Starting phenix.real_space_refine on Mon Aug 25 07:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eky_28217/08_2025/8eky_28217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eky_28217/08_2025/8eky_28217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eky_28217/08_2025/8eky_28217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eky_28217/08_2025/8eky_28217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eky_28217/08_2025/8eky_28217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eky_28217/08_2025/8eky_28217.map" } resolution = 3.47 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= -0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14407 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 9435 2.51 5 N 2451 2.21 5 O 2691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14605 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "B" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "C" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1493 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 12, 'TRANS': 174} Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "E" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "F" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "G" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1346 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain: "H" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1346 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain: "I" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "J" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 840 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.69, per 1000 atoms: 0.18 Number of scatterers: 14605 At special positions: 0 Unit cell: (85.32, 139.32, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 2691 8.00 N 2451 7.00 C 9435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 247 " - pdb=" SG CYS M 254 " distance=2.03 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: 0.86 Conformation dependent library (CDL) restraints added in 633.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 13 sheets defined 36.9% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 104 through 107 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.594A pdb=" N GLN A 166 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 224 through 241 removed outlier: 3.735A pdb=" N THR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 107 removed outlier: 3.620A pdb=" N ARG B 107 " --> pdb=" O THR B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.582A pdb=" N ILE B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 4.202A pdb=" N PHE B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 162 Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.557A pdb=" N GLN B 166 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 167 " --> pdb=" O ARG B 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 167' Processing helix chain 'B' and resid 182 through 189 removed outlier: 3.640A pdb=" N LYS B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 241 removed outlier: 3.622A pdb=" N THR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 107 removed outlier: 3.647A pdb=" N ARG C 107 " --> pdb=" O THR C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 107' Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.785A pdb=" N ILE C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.837A pdb=" N PHE C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.728A pdb=" N GLN C 166 " --> pdb=" O PRO C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 225 through 242 Processing helix chain 'D' and resid 104 through 107 removed outlier: 3.736A pdb=" N ARG D 107 " --> pdb=" O THR D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.850A pdb=" N PHE D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 162 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'D' and resid 224 through 241 removed outlier: 3.749A pdb=" N THR D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 107 Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.521A pdb=" N ILE E 129 " --> pdb=" O PRO E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 removed outlier: 3.879A pdb=" N PHE E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 162 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 224 through 241 removed outlier: 3.540A pdb=" N THR E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 107 Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.520A pdb=" N ARG F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.767A pdb=" N PHE F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 162 Processing helix chain 'F' and resid 163 through 167 Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'F' and resid 224 through 241 removed outlier: 3.720A pdb=" N THR F 228 " --> pdb=" O SER F 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 107 removed outlier: 3.589A pdb=" N ARG G 107 " --> pdb=" O THR G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 104 through 107' Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.677A pdb=" N ILE G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 140 removed outlier: 3.978A pdb=" N PHE G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 162 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 225 through 241 Processing helix chain 'H' and resid 104 through 107 removed outlier: 3.680A pdb=" N ARG H 107 " --> pdb=" O THR H 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 152 through 161 Processing helix chain 'H' and resid 182 through 188 Processing helix chain 'H' and resid 224 through 241 Processing helix chain 'I' and resid 104 through 107 removed outlier: 3.811A pdb=" N ARG I 107 " --> pdb=" O THR I 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 104 through 107' Processing helix chain 'I' and resid 125 through 134 removed outlier: 3.525A pdb=" N ILE I 129 " --> pdb=" O PRO I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 141 removed outlier: 3.585A pdb=" N ILE I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 162 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.567A pdb=" N GLN I 166 " --> pdb=" O PRO I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 189 Processing helix chain 'I' and resid 225 through 241 Processing helix chain 'J' and resid 104 through 107 Processing helix chain 'J' and resid 125 through 134 removed outlier: 3.791A pdb=" N ILE J 129 " --> pdb=" O PRO J 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG J 134 " --> pdb=" O ALA J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 141 Processing helix chain 'J' and resid 152 through 162 Processing helix chain 'J' and resid 163 through 167 Processing helix chain 'J' and resid 182 through 189 removed outlier: 3.692A pdb=" N LYS J 186 " --> pdb=" O HIS J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 241 Processing helix chain 'M' and resid 195 through 206 removed outlier: 4.674A pdb=" N GLU M 200 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU M 201 " --> pdb=" O SER M 197 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA M 204 " --> pdb=" O GLU M 200 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY M 206 " --> pdb=" O HIS M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 234 Proline residue: M 225 - end of helix Processing helix chain 'M' and resid 251 through 257 Processing helix chain 'M' and resid 282 through 295 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.660A pdb=" N TYR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 146 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 112 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N CYS A 148 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE A 114 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 201 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 202 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 214 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE A 204 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 214 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS B 83 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.660A pdb=" N TYR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 146 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 112 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N CYS A 148 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE A 114 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 201 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 202 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 214 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE A 204 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 214 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 204 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE B 214 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 202 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 201 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 110 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL B 146 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 112 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N CYS B 148 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE B 114 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU B 177 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 102 removed outlier: 5.065A pdb=" N THR C 91 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU C 177 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 147 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL C 146 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 112 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS C 148 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE C 114 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 201 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN C 213 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN D 213 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY D 201 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N LEU D 177 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA D 147 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR D 91 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 97 through 102 removed outlier: 5.195A pdb=" N THR E 91 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU E 177 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA E 147 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL E 146 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL E 112 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS E 148 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE E 114 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY E 201 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU E 202 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE E 214 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE E 204 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 214 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE J 214 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN J 213 " --> pdb=" O ILE J 204 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY J 201 " --> pdb=" O PHE J 115 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR J 110 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL J 146 " --> pdb=" O TYR J 110 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL J 112 " --> pdb=" O VAL J 146 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS J 148 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE J 114 " --> pdb=" O CYS J 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 97 through 102 removed outlier: 4.929A pdb=" N THR F 91 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU F 177 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA F 147 " --> pdb=" O LEU F 177 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR F 110 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL F 146 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL F 112 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS F 148 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE F 114 " --> pdb=" O CYS F 148 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY F 201 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU F 202 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE F 214 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE F 204 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G 213 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 204 " --> pdb=" O GLN G 213 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY G 201 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR G 110 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL G 146 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL G 112 " --> pdb=" O VAL G 146 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N CYS G 148 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE G 114 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU G 177 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA G 147 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU G 176 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL G 93 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR G 91 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 191 through 192 removed outlier: 3.602A pdb=" N HIS F 197 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 83 through 84 removed outlier: 4.163A pdb=" N LYS H 83 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN H 213 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY H 201 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR H 110 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL H 146 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL H 112 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS H 148 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE H 114 " --> pdb=" O CYS H 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 83 through 84 removed outlier: 4.163A pdb=" N LYS H 83 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE I 214 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN I 213 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG I 200 " --> pdb=" O ASN I 217 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY I 201 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR I 110 " --> pdb=" O GLU I 144 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL I 146 " --> pdb=" O TYR I 110 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL I 112 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS I 148 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE I 114 " --> pdb=" O CYS I 148 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LEU I 177 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA I 147 " --> pdb=" O LEU I 177 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 176 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL I 93 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER I 178 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR I 91 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 97 through 102 Processing sheet with id=AB3, first strand: chain 'J' and resid 97 through 102 removed outlier: 3.532A pdb=" N VAL J 93 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 176 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 192 through 194 removed outlier: 5.771A pdb=" N TYR M 192 " --> pdb=" O LYS M 244 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP M 246 " --> pdb=" O TYR M 192 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU M 194 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE M 209 " --> pdb=" O GLY M 243 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL M 245 " --> pdb=" O PHE M 209 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS M 211 " --> pdb=" O VAL M 245 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU M 265 " --> pdb=" O GLN M 276 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN M 276 " --> pdb=" O LEU M 265 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TRP M 267 " --> pdb=" O VAL M 274 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1533 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: 1.53 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4687 1.34 - 1.46: 3067 1.46 - 1.58: 7188 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 14970 Sorted by residual: bond pdb=" N THR C 255 " pdb=" CA THR C 255 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.35e+00 bond pdb=" C ALA J 85 " pdb=" N PRO J 86 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.32e-02 5.74e+03 5.23e+00 bond pdb=" CA ALA J 85 " pdb=" C ALA J 85 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.02e-02 9.61e+03 3.89e+00 bond pdb=" CA ILE C 257 " pdb=" CB ILE C 257 " ideal model delta sigma weight residual 1.534 1.547 -0.013 6.80e-03 2.16e+04 3.42e+00 bond pdb=" CA ILE C 256 " pdb=" C ILE C 256 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.27e-02 6.20e+03 2.87e+00 ... (remaining 14965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 19891 2.04 - 4.08: 341 4.08 - 6.13: 53 6.13 - 8.17: 13 8.17 - 10.21: 4 Bond angle restraints: 20302 Sorted by residual: angle pdb=" N GLU C 254 " pdb=" CA GLU C 254 " pdb=" C GLU C 254 " ideal model delta sigma weight residual 108.14 115.61 -7.47 1.52e+00 4.33e-01 2.41e+01 angle pdb=" C ILE C 257 " pdb=" N PRO C 258 " pdb=" CA PRO C 258 " ideal model delta sigma weight residual 119.90 115.00 4.90 1.05e+00 9.07e-01 2.18e+01 angle pdb=" N THR C 255 " pdb=" CA THR C 255 " pdb=" C THR C 255 " ideal model delta sigma weight residual 110.80 120.55 -9.75 2.13e+00 2.20e-01 2.10e+01 angle pdb=" N ILE J 141 " pdb=" CA ILE J 141 " pdb=" C ILE J 141 " ideal model delta sigma weight residual 111.91 108.37 3.54 8.90e-01 1.26e+00 1.58e+01 angle pdb=" CA GLU E 227 " pdb=" CB GLU E 227 " pdb=" CG GLU E 227 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 ... (remaining 20297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 7809 16.76 - 33.52: 772 33.52 - 50.27: 180 50.27 - 67.03: 31 67.03 - 83.79: 26 Dihedral angle restraints: 8818 sinusoidal: 3591 harmonic: 5227 Sorted by residual: dihedral pdb=" CB CYS M 247 " pdb=" SG CYS M 247 " pdb=" SG CYS M 254 " pdb=" CB CYS M 254 " ideal model delta sinusoidal sigma weight residual 93.00 171.42 -78.42 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" N THR C 255 " pdb=" C THR C 255 " pdb=" CA THR C 255 " pdb=" CB THR C 255 " ideal model delta harmonic sigma weight residual 123.40 135.65 -12.25 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C THR C 255 " pdb=" N THR C 255 " pdb=" CA THR C 255 " pdb=" CB THR C 255 " ideal model delta harmonic sigma weight residual -122.00 -133.99 11.99 0 2.50e+00 1.60e-01 2.30e+01 ... (remaining 8815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2145 0.105 - 0.210: 98 0.210 - 0.315: 3 0.315 - 0.420: 0 0.420 - 0.525: 1 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA THR C 255 " pdb=" N THR C 255 " pdb=" C THR C 255 " pdb=" CB THR C 255 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA LYS C 250 " pdb=" N LYS C 250 " pdb=" C LYS C 250 " pdb=" CB LYS C 250 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE E 141 " pdb=" CA ILE E 141 " pdb=" CG1 ILE E 141 " pdb=" CG2 ILE E 141 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2244 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 257 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.81e+00 pdb=" N PRO C 258 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 170 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO G 171 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 171 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 171 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 83 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO H 84 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 84 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 84 " -0.027 5.00e-02 4.00e+02 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1820 2.75 - 3.29: 14282 3.29 - 3.82: 23301 3.82 - 4.36: 27433 4.36 - 4.90: 48620 Nonbonded interactions: 115456 Sorted by model distance: nonbonded pdb=" OE2 GLU D 127 " pdb=" NH1 ARG D 200 " model vdw 2.211 3.120 nonbonded pdb=" NE2 GLN F 213 " pdb=" OD1 ASN G 217 " model vdw 2.228 3.120 nonbonded pdb=" OD2 ASP M 246 " pdb=" OG1 THR M 248 " model vdw 2.246 3.040 nonbonded pdb=" NE2 GLN A 213 " pdb=" OD1 ASN B 217 " model vdw 2.269 3.120 nonbonded pdb=" NE2 GLN C 213 " pdb=" OD1 ASN D 217 " model vdw 2.276 3.120 ... (remaining 115451 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 76 through 242) selection = (chain 'B' and resid 76 through 242) selection = (chain 'C' and resid 76 through 242) selection = (chain 'D' and resid 76 through 242) selection = (chain 'E' and resid 76 through 242) selection = (chain 'F' and resid 76 through 242) selection = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 76 through 242) selection = (chain 'J' and resid 76 through 242) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 10.820 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.037 14971 Z= 0.181 Angle : 0.681 10.209 20304 Z= 0.366 Chirality : 0.048 0.525 2247 Planarity : 0.005 0.065 2599 Dihedral : 14.659 83.790 5467 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: -0.33 (0.20), residues: 1793 helix: 0.68 (0.22), residues: 534 sheet: -0.89 (0.22), residues: 468 loop : -0.23 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 212 TYR 0.026 0.001 TYR J 116 PHE 0.015 0.001 PHE I 114 TRP 0.031 0.002 TRP G 88 HIS 0.010 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00403 (14970) covalent geometry : angle 0.68115 (20302) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.09291 ( 2) hydrogen bonds : bond 0.17616 ( 536) hydrogen bonds : angle 5.99175 ( 1533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8151 (tp40) cc_final: 0.7886 (tp-100) REVERT: A 237 TYR cc_start: 0.8472 (t80) cc_final: 0.8225 (t80) REVERT: B 179 ASP cc_start: 0.7489 (t70) cc_final: 0.6801 (t0) REVERT: C 179 ASP cc_start: 0.7972 (t0) cc_final: 0.7514 (t0) REVERT: D 109 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7742 (mmtt) REVERT: D 116 TYR cc_start: 0.9124 (p90) cc_final: 0.8886 (p90) REVERT: D 213 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8328 (tm-30) REVERT: E 227 GLU cc_start: 0.8123 (tp30) cc_final: 0.7669 (tp30) REVERT: E 231 LEU cc_start: 0.9174 (mp) cc_final: 0.8879 (mp) REVERT: H 142 ASN cc_start: 0.8825 (t0) cc_final: 0.8616 (t0) REVERT: H 195 SER cc_start: 0.8885 (t) cc_final: 0.8564 (t) REVERT: J 179 ASP cc_start: 0.7767 (t70) cc_final: 0.7168 (t0) REVERT: J 184 ILE cc_start: 0.9021 (mp) cc_final: 0.8623 (mt) REVERT: J 190 VAL cc_start: 0.9465 (m) cc_final: 0.9112 (p) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1294 time to fit residues: 54.2877 Evaluate side-chains 244 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS C 217 ASN C 241 HIS F 233 GLN H 217 ASN J 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.077158 restraints weight = 30301.587| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.98 r_work: 0.2886 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14971 Z= 0.174 Angle : 0.577 8.944 20304 Z= 0.299 Chirality : 0.045 0.160 2247 Planarity : 0.004 0.046 2599 Dihedral : 4.129 17.677 1983 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.32 % Allowed : 8.74 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: -0.09 (0.20), residues: 1793 helix: 1.05 (0.22), residues: 543 sheet: -1.01 (0.22), residues: 474 loop : -0.04 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 107 TYR 0.013 0.001 TYR E 237 PHE 0.011 0.001 PHE D 114 TRP 0.016 0.001 TRP G 159 HIS 0.006 0.001 HIS M 250 Details of bonding type rmsd covalent geometry : bond 0.00414 (14970) covalent geometry : angle 0.57717 (20302) SS BOND : bond 0.00430 ( 1) SS BOND : angle 1.20270 ( 2) hydrogen bonds : bond 0.03771 ( 536) hydrogen bonds : angle 4.74930 ( 1533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.9016 (tp30) cc_final: 0.8790 (tp30) REVERT: A 144 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8352 (mm-30) REVERT: A 183 GLN cc_start: 0.8250 (tp40) cc_final: 0.7955 (tp-100) REVERT: A 237 TYR cc_start: 0.9016 (t80) cc_final: 0.8619 (t80) REVERT: B 116 TYR cc_start: 0.9229 (p90) cc_final: 0.8947 (p90) REVERT: B 179 ASP cc_start: 0.8136 (t70) cc_final: 0.7149 (t0) REVERT: C 179 ASP cc_start: 0.8428 (t0) cc_final: 0.8064 (t0) REVERT: D 109 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7828 (mmtt) REVERT: D 116 TYR cc_start: 0.9320 (p90) cc_final: 0.9056 (p90) REVERT: D 179 ASP cc_start: 0.8931 (t0) cc_final: 0.8625 (t0) REVERT: E 227 GLU cc_start: 0.8371 (tp30) cc_final: 0.8051 (tp30) REVERT: G 95 ASP cc_start: 0.8024 (t70) cc_final: 0.7793 (t0) REVERT: H 195 SER cc_start: 0.9208 (t) cc_final: 0.8988 (t) REVERT: J 118 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8321 (mp) REVERT: J 190 VAL cc_start: 0.9524 (m) cc_final: 0.9178 (p) REVERT: M 251 TYR cc_start: 0.7349 (p90) cc_final: 0.7120 (p90) outliers start: 21 outliers final: 12 residues processed: 270 average time/residue: 0.1516 time to fit residues: 54.2049 Evaluate side-chains 259 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 33 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS C 197 HIS C 217 ASN C 241 HIS F 233 GLN H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078135 restraints weight = 30140.298| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.00 r_work: 0.2917 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14971 Z= 0.124 Angle : 0.545 8.502 20304 Z= 0.280 Chirality : 0.044 0.184 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.972 21.135 1983 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.26 % Allowed : 11.50 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: 0.11 (0.21), residues: 1793 helix: 1.32 (0.23), residues: 543 sheet: -0.94 (0.22), residues: 474 loop : 0.01 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 173 TYR 0.011 0.001 TYR B 237 PHE 0.008 0.001 PHE I 115 TRP 0.015 0.001 TRP G 88 HIS 0.004 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00297 (14970) covalent geometry : angle 0.54466 (20302) SS BOND : bond 0.00285 ( 1) SS BOND : angle 1.26378 ( 2) hydrogen bonds : bond 0.03170 ( 536) hydrogen bonds : angle 4.52032 ( 1533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8384 (mp0) cc_final: 0.7736 (mp0) REVERT: A 144 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8388 (mm-30) REVERT: A 183 GLN cc_start: 0.8225 (tp40) cc_final: 0.7946 (tp-100) REVERT: A 237 TYR cc_start: 0.9008 (t80) cc_final: 0.8636 (t80) REVERT: B 116 TYR cc_start: 0.9247 (p90) cc_final: 0.8926 (p90) REVERT: B 179 ASP cc_start: 0.8075 (t70) cc_final: 0.7142 (t70) REVERT: C 179 ASP cc_start: 0.8443 (t0) cc_final: 0.7980 (t0) REVERT: C 240 LYS cc_start: 0.8548 (tttt) cc_final: 0.8246 (ttmt) REVERT: D 116 TYR cc_start: 0.9306 (p90) cc_final: 0.9058 (p90) REVERT: D 178 SER cc_start: 0.9352 (p) cc_final: 0.9067 (p) REVERT: D 179 ASP cc_start: 0.8875 (t0) cc_final: 0.8471 (t0) REVERT: E 227 GLU cc_start: 0.8382 (tp30) cc_final: 0.8168 (tp30) REVERT: F 83 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8728 (mmmm) REVERT: G 95 ASP cc_start: 0.8040 (t70) cc_final: 0.7788 (t0) REVERT: H 142 ASN cc_start: 0.8884 (t0) cc_final: 0.8576 (t0) REVERT: H 195 SER cc_start: 0.9278 (t) cc_final: 0.9060 (t) REVERT: J 118 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8295 (mp) REVERT: J 179 ASP cc_start: 0.8473 (t70) cc_final: 0.7762 (t0) REVERT: J 190 VAL cc_start: 0.9522 (m) cc_final: 0.9178 (p) outliers start: 20 outliers final: 15 residues processed: 295 average time/residue: 0.1457 time to fit residues: 57.9595 Evaluate side-chains 266 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 250 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 161 ASN F 156 HIS F 233 GLN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** 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 = 0.3374 r_free = 0.3374 target = 0.099102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077988 restraints weight = 30017.574| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.89 r_work: 0.2919 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14971 Z= 0.190 Angle : 0.568 9.458 20304 Z= 0.294 Chirality : 0.045 0.171 2247 Planarity : 0.004 0.044 2599 Dihedral : 4.071 20.529 1983 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.95 % Allowed : 13.83 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: 0.07 (0.21), residues: 1793 helix: 1.32 (0.23), residues: 549 sheet: -1.04 (0.22), residues: 474 loop : 0.03 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 212 TYR 0.013 0.001 TYR E 237 PHE 0.012 0.001 PHE D 114 TRP 0.016 0.001 TRP G 88 HIS 0.005 0.001 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00455 (14970) covalent geometry : angle 0.56823 (20302) SS BOND : bond 0.00419 ( 1) SS BOND : angle 1.43269 ( 2) hydrogen bonds : bond 0.03274 ( 536) hydrogen bonds : angle 4.53778 ( 1533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8542 (mp0) cc_final: 0.7918 (mp0) REVERT: A 237 TYR cc_start: 0.9001 (t80) cc_final: 0.8694 (t80) REVERT: B 179 ASP cc_start: 0.8054 (t70) cc_final: 0.7276 (t0) REVERT: C 179 ASP cc_start: 0.8362 (t0) cc_final: 0.7995 (t0) REVERT: C 240 LYS cc_start: 0.8673 (tttt) cc_final: 0.8354 (ttmt) REVERT: D 179 ASP cc_start: 0.8800 (t0) cc_final: 0.8520 (t0) REVERT: E 233 GLN cc_start: 0.8433 (mt0) cc_final: 0.8210 (mt0) REVERT: F 144 GLU cc_start: 0.8072 (mp0) cc_final: 0.7783 (mp0) REVERT: G 95 ASP cc_start: 0.7970 (t70) cc_final: 0.7711 (t0) REVERT: G 150 VAL cc_start: 0.8851 (m) cc_final: 0.8563 (t) REVERT: H 134 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8589 (mtm110) REVERT: H 137 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: H 142 ASN cc_start: 0.8946 (t0) cc_final: 0.8626 (t0) REVERT: I 136 GLU cc_start: 0.8379 (mp0) cc_final: 0.8174 (mp0) REVERT: J 118 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8284 (mp) REVERT: J 179 ASP cc_start: 0.8398 (t70) cc_final: 0.7867 (t0) REVERT: J 190 VAL cc_start: 0.9518 (m) cc_final: 0.9190 (p) outliers start: 31 outliers final: 20 residues processed: 276 average time/residue: 0.1497 time to fit residues: 55.8087 Evaluate side-chains 265 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 241 HIS Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 4 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN H 217 ASN ** M 229 GLN ** 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 = 0.3369 r_free = 0.3369 target = 0.098927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.077447 restraints weight = 30101.682| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.97 r_work: 0.2895 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14971 Z= 0.136 Angle : 0.552 9.528 20304 Z= 0.284 Chirality : 0.044 0.193 2247 Planarity : 0.004 0.045 2599 Dihedral : 3.952 20.143 1983 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.14 % Allowed : 14.71 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: 0.21 (0.21), residues: 1793 helix: 1.52 (0.23), residues: 545 sheet: -0.99 (0.23), residues: 474 loop : 0.07 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 212 TYR 0.012 0.001 TYR B 237 PHE 0.010 0.001 PHE M 212 TRP 0.017 0.001 TRP G 88 HIS 0.005 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00327 (14970) covalent geometry : angle 0.55156 (20302) SS BOND : bond 0.00387 ( 1) SS BOND : angle 1.77670 ( 2) hydrogen bonds : bond 0.02950 ( 536) hydrogen bonds : angle 4.40915 ( 1533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8403 (mp0) cc_final: 0.7687 (mp0) REVERT: A 144 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8442 (mm-30) REVERT: A 237 TYR cc_start: 0.9017 (t80) cc_final: 0.8658 (t80) REVERT: B 179 ASP cc_start: 0.8209 (t70) cc_final: 0.7485 (t70) REVERT: C 179 ASP cc_start: 0.8444 (t0) cc_final: 0.8006 (t0) REVERT: C 210 ILE cc_start: 0.9405 (mm) cc_final: 0.8739 (tt) REVERT: C 240 LYS cc_start: 0.8577 (tttt) cc_final: 0.8275 (ttmt) REVERT: D 178 SER cc_start: 0.9381 (p) cc_final: 0.9057 (p) REVERT: D 179 ASP cc_start: 0.8838 (t0) cc_final: 0.8487 (t0) REVERT: D 213 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8778 (tm-30) REVERT: E 139 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8194 (mtt180) REVERT: E 143 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8487 (p) REVERT: E 183 GLN cc_start: 0.8290 (tp40) cc_final: 0.7902 (tp40) REVERT: E 233 GLN cc_start: 0.8575 (mt0) cc_final: 0.8324 (mt0) REVERT: F 137 GLU cc_start: 0.8422 (mp0) cc_final: 0.8069 (mp0) REVERT: G 95 ASP cc_start: 0.8036 (t70) cc_final: 0.7683 (t0) REVERT: G 137 GLU cc_start: 0.7995 (pm20) cc_final: 0.7756 (pm20) REVERT: G 150 VAL cc_start: 0.8915 (m) cc_final: 0.8612 (t) REVERT: H 134 ARG cc_start: 0.8893 (mtp-110) cc_final: 0.8524 (mtm110) REVERT: H 137 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: H 142 ASN cc_start: 0.8906 (t0) cc_final: 0.8554 (t0) REVERT: I 136 GLU cc_start: 0.8531 (mp0) cc_final: 0.8235 (mp0) REVERT: J 118 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8393 (mp) REVERT: J 179 ASP cc_start: 0.8499 (t70) cc_final: 0.7867 (t0) REVERT: J 190 VAL cc_start: 0.9530 (m) cc_final: 0.9172 (p) outliers start: 34 outliers final: 23 residues processed: 287 average time/residue: 0.1506 time to fit residues: 58.2156 Evaluate side-chains 276 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 0.0470 chunk 22 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN F 233 GLN F 241 HIS H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.077855 restraints weight = 30092.996| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.98 r_work: 0.2914 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14971 Z= 0.125 Angle : 0.547 10.349 20304 Z= 0.282 Chirality : 0.044 0.192 2247 Planarity : 0.004 0.045 2599 Dihedral : 3.887 19.719 1983 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.39 % Allowed : 15.78 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: 0.30 (0.21), residues: 1793 helix: 1.55 (0.23), residues: 549 sheet: -0.95 (0.23), residues: 474 loop : 0.15 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 212 TYR 0.015 0.001 TYR E 237 PHE 0.008 0.001 PHE D 114 TRP 0.019 0.001 TRP G 88 HIS 0.005 0.001 HIS H 197 Details of bonding type rmsd covalent geometry : bond 0.00299 (14970) covalent geometry : angle 0.54680 (20302) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.70181 ( 2) hydrogen bonds : bond 0.02837 ( 536) hydrogen bonds : angle 4.36418 ( 1533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8425 (mp0) cc_final: 0.7659 (mp0) REVERT: A 237 TYR cc_start: 0.9015 (t80) cc_final: 0.8658 (t80) REVERT: B 179 ASP cc_start: 0.8138 (t70) cc_final: 0.7417 (t70) REVERT: C 179 ASP cc_start: 0.8407 (t0) cc_final: 0.8017 (t0) REVERT: C 210 ILE cc_start: 0.9398 (mm) cc_final: 0.8736 (tt) REVERT: C 240 LYS cc_start: 0.8542 (tttt) cc_final: 0.8240 (ttmt) REVERT: D 178 SER cc_start: 0.9433 (p) cc_final: 0.9166 (p) REVERT: D 179 ASP cc_start: 0.8776 (t0) cc_final: 0.8376 (t0) REVERT: E 139 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8164 (mtt180) REVERT: E 143 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8504 (p) REVERT: E 183 GLN cc_start: 0.8299 (tp40) cc_final: 0.7881 (tp40) REVERT: E 227 GLU cc_start: 0.8295 (tp30) cc_final: 0.8030 (tp30) REVERT: E 231 LEU cc_start: 0.9080 (mp) cc_final: 0.8873 (mp) REVERT: E 233 GLN cc_start: 0.8563 (mt0) cc_final: 0.8312 (mt0) REVERT: F 137 GLU cc_start: 0.8448 (mp0) cc_final: 0.8110 (mp0) REVERT: F 144 GLU cc_start: 0.7954 (mp0) cc_final: 0.7637 (mp0) REVERT: G 95 ASP cc_start: 0.7931 (t70) cc_final: 0.7571 (t0) REVERT: G 137 GLU cc_start: 0.8112 (pm20) cc_final: 0.7843 (pm20) REVERT: G 150 VAL cc_start: 0.8896 (m) cc_final: 0.8567 (t) REVERT: H 137 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: H 142 ASN cc_start: 0.8897 (t0) cc_final: 0.8541 (t0) REVERT: I 136 GLU cc_start: 0.8511 (mp0) cc_final: 0.8219 (mp0) REVERT: J 118 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8399 (mp) REVERT: J 179 ASP cc_start: 0.8501 (t70) cc_final: 0.7853 (t0) REVERT: J 180 LEU cc_start: 0.9222 (tp) cc_final: 0.8965 (tt) REVERT: J 190 VAL cc_start: 0.9523 (m) cc_final: 0.9178 (p) outliers start: 38 outliers final: 24 residues processed: 284 average time/residue: 0.1565 time to fit residues: 59.1342 Evaluate side-chains 278 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain M residue 274 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 30.0000 chunk 5 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.077659 restraints weight = 30017.632| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.98 r_work: 0.2910 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14971 Z= 0.129 Angle : 0.558 8.453 20304 Z= 0.287 Chirality : 0.044 0.189 2247 Planarity : 0.004 0.045 2599 Dihedral : 3.860 19.571 1983 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.14 % Allowed : 16.34 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: 0.31 (0.21), residues: 1793 helix: 1.63 (0.23), residues: 545 sheet: -0.96 (0.23), residues: 474 loop : 0.11 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 134 TYR 0.013 0.001 TYR B 237 PHE 0.009 0.001 PHE D 114 TRP 0.021 0.001 TRP G 88 HIS 0.005 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00312 (14970) covalent geometry : angle 0.55818 (20302) SS BOND : bond 0.00320 ( 1) SS BOND : angle 1.64584 ( 2) hydrogen bonds : bond 0.02790 ( 536) hydrogen bonds : angle 4.34857 ( 1533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8423 (mp0) cc_final: 0.7642 (mp0) REVERT: A 237 TYR cc_start: 0.9001 (t80) cc_final: 0.8638 (t80) REVERT: B 179 ASP cc_start: 0.8117 (t70) cc_final: 0.7380 (t70) REVERT: B 240 LYS cc_start: 0.6593 (pptt) cc_final: 0.5138 (pptt) REVERT: C 165 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.8316 (tpp-160) REVERT: C 179 ASP cc_start: 0.8484 (t0) cc_final: 0.8035 (t0) REVERT: C 210 ILE cc_start: 0.9397 (mm) cc_final: 0.8753 (tt) REVERT: C 240 LYS cc_start: 0.8526 (tttt) cc_final: 0.8234 (ttmt) REVERT: D 178 SER cc_start: 0.9474 (p) cc_final: 0.9217 (p) REVERT: D 179 ASP cc_start: 0.8754 (t0) cc_final: 0.8329 (t0) REVERT: D 213 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8819 (tm-30) REVERT: E 127 GLU cc_start: 0.8573 (pm20) cc_final: 0.8329 (mm-30) REVERT: E 139 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8183 (mtt180) REVERT: E 143 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8494 (p) REVERT: E 183 GLN cc_start: 0.8345 (tp40) cc_final: 0.7939 (tp40) REVERT: E 233 GLN cc_start: 0.8563 (mt0) cc_final: 0.8325 (mt0) REVERT: F 137 GLU cc_start: 0.8494 (mp0) cc_final: 0.8182 (mp0) REVERT: F 144 GLU cc_start: 0.7975 (mp0) cc_final: 0.7621 (mp0) REVERT: G 95 ASP cc_start: 0.7908 (t70) cc_final: 0.7542 (t0) REVERT: G 150 VAL cc_start: 0.8873 (m) cc_final: 0.8555 (t) REVERT: H 134 ARG cc_start: 0.9070 (mtm110) cc_final: 0.8840 (mtm110) REVERT: H 142 ASN cc_start: 0.8873 (t0) cc_final: 0.8514 (t0) REVERT: I 136 GLU cc_start: 0.8525 (mp0) cc_final: 0.8221 (mp0) REVERT: J 118 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8448 (mp) REVERT: J 179 ASP cc_start: 0.8478 (t70) cc_final: 0.7908 (t0) REVERT: J 180 LEU cc_start: 0.9222 (tp) cc_final: 0.8952 (tt) REVERT: J 190 VAL cc_start: 0.9524 (m) cc_final: 0.9174 (p) outliers start: 34 outliers final: 24 residues processed: 284 average time/residue: 0.1581 time to fit residues: 59.8569 Evaluate side-chains 282 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain M residue 262 TYR Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 276 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.074494 restraints weight = 30695.834| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.92 r_work: 0.2846 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14971 Z= 0.266 Angle : 0.638 11.631 20304 Z= 0.331 Chirality : 0.047 0.211 2247 Planarity : 0.004 0.045 2599 Dihedral : 4.285 20.245 1983 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.39 % Allowed : 16.91 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: -0.11 (0.21), residues: 1793 helix: 1.17 (0.22), residues: 567 sheet: -1.21 (0.24), residues: 440 loop : -0.15 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 134 TYR 0.016 0.002 TYR E 237 PHE 0.015 0.002 PHE D 114 TRP 0.020 0.002 TRP G 88 HIS 0.008 0.001 HIS G 182 Details of bonding type rmsd covalent geometry : bond 0.00636 (14970) covalent geometry : angle 0.63807 (20302) SS BOND : bond 0.00408 ( 1) SS BOND : angle 1.53324 ( 2) hydrogen bonds : bond 0.03520 ( 536) hydrogen bonds : angle 4.65489 ( 1533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8441 (mp0) cc_final: 0.7674 (mp0) REVERT: A 237 TYR cc_start: 0.9021 (t80) cc_final: 0.8771 (t80) REVERT: B 179 ASP cc_start: 0.8398 (t70) cc_final: 0.7414 (t0) REVERT: C 165 ARG cc_start: 0.8721 (tpp-160) cc_final: 0.8483 (tpp-160) REVERT: C 179 ASP cc_start: 0.8484 (t0) cc_final: 0.8232 (t0) REVERT: C 240 LYS cc_start: 0.8666 (tttt) cc_final: 0.8371 (ttmt) REVERT: D 179 ASP cc_start: 0.8905 (t0) cc_final: 0.8558 (t0) REVERT: D 213 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8805 (tm-30) REVERT: E 127 GLU cc_start: 0.8722 (pm20) cc_final: 0.8364 (mm-30) REVERT: E 139 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8234 (mtt180) REVERT: E 143 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8461 (p) REVERT: E 227 GLU cc_start: 0.8344 (tp30) cc_final: 0.8098 (tp30) REVERT: E 233 GLN cc_start: 0.8575 (mt0) cc_final: 0.8338 (mt0) REVERT: F 137 GLU cc_start: 0.8539 (mp0) cc_final: 0.8158 (mp0) REVERT: G 95 ASP cc_start: 0.8005 (t70) cc_final: 0.7595 (t0) REVERT: H 134 ARG cc_start: 0.8923 (mtm110) cc_final: 0.8440 (ttp-110) REVERT: I 136 GLU cc_start: 0.8537 (mp0) cc_final: 0.8247 (mp0) REVERT: J 118 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8578 (mp) REVERT: J 179 ASP cc_start: 0.8503 (t70) cc_final: 0.8000 (t0) outliers start: 38 outliers final: 27 residues processed: 266 average time/residue: 0.1445 time to fit residues: 51.5609 Evaluate side-chains 259 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 276 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 173 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 9 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.076522 restraints weight = 30321.561| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.98 r_work: 0.2885 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14971 Z= 0.144 Angle : 0.582 8.376 20304 Z= 0.300 Chirality : 0.045 0.313 2247 Planarity : 0.004 0.046 2599 Dihedral : 4.054 19.981 1983 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.07 % Allowed : 17.54 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: 0.14 (0.21), residues: 1793 helix: 1.55 (0.23), residues: 544 sheet: -1.15 (0.23), residues: 474 loop : 0.03 (0.25), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 165 TYR 0.013 0.001 TYR B 237 PHE 0.008 0.001 PHE D 114 TRP 0.018 0.001 TRP G 88 HIS 0.006 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00348 (14970) covalent geometry : angle 0.58227 (20302) SS BOND : bond 0.00230 ( 1) SS BOND : angle 1.73533 ( 2) hydrogen bonds : bond 0.02959 ( 536) hydrogen bonds : angle 4.44471 ( 1533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8432 (mp0) cc_final: 0.7708 (mp0) REVERT: A 237 TYR cc_start: 0.9019 (t80) cc_final: 0.8714 (t80) REVERT: B 172 ILE cc_start: 0.9119 (mm) cc_final: 0.8903 (mm) REVERT: B 179 ASP cc_start: 0.8197 (t70) cc_final: 0.7468 (t70) REVERT: B 240 LYS cc_start: 0.6517 (pptt) cc_final: 0.5030 (pptt) REVERT: C 165 ARG cc_start: 0.8536 (tpp-160) cc_final: 0.8305 (tpp-160) REVERT: C 179 ASP cc_start: 0.8471 (t0) cc_final: 0.8043 (t0) REVERT: C 240 LYS cc_start: 0.8612 (tttt) cc_final: 0.8301 (ttmt) REVERT: D 179 ASP cc_start: 0.8777 (t0) cc_final: 0.8408 (t0) REVERT: D 213 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8778 (tm-30) REVERT: E 127 GLU cc_start: 0.8742 (pm20) cc_final: 0.8308 (mm-30) REVERT: E 136 GLU cc_start: 0.8362 (tp30) cc_final: 0.8060 (tp30) REVERT: E 139 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8197 (mtt180) REVERT: E 143 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8494 (p) REVERT: E 233 GLN cc_start: 0.8587 (mt0) cc_final: 0.8349 (mt0) REVERT: F 137 GLU cc_start: 0.8578 (mp0) cc_final: 0.8275 (mp0) REVERT: F 144 GLU cc_start: 0.8050 (mp0) cc_final: 0.7761 (mp0) REVERT: G 95 ASP cc_start: 0.7907 (t70) cc_final: 0.7461 (t0) REVERT: H 134 ARG cc_start: 0.8870 (mtm110) cc_final: 0.8388 (ttp-110) REVERT: H 142 ASN cc_start: 0.8925 (t0) cc_final: 0.8524 (t0) REVERT: I 136 GLU cc_start: 0.8513 (mp0) cc_final: 0.8214 (mp0) REVERT: I 179 ASP cc_start: 0.7843 (t70) cc_final: 0.7587 (t70) REVERT: J 118 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8522 (mp) REVERT: J 179 ASP cc_start: 0.8448 (t70) cc_final: 0.7963 (t0) REVERT: J 180 LEU cc_start: 0.9267 (tp) cc_final: 0.9056 (tt) outliers start: 33 outliers final: 24 residues processed: 276 average time/residue: 0.1500 time to fit residues: 55.4806 Evaluate side-chains 275 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 291 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 104 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN F 241 HIS ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.077602 restraints weight = 30036.534| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.97 r_work: 0.2903 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14971 Z= 0.123 Angle : 0.578 8.154 20304 Z= 0.297 Chirality : 0.045 0.308 2247 Planarity : 0.004 0.046 2599 Dihedral : 3.924 19.669 1983 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.95 % Allowed : 18.10 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: 0.26 (0.21), residues: 1793 helix: 1.58 (0.23), residues: 548 sheet: -1.07 (0.23), residues: 474 loop : 0.14 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 212 TYR 0.020 0.001 TYR E 237 PHE 0.010 0.001 PHE M 212 TRP 0.018 0.001 TRP G 88 HIS 0.006 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00300 (14970) covalent geometry : angle 0.57778 (20302) SS BOND : bond 0.00270 ( 1) SS BOND : angle 1.89622 ( 2) hydrogen bonds : bond 0.02802 ( 536) hydrogen bonds : angle 4.34667 ( 1533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8435 (mp0) cc_final: 0.7707 (mp0) REVERT: A 217 ASN cc_start: 0.8550 (m-40) cc_final: 0.8324 (t0) REVERT: A 237 TYR cc_start: 0.9007 (t80) cc_final: 0.8695 (t80) REVERT: B 172 ILE cc_start: 0.9112 (mm) cc_final: 0.8874 (mm) REVERT: B 179 ASP cc_start: 0.8100 (t70) cc_final: 0.7379 (t70) REVERT: B 240 LYS cc_start: 0.6443 (pptt) cc_final: 0.5002 (pptt) REVERT: C 165 ARG cc_start: 0.8517 (tpp-160) cc_final: 0.8316 (tpp-160) REVERT: C 179 ASP cc_start: 0.8370 (t0) cc_final: 0.7913 (t0) REVERT: C 240 LYS cc_start: 0.8542 (tttt) cc_final: 0.8250 (ttmt) REVERT: D 179 ASP cc_start: 0.8733 (t0) cc_final: 0.8369 (t0) REVERT: E 127 GLU cc_start: 0.8723 (pm20) cc_final: 0.8240 (mm-30) REVERT: E 139 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8183 (mtt180) REVERT: E 143 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8508 (p) REVERT: E 227 GLU cc_start: 0.8299 (tp30) cc_final: 0.8026 (tp30) REVERT: E 233 GLN cc_start: 0.8589 (mt0) cc_final: 0.8350 (mt0) REVERT: F 137 GLU cc_start: 0.8619 (mp0) cc_final: 0.8342 (mp0) REVERT: G 95 ASP cc_start: 0.7854 (t70) cc_final: 0.7392 (t0) REVERT: H 134 ARG cc_start: 0.8851 (mtm110) cc_final: 0.8540 (ttp80) REVERT: H 142 ASN cc_start: 0.8942 (t0) cc_final: 0.8588 (t0) REVERT: H 178 SER cc_start: 0.9151 (t) cc_final: 0.8630 (p) REVERT: I 136 GLU cc_start: 0.8525 (mp0) cc_final: 0.8231 (mp0) REVERT: J 179 ASP cc_start: 0.8425 (t70) cc_final: 0.7942 (t0) REVERT: J 180 LEU cc_start: 0.9228 (tp) cc_final: 0.9013 (tt) REVERT: J 227 GLU cc_start: 0.8044 (tp30) cc_final: 0.7844 (tp30) outliers start: 31 outliers final: 24 residues processed: 270 average time/residue: 0.1365 time to fit residues: 49.2929 Evaluate side-chains 272 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 262 TYR Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 291 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 98 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.077526 restraints weight = 29968.902| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.96 r_work: 0.2903 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14971 Z= 0.133 Angle : 0.595 9.083 20304 Z= 0.305 Chirality : 0.045 0.306 2247 Planarity : 0.004 0.046 2599 Dihedral : 3.910 19.420 1983 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.01 % Allowed : 17.79 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 aren not related in a simple way. whole: 0.27 (0.21), residues: 1793 helix: 1.63 (0.23), residues: 544 sheet: -1.04 (0.23), residues: 474 loop : 0.11 (0.25), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 223 TYR 0.013 0.001 TYR B 237 PHE 0.008 0.001 PHE D 114 TRP 0.024 0.001 TRP G 88 HIS 0.007 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00325 (14970) covalent geometry : angle 0.59512 (20302) SS BOND : bond 0.00170 ( 1) SS BOND : angle 1.59007 ( 2) hydrogen bonds : bond 0.02807 ( 536) hydrogen bonds : angle 4.32299 ( 1533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2568.50 seconds wall clock time: 44 minutes 59.54 seconds (2699.54 seconds total)