 ASN ** K 229 ASN ** 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 = 0.4261 r_free = 0.4261 target = 0.174842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.143052 restraints weight = 48307.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144422 restraints weight = 38337.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145705 restraints weight = 31445.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146937 restraints weight = 18924.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148450 restraints weight = 15998.329| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21497 Z= 0.116 Angle : 0.614 15.734 29108 Z= 0.312 Chirality : 0.042 0.259 3123 Planarity : 0.003 0.057 3807 Dihedral : 4.199 28.966 2862 Min Nonbonded Distance : 1.404 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.92 % Allowed : 27.17 % Favored : 69.91 % 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: -0.31 (0.17), residues: 2579 helix: 1.71 (0.16), residues: 1180 sheet: -2.12 (0.26), residues: 362 loop : -1.79 (0.17), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.032 0.001 TYR J 145 PHE 0.024 0.001 PHE F 150 TRP 0.015 0.001 TRP E 13 HIS 0.005 0.001 HIS K 241 Details of bonding type rmsd covalent geometry : bond 0.00257 (21497) covalent geometry : angle 0.61409 (29108) hydrogen bonds : bond 0.04138 ( 1004) hydrogen bonds : angle 4.33227 ( 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 393 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 326 time to evaluate : 0.909 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 188 LYS cc_start: 0.7835 (tmtt) cc_final: 0.6883 (ttmt) REVERT: A 195 LEU cc_start: 0.7544 (tt) cc_final: 0.6786 (pp) REVERT: A 218 TRP cc_start: 0.6289 (t-100) cc_final: 0.5659 (t-100) REVERT: B 217 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8809 (mm) REVERT: E 41 LYS cc_start: 0.7869 (tptp) cc_final: 0.7428 (mttt) REVERT: F 109 GLU cc_start: 0.6125 (tp30) cc_final: 0.5758 (tm-30) REVERT: F 245 MET cc_start: 0.7824 (tpp) cc_final: 0.7589 (tpp) REVERT: G 10 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6420 (mm) REVERT: G 66 MET cc_start: 0.7132 (mtm) cc_final: 0.6839 (tpt) REVERT: I 9 GLU cc_start: 0.6974 (pt0) cc_final: 0.6752 (pt0) REVERT: I 37 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: I 70 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.7094 (ttp80) REVERT: I 145 TYR cc_start: 0.7236 (m-10) cc_final: 0.6982 (m-10) REVERT: I 222 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7622 (tp40) REVERT: I 246 GLU cc_start: 0.7388 (tp30) cc_final: 0.7121 (tp30) REVERT: J 34 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7435 (tppt) REVERT: J 114 LEU cc_start: 0.8682 (mm) cc_final: 0.8353 (mp) REVERT: K 170 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8244 (mm) REVERT: L 253 ASP cc_start: 0.7473 (p0) cc_final: 0.7153 (p0) outliers start: 67 outliers final: 45 residues processed: 372 average time/residue: 0.1703 time to fit residues: 94.6077 Evaluate side-chains 345 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 202 LEU Chi-restraints excluded: chain B residue 217 LEU 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 126 VAL 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 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 G residue 10 LEU Chi-restraints excluded: chain G residue 15 GLU 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 42 GLU Chi-restraints excluded: chain I residue 61 GLN 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 222 GLN Chi-restraints excluded: chain I residue 257 VAL 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 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 L residue 55 CYS Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 159 VAL 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: 2.9990 chunk 248 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 147 optimal weight: 0.0770 chunk 51 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 249 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN E 232 ASN K 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.173762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138793 restraints weight = 55604.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139342 restraints weight = 28182.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140702 restraints weight = 23044.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.141326 restraints weight = 18097.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141627 restraints weight = 17018.240| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21497 Z= 0.127 Angle : 0.628 15.525 29108 Z= 0.317 Chirality : 0.042 0.277 3123 Planarity : 0.003 0.058 3807 Dihedral : 4.188 28.906 2862 Min Nonbonded Distance : 1.377 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.40 % Allowed : 26.73 % Favored : 69.86 % 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: -0.27 (0.17), residues: 2579 helix: 1.74 (0.16), residues: 1180 sheet: -2.12 (0.27), residues: 331 loop : -1.77 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 147 TYR 0.029 0.001 TYR J 145 PHE 0.023 0.001 PHE F 150 TRP 0.016 0.001 TRP E 13 HIS 0.007 0.001 HIS K 230 Details of bonding type rmsd covalent geometry : bond 0.00292 (21497) covalent geometry : angle 0.62761 (29108) hydrogen bonds : bond 0.04146 ( 1004) hydrogen bonds : angle 4.30793 ( 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 392 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 314 time to evaluate : 0.862 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: 0.7703 (OUTLIER) cc_final: 0.7045 (ptp-170) REVERT: A 188 LYS cc_start: 0.7992 (tmtt) cc_final: 0.7140 (ttmt) REVERT: A 195 LEU cc_start: 0.7818 (tt) cc_final: 0.6983 (pp) REVERT: A 218 TRP cc_start: 0.6599 (t-100) cc_final: 0.5841 (t-100) REVERT: B 217 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8908 (mm) REVERT: D 86 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7457 (p90) REVERT: D 239 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.6054 (ptm160) REVERT: E 41 LYS cc_start: 0.7888 (tptp) cc_final: 0.7430 (mttt) REVERT: E 104 LYS cc_start: 0.6570 (tptm) cc_final: 0.6337 (tppt) REVERT: F 69 PHE cc_start: 0.5068 (OUTLIER) cc_final: 0.3839 (m-10) REVERT: F 109 GLU cc_start: 0.6129 (tp30) cc_final: 0.5690 (tm-30) REVERT: F 245 MET cc_start: 0.8105 (tpp) cc_final: 0.7863 (tpp) REVERT: G 66 MET cc_start: 0.7388 (mtm) cc_final: 0.6878 (tpt) REVERT: G 282 LEU cc_start: 0.6634 (tp) cc_final: 0.6058 (tp) REVERT: I 9 GLU cc_start: 0.7036 (pt0) cc_final: 0.6787 (pt0) REVERT: I 37 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: I 222 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7648 (tp40) REVERT: I 246 GLU cc_start: 0.7324 (tp30) cc_final: 0.6510 (tp30) REVERT: J 114 LEU cc_start: 0.8733 (mm) cc_final: 0.8382 (mp) REVERT: K 139 ASN cc_start: 0.7315 (p0) cc_final: 0.7020 (p0) REVERT: K 170 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8244 (mm) REVERT: L 67 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: L 179 HIS cc_start: 0.6751 (m90) cc_final: 0.6347 (m170) REVERT: L 248 TYR cc_start: 0.7898 (p90) cc_final: 0.7444 (p90) REVERT: L 290 ASP cc_start: 0.8061 (m-30) cc_final: 0.7514 (m-30) outliers start: 78 outliers final: 61 residues processed: 372 average time/residue: 0.1755 time to fit residues: 97.1156 Evaluate side-chains 363 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 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 D residue 239 ARG 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 166 LEU Chi-restraints excluded: chain E residue 170 LEU 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 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 G residue 5 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 15 GLU 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 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 42 GLU Chi-restraints excluded: chain I residue 61 GLN 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 222 GLN Chi-restraints excluded: chain I residue 257 VAL 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 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 K residue 282 LEU 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 86 TYR Chi-restraints excluded: chain L residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 190 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 126 optimal weight: 6.9990 chunk 204 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN E 232 ASN F 229 ASN ** J 232 ASN ** 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 = 0.4230 r_free = 0.4230 target = 0.172244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138716 restraints weight = 65102.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139842 restraints weight = 43610.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141942 restraints weight = 31599.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143318 restraints weight = 20519.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144901 restraints weight = 17629.072| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2668 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= 0.144 Angle : 0.644 15.561 29108 Z= 0.328 Chirality : 0.043 0.294 3123 Planarity : 0.004 0.058 3807 Dihedral : 4.285 29.376 2862 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: -0.30 (0.17), residues: 2579 helix: 1.69 (0.15), residues: 1180 sheet: -1.99 (0.26), residues: 364 loop : -1.79 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.036 0.001 TYR J 145 PHE 0.022 0.001 PHE F 150 TRP 0.014 0.001 TRP A 218 HIS 0.006 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00336 (21497) covalent geometry : angle 0.64402 (29108) hydrogen bonds : bond 0.04250 ( 1004) hydrogen bonds : angle 4.36537 ( 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 393 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 303 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: A 92 ARG cc_start: 0.7742 (mmp80) cc_final: 0.7528 (mmp80) REVERT: A 147 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6950 (ptp-170) REVERT: A 175 MET cc_start: 0.7553 (ppp) cc_final: 0.7351 (ppp) REVERT: A 188 LYS cc_start: 0.8055 (tmtt) cc_final: 0.7248 (ttmt) REVERT: A 195 LEU cc_start: 0.7789 (tt) cc_final: 0.6944 (pp) REVERT: B 217 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8779 (mm) REVERT: D 86 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7524 (p90) REVERT: E 41 LYS cc_start: 0.7887 (tptp) cc_final: 0.7432 (mttt) REVERT: F 69 PHE cc_start: 0.5163 (OUTLIER) cc_final: 0.3777 (m-10) REVERT: G 282 LEU cc_start: 0.6418 (tp) cc_final: 0.5794 (tp) REVERT: I 37 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: I 70 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.7235 (ttp80) REVERT: I 151 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: I 222 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: I 246 GLU cc_start: 0.7381 (tp30) cc_final: 0.6615 (tp30) REVERT: J 34 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7452 (tppt) REVERT: J 114 LEU cc_start: 0.8748 (mm) cc_final: 0.8358 (mp) REVERT: K 170 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8278 (mm) REVERT: L 67 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: L 248 TYR cc_start: 0.7998 (p90) cc_final: 0.7529 (p90) outliers start: 90 outliers final: 66 residues processed: 370 average time/residue: 0.1725 time to fit residues: 94.5999 Evaluate side-chains 371 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 296 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 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 91 TYR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 170 LEU 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 15 GLU 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 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 61 GLN 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 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 71 ILE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 118 HIS Chi-restraints excluded: chain K residue 126 VAL 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 282 LEU 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 86 TYR Chi-restraints excluded: chain L residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 65 optimal weight: 1.9990 chunk 241 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 186 optimal weight: 0.2980 chunk 242 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** 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 = 0.4186 r_free = 0.4186 target = 0.169800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130430 restraints weight = 79657.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133899 restraints weight = 32870.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135474 restraints weight = 21012.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136534 restraints weight = 17365.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136959 restraints weight = 15027.965| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2723 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= 0.132 Angle : 0.656 15.951 29108 Z= 0.331 Chirality : 0.043 0.315 3123 Planarity : 0.004 0.058 3807 Dihedral : 4.236 29.144 2862 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.62 % Allowed : 26.95 % 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: -0.26 (0.17), residues: 2579 helix: 1.73 (0.15), residues: 1180 sheet: -1.98 (0.27), residues: 354 loop : -1.77 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 110 TYR 0.036 0.001 TYR J 145 PHE 0.021 0.001 PHE F 150 TRP 0.026 0.001 TRP A 218 HIS 0.006 0.001 HIS F 230 Details of bonding type rmsd covalent geometry : bond 0.00306 (21497) covalent geometry : angle 0.65625 (29108) hydrogen bonds : bond 0.04174 ( 1004) hydrogen bonds : angle 4.34669 ( 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 394 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 311 time to evaluate : 0.852 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 147 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7097 (ptp-170) REVERT: A 188 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7218 (ttmt) REVERT: A 195 LEU cc_start: 0.7879 (tt) cc_final: 0.7051 (pp) REVERT: B 217 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8941 (mm) REVERT: D 86 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7553 (p90) REVERT: E 41 LYS cc_start: 0.7968 (tptp) cc_final: 0.7445 (mttt) REVERT: F 69 PHE cc_start: 0.5132 (OUTLIER) cc_final: 0.3984 (m-10) REVERT: G 282 LEU cc_start: 0.6646 (tp) cc_final: 0.6072 (tp) REVERT: I 37 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: I 70 ARG cc_start: 0.7719 (ttp-110) cc_final: 0.7396 (ttp80) REVERT: I 151 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6546 (m-30) REVERT: I 222 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7533 (tp40) REVERT: I 246 GLU cc_start: 0.7551 (tp30) cc_final: 0.6691 (tp30) REVERT: J 34 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7464 (tppt) REVERT: J 114 LEU cc_start: 0.8762 (mm) cc_final: 0.8422 (mp) REVERT: K 170 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8234 (mm) REVERT: L 67 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: L 179 HIS cc_start: 0.6885 (m90) cc_final: 0.6461 (m170) REVERT: L 248 TYR cc_start: 0.8012 (p90) cc_final: 0.7449 (p90) outliers start: 83 outliers final: 67 residues processed: 372 average time/residue: 0.1743 time to fit residues: 96.6735 Evaluate side-chains 374 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 298 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 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 91 TYR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 170 LEU 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 15 GLU 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 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 42 GLU Chi-restraints excluded: chain I residue 61 GLN 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 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 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 282 LEU 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 86 TYR Chi-restraints excluded: chain L residue 108 ARG Chi-restraints excluded: chain L residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 178 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 0.0000 chunk 187 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 45 optimal weight: 0.0030 chunk 92 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN E 232 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** 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 = 0.4209 r_free = 0.4209 target = 0.171928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.133126 restraints weight = 69287.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136801 restraints weight = 28899.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138133 restraints weight = 18839.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.138925 restraints weight = 15792.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139473 restraints weight = 13904.642| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2756 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= 0.119 Angle : 0.657 16.460 29108 Z= 0.331 Chirality : 0.043 0.420 3123 Planarity : 0.003 0.058 3807 Dihedral : 4.158 28.228 2862 Min Nonbonded Distance : 1.415 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.79 % Allowed : 27.78 % 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: -0.16 (0.17), residues: 2579 helix: 1.76 (0.16), residues: 1180 sheet: -1.99 (0.26), residues: 367 loop : -1.62 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 110 TYR 0.034 0.001 TYR J 145 PHE 0.039 0.001 PHE G 146 TRP 0.026 0.001 TRP A 218 HIS 0.005 0.001 HIS F 230 Details of bonding type rmsd covalent geometry : bond 0.00266 (21497) covalent geometry : angle 0.65729 (29108) hydrogen bonds : bond 0.04056 ( 1004) hydrogen bonds : angle 4.25990 ( 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 379 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 315 time to evaluate : 0.611 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: 0.7814 (mmp80) cc_final: 0.7435 (mmp80) REVERT: A 147 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7065 (ptp-170) REVERT: A 188 LYS cc_start: 0.7925 (tmtt) cc_final: 0.7178 (ttmt) REVERT: A 195 LEU cc_start: 0.7856 (tt) cc_final: 0.7080 (pp) REVERT: B 217 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8935 (mm) REVERT: D 66 MET cc_start: 0.7694 (mmt) cc_final: 0.7478 (mmm) REVERT: E 41 LYS cc_start: 0.7831 (tptp) cc_final: 0.7361 (mttt) REVERT: E 115 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7321 (ttp-170) REVERT: F 245 MET cc_start: 0.7395 (mmm) cc_final: 0.6687 (pmm) REVERT: G 66 MET cc_start: 0.7285 (mtm) cc_final: 0.6780 (tpt) REVERT: I 37 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: I 70 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7390 (ttp80) REVERT: I 151 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6425 (m-30) REVERT: I 222 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7616 (tp40) REVERT: I 246 GLU cc_start: 0.7516 (tp30) cc_final: 0.7048 (tp30) REVERT: J 34 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7407 (tppt) REVERT: J 114 LEU cc_start: 0.8726 (mm) cc_final: 0.8431 (mp) REVERT: K 170 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8209 (mm) REVERT: L 179 HIS cc_start: 0.6769 (m90) cc_final: 0.6419 (m170) REVERT: L 248 TYR cc_start: 0.7920 (p90) cc_final: 0.7323 (p90) outliers start: 64 outliers final: 53 residues processed: 360 average time/residue: 0.1710 time to fit residues: 91.1906 Evaluate side-chains 355 residues out of total 2305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE 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 94 VAL Chi-restraints excluded: chain D residue 147 THR 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 244 VAL 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 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 54 VAL Chi-restraints excluded: chain G residue 123 ILE 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 9 GLU Chi-restraints excluded: chain I residue 37 GLU 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 197 ASP Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 257 VAL 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 284 TYR Chi-restraints excluded: chain J residue 290 ASP 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 K residue 282 LEU Chi-restraints excluded: chain L residue 6 PHE Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 108 ARG Chi-restraints excluded: chain L residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 189 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 85 optimal weight: 0.1980 chunk 128 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN E 232 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 GLN J 191 HIS ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN K 230 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.170396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130848 restraints weight = 67316.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134159 restraints weight = 30728.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135577 restraints weight = 19934.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136460 restraints weight = 16895.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136950 restraints weight = 14480.144| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2796 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= 0.136 Angle : 0.671 16.394 29108 Z= 0.338 Chirality : 0.044 0.352 3123 Planarity : 0.004 0.058 3807 Dihedral : 4.232 28.595 2862 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.97 % Allowed : 27.69 % Favored : 69.34 % 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: -0.16 (0.17), residues: 2579 helix: 1.75 (0.16), residues: 1181 sheet: -1.94 (0.28), residues: 337 loop : -1.65 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.034 0.001 TYR J 145 PHE 0.043 0.001 PHE G 146 TRP 0.026 0.001 TRP A 218 HIS 0.009 0.001 HIS J 252 Details of bonding type rmsd covalent geometry : bond 0.00315 (21497) covalent geometry : angle 0.67134 (29108) hydrogen bonds : bond 0.04147 ( 1004) hydrogen bonds : angle 4.31973 ( 2831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.20 seconds wall clock time: 70 minutes 1.48 seconds (4201.48 seconds total)