Starting phenix.real_space_refine on Sun May 25 01:34:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eky_28217/05_2025/8eky_28217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eky_28217/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8eky_28217/05_2025/8eky_28217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eky_28217/05_2025/8eky_28217.map" model { file = "/net/cci-nas-00/data/ceres_data/8eky_28217/05_2025/8eky_28217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eky_28217/05_2025/8eky_28217.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.60, per 1000 atoms: 0.52 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: 3.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.74 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: 3.82 Time building geometry restraints manager: 3.62 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.610 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), 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 TRP 0.031 0.002 TRP G 88 HIS 0.010 0.001 HIS F 241 PHE 0.015 0.001 PHE I 114 TYR 0.026 0.001 TYR J 116 ARG 0.010 0.001 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.17616 ( 536) hydrogen bonds : angle 5.99175 ( 1533) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.09291 ( 2) covalent geometry : bond 0.00403 (14970) covalent geometry : angle 0.68115 (20302) *********************** 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 : 1.666 Fit side-chains 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: 0.7743 (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: 0.8565 (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: 0.8622 (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: 0.3419 time to fit residues: 142.4813 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 : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 ASN C 241 HIS F 233 GLN H 217 ASN J 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.077796 restraints weight = 30223.276| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.03 r_work: 0.2904 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14971 Z= 0.149 Angle : 0.567 9.034 20304 Z= 0.294 Chirality : 0.044 0.162 2247 Planarity : 0.004 0.045 2599 Dihedral : 4.062 17.477 1983 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.13 % Allowed : 9.05 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1793 helix: 1.07 (0.22), residues: 543 sheet: -0.95 (0.22), residues: 474 loop : -0.03 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 159 HIS 0.006 0.001 HIS M 250 PHE 0.010 0.001 PHE I 114 TYR 0.012 0.001 TYR E 237 ARG 0.007 0.000 ARG E 107 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 536) hydrogen bonds : angle 4.71455 ( 1533) SS BOND : bond 0.00401 ( 1) SS BOND : angle 1.17774 ( 2) covalent geometry : bond 0.00353 (14970) covalent geometry : angle 0.56692 (20302) *********************** 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 282 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.9009 (tp30) cc_final: 0.8780 (tp30) REVERT: A 144 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 183 GLN cc_start: 0.8228 (tp40) cc_final: 0.7923 (tp-100) REVERT: A 237 TYR cc_start: 0.9012 (t80) cc_final: 0.8604 (t80) REVERT: B 116 TYR cc_start: 0.9244 (p90) cc_final: 0.9033 (p90) REVERT: B 179 ASP cc_start: 0.8082 (t70) cc_final: 0.7127 (t0) REVERT: C 179 ASP cc_start: 0.8417 (t0) cc_final: 0.8000 (t0) REVERT: D 116 TYR cc_start: 0.9314 (p90) cc_final: 0.9032 (p90) REVERT: D 178 SER cc_start: 0.9182 (p) cc_final: 0.8851 (p) REVERT: D 179 ASP cc_start: 0.8900 (t0) cc_final: 0.8572 (t0) REVERT: E 227 GLU cc_start: 0.8353 (tp30) cc_final: 0.8043 (tp30) REVERT: H 142 ASN cc_start: 0.8824 (t0) cc_final: 0.8545 (t0) REVERT: H 195 SER cc_start: 0.9215 (t) cc_final: 0.8997 (t) REVERT: J 190 VAL cc_start: 0.9518 (m) cc_final: 0.9181 (p) REVERT: M 251 TYR cc_start: 0.7376 (p90) cc_final: 0.7138 (p90) outliers start: 18 outliers final: 10 residues processed: 273 average time/residue: 0.3604 time to fit residues: 131.1417 Evaluate side-chains 262 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 252 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS 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 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 145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 48 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.099285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.077614 restraints weight = 30102.029| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.00 r_work: 0.2899 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14971 Z= 0.146 Angle : 0.552 8.379 20304 Z= 0.284 Chirality : 0.044 0.186 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.997 21.678 1983 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.45 % Allowed : 11.82 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1793 helix: 1.31 (0.22), residues: 543 sheet: -0.95 (0.22), residues: 474 loop : -0.03 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 88 HIS 0.004 0.001 HIS F 241 PHE 0.010 0.001 PHE I 114 TYR 0.011 0.001 TYR B 237 ARG 0.005 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 536) hydrogen bonds : angle 4.53136 ( 1533) SS BOND : bond 0.00355 ( 1) SS BOND : angle 1.29677 ( 2) covalent geometry : bond 0.00351 (14970) covalent geometry : angle 0.55164 (20302) *********************** 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 298 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8385 (mp0) cc_final: 0.7718 (mp0) REVERT: A 144 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 183 GLN cc_start: 0.8221 (tp40) cc_final: 0.7928 (tp-100) REVERT: A 237 TYR cc_start: 0.9019 (t80) cc_final: 0.8648 (t80) REVERT: B 116 TYR cc_start: 0.9256 (p90) cc_final: 0.8928 (p90) REVERT: B 179 ASP cc_start: 0.8214 (t70) cc_final: 0.7179 (t0) REVERT: C 179 ASP cc_start: 0.8455 (t0) cc_final: 0.8008 (t0) REVERT: C 195 SER cc_start: 0.9090 (t) cc_final: 0.8889 (m) REVERT: C 240 LYS cc_start: 0.8584 (tttt) cc_final: 0.8282 (ttmt) REVERT: D 116 TYR cc_start: 0.9312 (p90) cc_final: 0.9065 (p90) REVERT: D 178 SER cc_start: 0.9302 (p) cc_final: 0.8978 (p) REVERT: D 179 ASP cc_start: 0.8884 (t0) cc_final: 0.8459 (t0) REVERT: E 136 GLU cc_start: 0.8291 (tp30) cc_final: 0.7978 (tp30) REVERT: E 227 GLU cc_start: 0.8426 (tp30) cc_final: 0.8199 (tp30) REVERT: F 83 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8726 (mmmm) REVERT: H 142 ASN cc_start: 0.8875 (t0) cc_final: 0.8565 (t0) REVERT: H 195 SER cc_start: 0.9278 (t) cc_final: 0.9057 (t) REVERT: J 118 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8420 (mp) REVERT: J 179 ASP cc_start: 0.8498 (t70) cc_final: 0.7791 (t0) REVERT: J 190 VAL cc_start: 0.9524 (m) cc_final: 0.9172 (p) outliers start: 23 outliers final: 17 residues processed: 291 average time/residue: 0.3459 time to fit residues: 134.5166 Evaluate side-chains 265 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 G residue 118 LEU 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 165 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 171 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 3 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS E 161 ASN F 233 GLN ** 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 = 0.3383 r_free = 0.3383 target = 0.099745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078639 restraints weight = 29765.836| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.82 r_work: 0.2933 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1509 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= 0.164 Angle : 0.553 9.481 20304 Z= 0.286 Chirality : 0.044 0.157 2247 Planarity : 0.004 0.044 2599 Dihedral : 4.005 20.559 1983 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.01 % Allowed : 13.45 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1793 helix: 1.38 (0.23), residues: 549 sheet: -0.98 (0.22), residues: 474 loop : 0.06 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 88 HIS 0.005 0.001 HIS B 182 PHE 0.010 0.001 PHE D 114 TYR 0.013 0.001 TYR E 237 ARG 0.005 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 536) hydrogen bonds : angle 4.47777 ( 1533) SS BOND : bond 0.00432 ( 1) SS BOND : angle 1.53817 ( 2) covalent geometry : bond 0.00393 (14970) covalent geometry : angle 0.55275 (20302) *********************** 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 293 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 1.717 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8512 (mp0) cc_final: 0.7865 (mp0) REVERT: A 183 GLN cc_start: 0.8399 (tp40) cc_final: 0.8160 (tp-100) REVERT: A 237 TYR cc_start: 0.8978 (t80) cc_final: 0.8665 (t80) REVERT: B 179 ASP cc_start: 0.8043 (t70) cc_final: 0.7308 (t70) REVERT: C 179 ASP cc_start: 0.8337 (t0) cc_final: 0.7965 (t0) REVERT: C 240 LYS cc_start: 0.8664 (tttt) cc_final: 0.8344 (ttmt) REVERT: D 178 SER cc_start: 0.9308 (p) cc_final: 0.9074 (p) REVERT: D 179 ASP cc_start: 0.8777 (t0) cc_final: 0.8497 (t0) REVERT: E 183 GLN cc_start: 0.8499 (tp40) cc_final: 0.8138 (tp40) REVERT: F 144 GLU cc_start: 0.8051 (mp0) cc_final: 0.7762 (mp0) REVERT: F 173 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7712 (mtm180) REVERT: G 150 VAL cc_start: 0.8830 (m) cc_final: 0.8540 (t) REVERT: H 137 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: H 142 ASN cc_start: 0.8922 (t0) cc_final: 0.8600 (t0) REVERT: J 118 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8367 (mp) REVERT: J 179 ASP cc_start: 0.8379 (t70) cc_final: 0.7796 (t0) REVERT: J 190 VAL cc_start: 0.9510 (m) cc_final: 0.9186 (p) outliers start: 32 outliers final: 22 residues processed: 282 average time/residue: 0.3785 time to fit residues: 143.6915 Evaluate side-chains 265 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 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 G residue 118 LEU Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 97 GLU 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 5 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.0060 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 170 optimal weight: 0.0980 chunk 144 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3413 r_free = 0.3413 target = 0.101996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.080425 restraints weight = 29953.651| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.96 r_work: 0.2946 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14971 Z= 0.096 Angle : 0.533 10.196 20304 Z= 0.274 Chirality : 0.043 0.186 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.782 19.973 1983 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.45 % Allowed : 14.64 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1793 helix: 1.63 (0.23), residues: 545 sheet: -0.81 (0.23), residues: 474 loop : 0.16 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 88 HIS 0.004 0.001 HIS H 197 PHE 0.007 0.001 PHE J 154 TYR 0.013 0.001 TYR B 237 ARG 0.007 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.02628 ( 536) hydrogen bonds : angle 4.29478 ( 1533) SS BOND : bond 0.00272 ( 1) SS BOND : angle 1.64142 ( 2) covalent geometry : bond 0.00220 (14970) covalent geometry : angle 0.53312 (20302) *********************** 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 303 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8391 (mp0) cc_final: 0.7665 (mp0) REVERT: A 217 ASN cc_start: 0.8540 (m-40) cc_final: 0.8192 (t0) REVERT: A 237 TYR cc_start: 0.8999 (t80) cc_final: 0.8619 (t80) REVERT: B 179 ASP cc_start: 0.8113 (t70) cc_final: 0.7345 (t70) REVERT: C 179 ASP cc_start: 0.8370 (t0) cc_final: 0.7960 (t0) REVERT: C 240 LYS cc_start: 0.8499 (tttt) cc_final: 0.8194 (ttmt) REVERT: D 178 SER cc_start: 0.9422 (p) cc_final: 0.9167 (p) REVERT: D 179 ASP cc_start: 0.8706 (t0) cc_final: 0.8393 (t0) REVERT: E 127 GLU cc_start: 0.8608 (pm20) cc_final: 0.8229 (mm-30) REVERT: E 139 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8175 (mtt180) REVERT: E 183 GLN cc_start: 0.8284 (tp40) cc_final: 0.7812 (tp40) REVERT: G 137 GLU cc_start: 0.8151 (pm20) cc_final: 0.7927 (pm20) REVERT: H 137 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: H 142 ASN cc_start: 0.8869 (t0) cc_final: 0.8531 (t0) REVERT: J 179 ASP cc_start: 0.8495 (t70) cc_final: 0.7727 (t0) REVERT: J 180 LEU cc_start: 0.9105 (tp) cc_final: 0.8848 (tt) REVERT: J 190 VAL cc_start: 0.9491 (m) cc_final: 0.9160 (p) outliers start: 23 outliers final: 11 residues processed: 295 average time/residue: 0.3540 time to fit residues: 139.9678 Evaluate side-chains 268 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 139 ARG 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 J residue 82 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 121 optimal weight: 0.0000 chunk 76 optimal weight: 0.7980 chunk 18 optimal weight: 0.0770 chunk 132 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN C 217 ASN F 156 HIS F 233 GLN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN 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 = 0.3385 r_free = 0.3385 target = 0.099959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.078334 restraints weight = 30170.840| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.99 r_work: 0.2917 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14971 Z= 0.124 Angle : 0.541 8.727 20304 Z= 0.278 Chirality : 0.044 0.187 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.770 19.640 1983 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.14 % Allowed : 15.71 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1793 helix: 1.64 (0.23), residues: 547 sheet: -0.82 (0.23), residues: 470 loop : 0.15 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 88 HIS 0.005 0.001 HIS H 197 PHE 0.011 0.001 PHE A 122 TYR 0.023 0.001 TYR E 116 ARG 0.006 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.02733 ( 536) hydrogen bonds : angle 4.31152 ( 1533) SS BOND : bond 0.00339 ( 1) SS BOND : angle 1.52278 ( 2) covalent geometry : bond 0.00299 (14970) covalent geometry : angle 0.54049 (20302) *********************** 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: 34 poor density : 260 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8421 (mp0) cc_final: 0.7653 (mp0) REVERT: A 217 ASN cc_start: 0.8601 (m-40) cc_final: 0.8272 (t0) REVERT: A 237 TYR cc_start: 0.9010 (t80) cc_final: 0.8633 (t80) REVERT: B 179 ASP cc_start: 0.8181 (t70) cc_final: 0.7459 (t70) REVERT: C 179 ASP cc_start: 0.8490 (t0) cc_final: 0.8019 (t0) REVERT: C 210 ILE cc_start: 0.9411 (mm) cc_final: 0.8770 (tt) REVERT: C 240 LYS cc_start: 0.8526 (tttt) cc_final: 0.8229 (ttmt) REVERT: D 178 SER cc_start: 0.9466 (p) cc_final: 0.9209 (p) REVERT: D 179 ASP cc_start: 0.8738 (t0) cc_final: 0.8315 (t0) REVERT: D 213 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8780 (tm-30) REVERT: E 139 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8202 (mtt180) REVERT: E 143 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8486 (p) REVERT: E 227 GLU cc_start: 0.8297 (tp30) cc_final: 0.8033 (tp30) REVERT: F 144 GLU cc_start: 0.7937 (mp0) cc_final: 0.7623 (mp0) REVERT: G 150 VAL cc_start: 0.8895 (m) cc_final: 0.8566 (t) REVERT: H 134 ARG cc_start: 0.8965 (mtp-110) cc_final: 0.8748 (mtm110) REVERT: H 137 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: H 142 ASN cc_start: 0.8880 (t0) cc_final: 0.8534 (t0) REVERT: J 144 GLU cc_start: 0.7747 (tp30) cc_final: 0.7485 (mm-30) REVERT: J 179 ASP cc_start: 0.8472 (t70) cc_final: 0.7796 (t0) REVERT: J 180 LEU cc_start: 0.9188 (tp) cc_final: 0.8924 (tt) REVERT: J 190 VAL cc_start: 0.9511 (m) cc_final: 0.9178 (p) outliers start: 34 outliers final: 23 residues processed: 283 average time/residue: 0.3464 time to fit residues: 131.1089 Evaluate side-chains 275 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 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 E residue 149 SER 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 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 M residue 262 TYR 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 20 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 162 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 93 optimal weight: 0.0270 chunk 127 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 137 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 overall best weight: 0.8356 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3396 r_free = 0.3396 target = 0.100702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079085 restraints weight = 30000.408| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.98 r_work: 0.2928 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14971 Z= 0.108 Angle : 0.543 10.634 20304 Z= 0.279 Chirality : 0.043 0.180 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.711 19.270 1983 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.63 % Allowed : 16.47 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1793 helix: 1.69 (0.23), residues: 546 sheet: -0.78 (0.23), residues: 470 loop : 0.17 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 88 HIS 0.005 0.001 HIS H 197 PHE 0.009 0.001 PHE A 122 TYR 0.013 0.001 TYR B 237 ARG 0.007 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.02574 ( 536) hydrogen bonds : angle 4.26269 ( 1533) SS BOND : bond 0.00274 ( 1) SS BOND : angle 1.56549 ( 2) covalent geometry : bond 0.00260 (14970) covalent geometry : angle 0.54248 (20302) *********************** 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 287 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8406 (mp0) cc_final: 0.7621 (mp0) REVERT: A 217 ASN cc_start: 0.8549 (m-40) cc_final: 0.8267 (t0) REVERT: A 237 TYR cc_start: 0.8983 (t80) cc_final: 0.8619 (t80) REVERT: B 179 ASP cc_start: 0.8157 (t70) cc_final: 0.7436 (t70) REVERT: B 240 LYS cc_start: 0.6535 (pptt) cc_final: 0.5118 (pptt) REVERT: C 179 ASP cc_start: 0.8461 (t0) cc_final: 0.7970 (t0) REVERT: C 210 ILE cc_start: 0.9400 (mm) cc_final: 0.8749 (tt) REVERT: C 240 LYS cc_start: 0.8509 (tttt) cc_final: 0.8218 (ttmt) REVERT: D 178 SER cc_start: 0.9472 (p) cc_final: 0.9225 (p) REVERT: D 179 ASP cc_start: 0.8670 (t0) cc_final: 0.8236 (t0) REVERT: E 127 GLU cc_start: 0.8596 (pm20) cc_final: 0.8317 (mm-30) REVERT: E 139 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8159 (mtt180) REVERT: E 143 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8522 (p) REVERT: F 144 GLU cc_start: 0.7975 (mp0) cc_final: 0.7625 (mp0) REVERT: G 150 VAL cc_start: 0.8867 (m) cc_final: 0.8532 (t) REVERT: H 134 ARG cc_start: 0.8957 (mtp-110) cc_final: 0.8644 (mtm110) REVERT: H 137 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8288 (pt0) REVERT: H 142 ASN cc_start: 0.8839 (t0) cc_final: 0.8520 (t0) REVERT: H 178 SER cc_start: 0.9179 (t) cc_final: 0.8627 (p) REVERT: J 144 GLU cc_start: 0.7754 (tp30) cc_final: 0.7498 (mm-30) REVERT: J 179 ASP cc_start: 0.8511 (t70) cc_final: 0.7795 (t0) REVERT: J 180 LEU cc_start: 0.9164 (tp) cc_final: 0.8902 (tt) REVERT: J 190 VAL cc_start: 0.9507 (m) cc_final: 0.9175 (p) outliers start: 26 outliers final: 18 residues processed: 279 average time/residue: 0.3553 time to fit residues: 132.3264 Evaluate side-chains 275 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU 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 E residue 149 SER 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.076764 restraints weight = 30096.603| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.97 r_work: 0.2892 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14971 Z= 0.183 Angle : 0.572 7.859 20304 Z= 0.296 Chirality : 0.045 0.181 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.911 19.657 1983 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.39 % Allowed : 16.15 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1793 helix: 1.60 (0.23), residues: 548 sheet: -0.93 (0.23), residues: 474 loop : 0.14 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 88 HIS 0.005 0.001 HIS B 182 PHE 0.012 0.001 PHE D 114 TYR 0.022 0.001 TYR E 116 ARG 0.007 0.000 ARG E 223 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 536) hydrogen bonds : angle 4.40596 ( 1533) SS BOND : bond 0.00385 ( 1) SS BOND : angle 1.43367 ( 2) covalent geometry : bond 0.00439 (14970) covalent geometry : angle 0.57221 (20302) *********************** 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 288 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8411 (mp0) cc_final: 0.7643 (mp0) REVERT: A 183 GLN cc_start: 0.8263 (tp40) cc_final: 0.7957 (tp-100) REVERT: A 237 TYR cc_start: 0.9011 (t80) cc_final: 0.8713 (t80) REVERT: B 179 ASP cc_start: 0.8268 (t70) cc_final: 0.7269 (t0) REVERT: C 179 ASP cc_start: 0.8497 (t0) cc_final: 0.8031 (t0) REVERT: C 240 LYS cc_start: 0.8602 (tttt) cc_final: 0.8284 (ttmt) REVERT: D 78 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8341 (tptt) REVERT: D 179 ASP cc_start: 0.8796 (t0) cc_final: 0.8385 (t0) REVERT: D 213 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8805 (tm-30) REVERT: E 139 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8218 (mtt180) REVERT: E 143 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8494 (p) REVERT: F 144 GLU cc_start: 0.8072 (mp0) cc_final: 0.7678 (mp0) REVERT: H 134 ARG cc_start: 0.8960 (mtp-110) cc_final: 0.8664 (mtm110) REVERT: H 137 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8241 (pt0) REVERT: H 142 ASN cc_start: 0.8903 (t0) cc_final: 0.8565 (t0) REVERT: J 179 ASP cc_start: 0.8470 (t70) cc_final: 0.7852 (t0) REVERT: J 180 LEU cc_start: 0.9247 (tp) cc_final: 0.8994 (tt) outliers start: 38 outliers final: 29 residues processed: 276 average time/residue: 0.3561 time to fit residues: 130.8147 Evaluate side-chains 275 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 178 SER Chi-restraints excluded: chain C residue 140 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 E residue 149 SER Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 178 SER 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 250 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 101 optimal weight: 0.0470 chunk 7 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- 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 ** 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 = 0.3395 r_free = 0.3395 target = 0.100502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.078866 restraints weight = 29891.138| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.00 r_work: 0.2924 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14971 Z= 0.107 Angle : 0.562 8.147 20304 Z= 0.289 Chirality : 0.044 0.295 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.754 19.292 1983 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.63 % Allowed : 17.72 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1793 helix: 1.70 (0.23), residues: 546 sheet: -0.85 (0.23), residues: 468 loop : 0.18 (0.25), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 88 HIS 0.005 0.001 HIS F 241 PHE 0.007 0.001 PHE A 122 TYR 0.013 0.001 TYR B 237 ARG 0.007 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.02602 ( 536) hydrogen bonds : angle 4.25844 ( 1533) SS BOND : bond 0.00216 ( 1) SS BOND : angle 1.61692 ( 2) covalent geometry : bond 0.00258 (14970) covalent geometry : angle 0.56153 (20302) *********************** 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 295 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8401 (mp0) cc_final: 0.7610 (mp0) REVERT: A 217 ASN cc_start: 0.8519 (m-40) cc_final: 0.8219 (t0) REVERT: A 237 TYR cc_start: 0.8981 (t80) cc_final: 0.8636 (t80) REVERT: B 172 ILE cc_start: 0.9092 (mm) cc_final: 0.8851 (mm) REVERT: B 179 ASP cc_start: 0.8155 (t70) cc_final: 0.7441 (t70) REVERT: B 240 LYS cc_start: 0.6447 (pptt) cc_final: 0.5023 (pptt) REVERT: C 179 ASP cc_start: 0.8340 (t0) cc_final: 0.7871 (t0) REVERT: C 240 LYS cc_start: 0.8536 (tttt) cc_final: 0.8219 (ttmt) REVERT: D 78 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8276 (tptt) REVERT: D 178 SER cc_start: 0.9413 (p) cc_final: 0.9160 (p) REVERT: D 179 ASP cc_start: 0.8674 (t0) cc_final: 0.8270 (t0) REVERT: D 213 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8800 (tm-30) REVERT: E 127 GLU cc_start: 0.8612 (pm20) cc_final: 0.8289 (mm-30) REVERT: E 139 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8133 (mtt180) REVERT: E 143 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8497 (p) REVERT: F 144 GLU cc_start: 0.8071 (mp0) cc_final: 0.7680 (mp0) REVERT: H 134 ARG cc_start: 0.8947 (mtp-110) cc_final: 0.8744 (mtm110) REVERT: H 137 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: H 142 ASN cc_start: 0.8866 (t0) cc_final: 0.8538 (t0) REVERT: H 178 SER cc_start: 0.9173 (t) cc_final: 0.8665 (p) REVERT: J 144 GLU cc_start: 0.7709 (tp30) cc_final: 0.7420 (mm-30) REVERT: J 179 ASP cc_start: 0.8448 (t70) cc_final: 0.7780 (t0) REVERT: J 180 LEU cc_start: 0.9162 (tp) cc_final: 0.8926 (tt) outliers start: 26 outliers final: 19 residues processed: 284 average time/residue: 0.3694 time to fit residues: 139.2472 Evaluate side-chains 280 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 140 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 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 E residue 149 SER Chi-restraints excluded: chain F residue 178 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** 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 = 0.3392 r_free = 0.3392 target = 0.100417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.078850 restraints weight = 29818.004| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.98 r_work: 0.2925 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2060 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= 0.116 Angle : 0.565 8.316 20304 Z= 0.290 Chirality : 0.044 0.302 2247 Planarity : 0.004 0.045 2599 Dihedral : 3.728 19.240 1983 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.76 % Allowed : 17.47 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1793 helix: 1.67 (0.23), residues: 546 sheet: -0.84 (0.23), residues: 468 loop : 0.19 (0.25), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 88 HIS 0.005 0.001 HIS F 241 PHE 0.010 0.001 PHE M 212 TYR 0.023 0.001 TYR E 116 ARG 0.007 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.02615 ( 536) hydrogen bonds : angle 4.25247 ( 1533) SS BOND : bond 0.00306 ( 1) SS BOND : angle 1.73217 ( 2) covalent geometry : bond 0.00281 (14970) covalent geometry : angle 0.56515 (20302) ********************** 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 291 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8413 (mp0) cc_final: 0.7622 (mp0) REVERT: A 217 ASN cc_start: 0.8528 (m-40) cc_final: 0.8240 (t0) REVERT: A 237 TYR cc_start: 0.8990 (t80) cc_final: 0.8624 (t80) REVERT: B 172 ILE cc_start: 0.9073 (mm) cc_final: 0.8813 (mm) REVERT: B 179 ASP cc_start: 0.8153 (t70) cc_final: 0.7442 (t70) REVERT: B 240 LYS cc_start: 0.6488 (pptt) cc_final: 0.5105 (pptt) REVERT: C 179 ASP cc_start: 0.8353 (t0) cc_final: 0.7877 (t0) REVERT: C 240 LYS cc_start: 0.8521 (tttt) cc_final: 0.8213 (ttmt) REVERT: D 78 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8267 (tptt) REVERT: D 178 SER cc_start: 0.9436 (p) cc_final: 0.9199 (p) REVERT: D 179 ASP cc_start: 0.8684 (t0) cc_final: 0.8270 (t0) REVERT: D 213 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8805 (tm-30) REVERT: E 127 GLU cc_start: 0.8641 (pm20) cc_final: 0.8270 (mm-30) REVERT: E 139 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8143 (mtt180) REVERT: E 143 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8490 (p) REVERT: F 83 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8738 (mmmm) REVERT: F 144 GLU cc_start: 0.8071 (mp0) cc_final: 0.7672 (mp0) REVERT: G 179 ASP cc_start: 0.8201 (t0) cc_final: 0.7985 (t0) REVERT: H 134 ARG cc_start: 0.8984 (mtp-110) cc_final: 0.8780 (mtm110) REVERT: H 137 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: H 142 ASN cc_start: 0.8855 (t0) cc_final: 0.8539 (t0) REVERT: H 178 SER cc_start: 0.9200 (t) cc_final: 0.8677 (p) REVERT: J 144 GLU cc_start: 0.7722 (tp30) cc_final: 0.7424 (mm-30) REVERT: J 179 ASP cc_start: 0.8467 (t70) cc_final: 0.7802 (t0) outliers start: 28 outliers final: 22 residues processed: 282 average time/residue: 0.3626 time to fit residues: 135.2742 Evaluate side-chains 279 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 140 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 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 E residue 149 SER 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 H residue 225 VAL Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL 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 J residue 152 SER Chi-restraints excluded: chain M residue 262 TYR Chi-restraints excluded: chain M residue 274 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 114 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** 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 = 0.3370 r_free = 0.3370 target = 0.098839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.077301 restraints weight = 30320.773| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.98 r_work: 0.2894 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14971 Z= 0.156 Angle : 0.593 8.201 20304 Z= 0.304 Chirality : 0.045 0.301 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.870 19.540 1983 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.01 % Allowed : 17.41 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1793 helix: 1.63 (0.23), residues: 544 sheet: -0.94 (0.23), residues: 472 loop : 0.17 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 88 HIS 0.005 0.001 HIS F 241 PHE 0.010 0.001 PHE D 114 TYR 0.018 0.001 TYR C 110 ARG 0.007 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 536) hydrogen bonds : angle 4.33688 ( 1533) SS BOND : bond 0.00362 ( 1) SS BOND : angle 1.57635 ( 2) covalent geometry : bond 0.00380 (14970) covalent geometry : angle 0.59239 (20302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6146.04 seconds wall clock time: 107 minutes 44.95 seconds (6464.95 seconds total)