Starting phenix.real_space_refine on Fri Sep 27 13:01:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/09_2024/8bjm_16089.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/09_2024/8bjm_16089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/09_2024/8bjm_16089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/09_2024/8bjm_16089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/09_2024/8bjm_16089.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/09_2024/8bjm_16089.cif" } resolution = 2.2 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= -0.011 sd= 0.919 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 10122 2.51 5 N 2909 2.21 5 O 3536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16655 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "B" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "C" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "D" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1464 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "G" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "H" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "I" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1475 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "K" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "K" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 10.13, per 1000 atoms: 0.61 Number of scatterers: 16655 At special positions: 0 Unit cell: (133.042, 133.042, 77.486, 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 88 16.00 O 3536 8.00 N 2909 7.00 C 10122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.1 seconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 22 sheets defined 47.5% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 removed outlier: 3.778A pdb=" N ARG A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 134 through 157 removed outlier: 3.876A pdb=" N SER A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 removed outlier: 6.563A pdb=" N ALA A 161 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN A 164 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS A 165 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.572A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.699A pdb=" N ARG B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 67 through 80 Processing helix chain 'B' and resid 134 through 157 removed outlier: 3.829A pdb=" N SER B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 6.551A pdb=" N ALA B 161 " --> pdb=" O PHE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 197 through 209 removed outlier: 4.222A pdb=" N ARG B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 44 removed outlier: 3.732A pdb=" N ARG C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 67 through 80 Processing helix chain 'C' and resid 134 through 157 removed outlier: 3.846A pdb=" N SER C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 167 removed outlier: 6.573A pdb=" N ALA C 161 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN C 164 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS C 165 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 167 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.736A pdb=" N ARG D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 67 through 80 Processing helix chain 'D' and resid 134 through 157 removed outlier: 3.882A pdb=" N SER D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 167 removed outlier: 6.594A pdb=" N ALA D 161 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN D 164 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS D 165 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 167 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'E' and resid 32 through 44 removed outlier: 3.731A pdb=" N ARG E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 Processing helix chain 'E' and resid 67 through 80 Processing helix chain 'E' and resid 134 through 157 removed outlier: 3.863A pdb=" N SER E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 167 removed outlier: 6.535A pdb=" N ALA E 161 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN E 164 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS E 165 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 167 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 178 Processing helix chain 'E' and resid 197 through 208 Processing helix chain 'F' and resid 32 through 44 removed outlier: 3.771A pdb=" N ARG F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 67 through 80 Processing helix chain 'F' and resid 134 through 157 removed outlier: 3.884A pdb=" N SER F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 removed outlier: 6.530A pdb=" N ALA F 161 " --> pdb=" O PHE F 158 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN F 164 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS F 165 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 Processing helix chain 'F' and resid 197 through 209 removed outlier: 3.827A pdb=" N ARG F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.695A pdb=" N ARG G 44 " --> pdb=" O GLN G 40 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 67 through 80 Processing helix chain 'G' and resid 134 through 157 removed outlier: 3.843A pdb=" N SER G 157 " --> pdb=" O ARG G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 removed outlier: 6.547A pdb=" N ALA G 161 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN G 164 " --> pdb=" O ALA G 161 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS G 165 " --> pdb=" O LEU G 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 167 " --> pdb=" O ASN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 197 through 208 Processing helix chain 'H' and resid 32 through 44 removed outlier: 3.794A pdb=" N ARG H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 80 Processing helix chain 'H' and resid 134 through 157 removed outlier: 3.882A pdb=" N SER H 157 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 removed outlier: 6.564A pdb=" N ALA H 161 " --> pdb=" O PHE H 158 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASN H 164 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS H 165 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 178 removed outlier: 3.604A pdb=" N LEU H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 208 Processing helix chain 'I' and resid 32 through 45 WARNING: missing atoms! removed outlier: 3.680A pdb=" N ARG I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 Processing helix chain 'I' and resid 67 through 80 Processing helix chain 'I' and resid 134 through 157 removed outlier: 3.866A pdb=" N SER I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 167 removed outlier: 6.563A pdb=" N ALA I 161 " --> pdb=" O PHE I 158 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN I 164 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS I 165 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU I 167 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 177 removed outlier: 3.565A pdb=" N LYS I 177 " --> pdb=" O ARG I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 208 Processing helix chain 'J' and resid 32 through 43 Processing helix chain 'J' and resid 48 through 52 Processing helix chain 'J' and resid 67 through 80 Processing helix chain 'J' and resid 134 through 157 removed outlier: 3.848A pdb=" N SER J 157 " --> pdb=" O ARG J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 167 removed outlier: 6.581A pdb=" N ALA J 161 " --> pdb=" O PHE J 158 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASN J 164 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS J 165 " --> pdb=" O LEU J 162 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 167 " --> pdb=" O ASN J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 177 removed outlier: 3.518A pdb=" N LYS J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 208 Processing helix chain 'K' and resid 32 through 44 removed outlier: 3.738A pdb=" N ARG K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 52 Processing helix chain 'K' and resid 67 through 80 Processing helix chain 'K' and resid 134 through 157 removed outlier: 3.859A pdb=" N SER K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 167 removed outlier: 6.549A pdb=" N ALA K 161 " --> pdb=" O PHE K 158 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN K 164 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS K 165 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU K 167 " --> pdb=" O ASN K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 178 removed outlier: 3.526A pdb=" N LEU K 178 " --> pdb=" O SER K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 209 removed outlier: 4.133A pdb=" N ARG K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 99 removed outlier: 5.350A pdb=" N HIS A 86 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN A 114 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG A 112 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 90 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY A 106 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 96 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR A 104 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A 98 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE A 103 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 99 removed outlier: 5.359A pdb=" N HIS B 86 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN B 114 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG B 112 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 90 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY B 106 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 96 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 104 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 98 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE B 103 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 99 removed outlier: 5.363A pdb=" N HIS C 86 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLN C 114 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE C 88 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG C 112 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 90 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY C 106 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL C 96 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR C 104 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 98 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE C 103 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 84 through 99 removed outlier: 5.352A pdb=" N HIS D 86 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLN D 114 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE D 88 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG D 112 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 90 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY D 106 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL D 96 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR D 104 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU D 98 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE D 103 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 57 removed outlier: 3.654A pdb=" N ALA E 57 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 84 through 99 removed outlier: 5.357A pdb=" N HIS E 86 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN E 114 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE E 88 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG E 112 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 90 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY E 106 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 96 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR E 104 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU E 98 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE E 103 " --> pdb=" O GLY E 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 84 through 99 removed outlier: 5.368A pdb=" N HIS F 86 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN F 114 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE F 88 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG F 112 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 90 " --> pdb=" O PHE F 110 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY F 106 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL F 96 " --> pdb=" O TYR F 104 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR F 104 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU F 98 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE F 103 " --> pdb=" O GLY F 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'G' and resid 84 through 99 removed outlier: 5.356A pdb=" N HIS G 86 " --> pdb=" O GLN G 114 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN G 114 " --> pdb=" O HIS G 86 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE G 88 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG G 112 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN G 90 " --> pdb=" O PHE G 110 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY G 106 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL G 96 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR G 104 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU G 98 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE G 103 " --> pdb=" O GLY G 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'H' and resid 84 through 99 removed outlier: 5.341A pdb=" N HIS H 86 " --> pdb=" O GLN H 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN H 114 " --> pdb=" O HIS H 86 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE H 88 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG H 112 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN H 90 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY H 106 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 96 " --> pdb=" O TYR H 104 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR H 104 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU H 98 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE H 103 " --> pdb=" O GLY H 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'I' and resid 84 through 99 removed outlier: 5.351A pdb=" N HIS I 86 " --> pdb=" O GLN I 114 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLN I 114 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE I 88 " --> pdb=" O ARG I 112 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG I 112 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN I 90 " --> pdb=" O PHE I 110 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY I 106 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL I 96 " --> pdb=" O TYR I 104 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR I 104 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU I 98 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS I 102 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N PHE I 103 " --> pdb=" O GLY I 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 53 through 56 Processing sheet with id=AC2, first strand: chain 'J' and resid 84 through 99 removed outlier: 5.353A pdb=" N HIS J 86 " --> pdb=" O GLN J 114 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN J 114 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE J 88 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG J 112 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN J 90 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY J 106 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL J 96 " --> pdb=" O TYR J 104 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR J 104 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU J 98 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE J 103 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'K' and resid 84 through 99 removed outlier: 5.369A pdb=" N HIS K 86 " --> pdb=" O GLN K 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN K 114 " --> pdb=" O HIS K 86 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE K 88 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG K 112 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN K 90 " --> pdb=" O PHE K 110 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY K 106 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL K 96 " --> pdb=" O TYR K 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR K 104 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU K 98 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE K 103 " --> pdb=" O GLY K 131 " (cutoff:3.500A) 822 hydrogen bonds defined for protein. 2271 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: 4.70 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3186 1.32 - 1.45: 3905 1.45 - 1.57: 9220 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 16421 Sorted by residual: bond pdb=" C TYR K 171 " pdb=" O TYR K 171 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.19e-02 7.06e+03 8.69e+00 bond pdb=" C TYR H 171 " pdb=" O TYR H 171 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.19e-02 7.06e+03 6.65e+00 bond pdb=" C TYR H 171 " pdb=" N LEU H 172 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.31e-02 5.83e+03 2.33e+00 bond pdb=" C ASP K 170 " pdb=" N TYR K 171 " ideal model delta sigma weight residual 1.335 1.315 0.019 1.36e-02 5.41e+03 2.01e+00 bond pdb=" C TYR K 171 " pdb=" N LEU K 172 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.31e-02 5.83e+03 1.94e+00 ... (remaining 16416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 20520 0.96 - 1.93: 1279 1.93 - 2.89: 197 2.89 - 3.85: 68 3.85 - 4.82: 10 Bond angle restraints: 22074 Sorted by residual: angle pdb=" N TYR H 171 " pdb=" CA TYR H 171 " pdb=" C TYR H 171 " ideal model delta sigma weight residual 111.36 108.79 2.57 1.09e+00 8.42e-01 5.55e+00 angle pdb=" CA TYR H 36 " pdb=" CB TYR H 36 " pdb=" CG TYR H 36 " ideal model delta sigma weight residual 113.90 109.79 4.11 1.80e+00 3.09e-01 5.20e+00 angle pdb=" CA TYR F 36 " pdb=" CB TYR F 36 " pdb=" CG TYR F 36 " ideal model delta sigma weight residual 113.90 109.81 4.09 1.80e+00 3.09e-01 5.16e+00 angle pdb=" CA TYR J 36 " pdb=" CB TYR J 36 " pdb=" CG TYR J 36 " ideal model delta sigma weight residual 113.90 109.98 3.92 1.80e+00 3.09e-01 4.75e+00 angle pdb=" C ALA F 85 " pdb=" N HIS F 86 " pdb=" CA HIS F 86 " ideal model delta sigma weight residual 121.94 118.13 3.81 1.76e+00 3.23e-01 4.70e+00 ... (remaining 22069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 9189 17.59 - 35.17: 540 35.17 - 52.76: 120 52.76 - 70.35: 62 70.35 - 87.93: 21 Dihedral angle restraints: 9932 sinusoidal: 4057 harmonic: 5875 Sorted by residual: dihedral pdb=" CB ARG I 193 " pdb=" CG ARG I 193 " pdb=" CD ARG I 193 " pdb=" NE ARG I 193 " ideal model delta sinusoidal sigma weight residual 60.00 119.40 -59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU B 178 " pdb=" CA LEU B 178 " pdb=" CB LEU B 178 " pdb=" CG LEU B 178 " ideal model delta sinusoidal sigma weight residual -180.00 -122.09 -57.91 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB GLU D 145 " pdb=" CG GLU D 145 " pdb=" CD GLU D 145 " pdb=" OE1 GLU D 145 " ideal model delta sinusoidal sigma weight residual 0.00 83.45 -83.45 1 3.00e+01 1.11e-03 9.45e+00 ... (remaining 9929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1272 0.028 - 0.057: 658 0.057 - 0.085: 274 0.085 - 0.113: 109 0.113 - 0.142: 34 Chirality restraints: 2347 Sorted by residual: chirality pdb=" CA VAL H 96 " pdb=" N VAL H 96 " pdb=" C VAL H 96 " pdb=" CB VAL H 96 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VAL E 96 " pdb=" N VAL E 96 " pdb=" C VAL E 96 " pdb=" CB VAL E 96 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA VAL D 96 " pdb=" N VAL D 96 " pdb=" C VAL D 96 " pdb=" CB VAL D 96 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 2344 not shown) Planarity restraints: 2910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 36 " 0.024 2.00e-02 2.50e+03 1.27e-02 3.23e+00 pdb=" CG TYR F 36 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR F 36 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR F 36 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 36 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 36 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 36 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 36 " -0.023 2.00e-02 2.50e+03 1.22e-02 3.00e+00 pdb=" CG TYR H 36 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 36 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR H 36 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 36 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 36 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 36 " 0.023 2.00e-02 2.50e+03 1.22e-02 2.97e+00 pdb=" CG TYR C 36 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 36 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 36 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 36 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 36 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 36 " 0.006 2.00e-02 2.50e+03 ... (remaining 2907 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1412 2.74 - 3.28: 15913 3.28 - 3.82: 31105 3.82 - 4.36: 37928 4.36 - 4.90: 60876 Nonbonded interactions: 147234 Sorted by model distance: nonbonded pdb=" O LEU E 47 " pdb=" OH TYR E 171 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP B 123 " pdb=" O HOH B 501 " model vdw 2.211 3.040 nonbonded pdb=" O LEU B 47 " pdb=" OH TYR B 171 " model vdw 2.213 3.040 nonbonded pdb=" OD2 ASP E 123 " pdb=" O HOH E 501 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU B 35 " pdb=" O HOH B 502 " model vdw 2.218 3.040 ... (remaining 147229 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 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'B' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'C' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'D' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 208)) selection = (chain 'E' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'F' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'G' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'H' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'I' and (resid 23 through 51 or (resid 52 and (name N or name CA or name \ C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'J' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'K' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) } 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.930 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 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:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 : 0.005 0.035 16421 Z= 0.313 Angle : 0.548 4.817 22074 Z= 0.311 Chirality : 0.043 0.142 2347 Planarity : 0.004 0.043 2910 Dihedral : 13.854 87.934 6206 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.17 % Allowed : 4.86 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.18), residues: 2028 helix: 1.92 (0.18), residues: 777 sheet: 1.90 (0.23), residues: 424 loop : 0.69 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP D 84 HIS 0.006 0.002 HIS F 86 PHE 0.012 0.002 PHE K 110 TYR 0.024 0.003 TYR F 36 ARG 0.004 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 287 time to evaluate : 1.903 Fit side-chains REVERT: B 41 LYS cc_start: 0.9005 (mttp) cc_final: 0.8469 (mppt) REVERT: C 133 LYS cc_start: 0.8670 (mptm) cc_final: 0.8097 (mppt) REVERT: C 194 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6837 (pp30) REVERT: C 196 LEU cc_start: 0.8214 (mt) cc_final: 0.7725 (mm) REVERT: C 206 ASN cc_start: 0.8725 (m-40) cc_final: 0.8493 (m-40) REVERT: E 192 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7424 (tttm) REVERT: H 196 LEU cc_start: 0.8190 (mt) cc_final: 0.7828 (mm) REVERT: I 192 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7620 (tttm) REVERT: J 196 LEU cc_start: 0.8619 (mt) cc_final: 0.8417 (mm) outliers start: 20 outliers final: 2 residues processed: 299 average time/residue: 1.4486 time to fit residues: 475.3894 Evaluate side-chains 256 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 251 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 179 optimal weight: 20.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 45 GLN A 69 HIS A 90 GLN A 114 GLN A 164 ASN B 30 GLN B 40 GLN B 90 GLN B 114 GLN B 176 ASN C 28 GLN C 40 GLN C 114 GLN C 176 ASN D 90 GLN D 114 GLN D 194 GLN E 30 GLN E 40 GLN E 90 GLN E 114 GLN E 176 ASN F 40 GLN F 45 GLN F 90 GLN F 114 GLN G 28 GLN G 40 GLN G 90 GLN G 100 ASN G 114 GLN G 194 GLN H 28 GLN H 40 GLN H 90 GLN H 99 ASN H 114 GLN I 30 GLN I 40 GLN I 90 GLN I 114 GLN J 28 GLN J 30 GLN J 40 GLN J 90 GLN J 114 GLN K 28 GLN K 40 GLN K 45 GLN K 114 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16421 Z= 0.224 Angle : 0.503 4.412 22074 Z= 0.277 Chirality : 0.040 0.129 2347 Planarity : 0.003 0.027 2910 Dihedral : 5.023 67.430 2299 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.81 % Allowed : 8.07 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.29 (0.18), residues: 2028 helix: 2.26 (0.18), residues: 783 sheet: 1.86 (0.23), residues: 424 loop : 0.70 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 84 HIS 0.005 0.001 HIS D 86 PHE 0.011 0.002 PHE F 110 TYR 0.023 0.002 TYR F 36 ARG 0.003 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 281 time to evaluate : 1.987 Fit side-chains REVERT: A 130 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: B 41 LYS cc_start: 0.9000 (mttp) cc_final: 0.8483 (mppt) REVERT: C 55 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7500 (mtm-85) REVERT: C 196 LEU cc_start: 0.8184 (mt) cc_final: 0.7891 (mm) REVERT: C 206 ASN cc_start: 0.8678 (m-40) cc_final: 0.8416 (m-40) REVERT: F 174 SER cc_start: 0.8174 (m) cc_final: 0.7968 (t) REVERT: G 56 MET cc_start: 0.7864 (tpp) cc_final: 0.7482 (mmm) REVERT: H 56 MET cc_start: 0.7634 (tpp) cc_final: 0.7238 (tpp) REVERT: H 196 LEU cc_start: 0.8238 (mt) cc_final: 0.7903 (mm) REVERT: H 202 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6891 (mm-30) REVERT: I 192 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7624 (tttm) REVERT: J 196 LEU cc_start: 0.8639 (mt) cc_final: 0.8376 (mm) REVERT: K 196 LEU cc_start: 0.8448 (mt) cc_final: 0.8243 (mm) outliers start: 31 outliers final: 6 residues processed: 293 average time/residue: 1.4265 time to fit residues: 459.9959 Evaluate side-chains 272 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 149 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 chunk 178 optimal weight: 40.0000 chunk 61 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 overall best weight: 6.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 99 ASN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 28 GLN D 90 GLN E 90 GLN E 176 ASN F 28 GLN F 45 GLN F 90 GLN F 176 ASN G 100 ASN G 194 GLN H 90 GLN H 206 ASN I 30 GLN I 90 GLN J 30 GLN J 90 GLN K 176 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16421 Z= 0.359 Angle : 0.573 5.045 22074 Z= 0.315 Chirality : 0.044 0.128 2347 Planarity : 0.004 0.044 2910 Dihedral : 4.735 56.100 2291 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.05 % Allowed : 9.60 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.13 (0.18), residues: 2028 helix: 2.12 (0.18), residues: 783 sheet: 1.81 (0.23), residues: 424 loop : 0.59 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 84 HIS 0.006 0.002 HIS D 86 PHE 0.013 0.003 PHE F 110 TYR 0.028 0.003 TYR F 36 ARG 0.004 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 267 time to evaluate : 2.016 Fit side-chains REVERT: A 130 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: B 41 LYS cc_start: 0.9007 (mttp) cc_final: 0.8463 (mppt) REVERT: B 201 GLU cc_start: 0.8166 (tp30) cc_final: 0.7376 (mm-30) REVERT: C 55 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7519 (mtm-85) REVERT: C 194 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6780 (pp30) REVERT: C 196 LEU cc_start: 0.8241 (mt) cc_final: 0.7712 (mm) REVERT: C 206 ASN cc_start: 0.8653 (m-40) cc_final: 0.8396 (m-40) REVERT: D 56 MET cc_start: 0.7883 (tpp) cc_final: 0.7594 (tpp) REVERT: F 56 MET cc_start: 0.7669 (tpp) cc_final: 0.7400 (mmm) REVERT: H 56 MET cc_start: 0.7670 (tpp) cc_final: 0.7235 (tpp) REVERT: H 196 LEU cc_start: 0.8245 (mt) cc_final: 0.7871 (mm) REVERT: I 192 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7668 (tttm) REVERT: K 56 MET cc_start: 0.7465 (tpp) cc_final: 0.6910 (tpp) REVERT: K 196 LEU cc_start: 0.8463 (mt) cc_final: 0.8244 (mm) outliers start: 35 outliers final: 7 residues processed: 284 average time/residue: 1.4073 time to fit residues: 439.3211 Evaluate side-chains 268 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 194 GLN Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 30.0000 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 28 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 90 GLN E 90 GLN E 176 ASN F 28 GLN F 176 ASN G 100 ASN G 194 GLN H 90 GLN H 99 ASN H 176 ASN I 28 GLN I 30 GLN I 90 GLN J 30 GLN J 90 GLN K 176 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16421 Z= 0.169 Angle : 0.462 7.136 22074 Z= 0.252 Chirality : 0.039 0.125 2347 Planarity : 0.003 0.024 2910 Dihedral : 4.354 59.875 2291 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.93 % Allowed : 10.42 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.44 (0.18), residues: 2028 helix: 2.47 (0.18), residues: 787 sheet: 1.92 (0.23), residues: 421 loop : 0.68 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 84 HIS 0.003 0.001 HIS D 86 PHE 0.009 0.001 PHE F 110 TYR 0.020 0.002 TYR F 36 ARG 0.002 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 287 time to evaluate : 2.074 Fit side-chains REVERT: A 130 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: A 196 LEU cc_start: 0.8221 (mm) cc_final: 0.7962 (mt) REVERT: B 41 LYS cc_start: 0.9000 (mttp) cc_final: 0.8498 (mppt) REVERT: C 55 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7534 (mtm-85) REVERT: C 194 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6773 (pp30) REVERT: C 196 LEU cc_start: 0.8184 (mt) cc_final: 0.7622 (mm) REVERT: C 206 ASN cc_start: 0.8626 (m-40) cc_final: 0.8332 (m-40) REVERT: D 56 MET cc_start: 0.7800 (tpp) cc_final: 0.7375 (tpp) REVERT: F 56 MET cc_start: 0.7510 (tpp) cc_final: 0.7187 (mmm) REVERT: F 192 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.5626 (tptt) REVERT: H 56 MET cc_start: 0.7525 (tpp) cc_final: 0.7160 (tpp) REVERT: H 196 LEU cc_start: 0.8227 (mt) cc_final: 0.7910 (mm) REVERT: J 56 MET cc_start: 0.7616 (tpp) cc_final: 0.7347 (tpp) REVERT: K 56 MET cc_start: 0.7495 (tpp) cc_final: 0.6915 (tpp) REVERT: K 196 LEU cc_start: 0.8450 (mt) cc_final: 0.8206 (mm) outliers start: 33 outliers final: 7 residues processed: 300 average time/residue: 1.3838 time to fit residues: 458.3640 Evaluate side-chains 283 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 273 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 142 optimal weight: 50.0000 chunk 78 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN B 90 GLN B 176 ASN C 90 GLN C 176 ASN D 28 GLN D 90 GLN D 181 GLN E 90 GLN E 176 ASN F 176 ASN G 100 ASN G 194 GLN H 28 GLN H 90 GLN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 90 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16421 Z= 0.248 Angle : 0.511 8.083 22074 Z= 0.278 Chirality : 0.041 0.125 2347 Planarity : 0.003 0.030 2910 Dihedral : 4.196 30.449 2287 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.05 % Allowed : 11.06 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.37 (0.18), residues: 2028 helix: 2.41 (0.18), residues: 786 sheet: 1.87 (0.23), residues: 424 loop : 0.66 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 84 HIS 0.005 0.001 HIS D 86 PHE 0.010 0.002 PHE F 110 TYR 0.024 0.002 TYR F 36 ARG 0.003 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 278 time to evaluate : 2.259 Fit side-chains REVERT: A 130 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: A 196 LEU cc_start: 0.8249 (mm) cc_final: 0.7994 (mt) REVERT: B 41 LYS cc_start: 0.9002 (mttp) cc_final: 0.8492 (mppt) REVERT: C 194 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6803 (pp30) REVERT: C 196 LEU cc_start: 0.8216 (mt) cc_final: 0.7668 (mm) REVERT: C 206 ASN cc_start: 0.8583 (m-40) cc_final: 0.8278 (m-40) REVERT: F 56 MET cc_start: 0.7521 (tpp) cc_final: 0.7240 (mmm) REVERT: F 192 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.5672 (tptt) REVERT: G 56 MET cc_start: 0.7520 (mmm) cc_final: 0.6993 (tpp) REVERT: H 56 MET cc_start: 0.7554 (tpp) cc_final: 0.7169 (tpp) REVERT: H 196 LEU cc_start: 0.8225 (mt) cc_final: 0.7878 (mm) REVERT: J 56 MET cc_start: 0.7718 (tpp) cc_final: 0.7382 (tpp) REVERT: K 56 MET cc_start: 0.7470 (tpp) cc_final: 0.7089 (tpp) REVERT: K 196 LEU cc_start: 0.8387 (mt) cc_final: 0.8125 (mm) outliers start: 35 outliers final: 8 residues processed: 294 average time/residue: 1.4289 time to fit residues: 462.6545 Evaluate side-chains 277 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 266 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 28 GLN D 90 GLN E 90 GLN E 176 ASN F 176 ASN G 100 ASN G 194 GLN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 90 GLN K 194 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16421 Z= 0.258 Angle : 0.524 9.291 22074 Z= 0.284 Chirality : 0.041 0.126 2347 Planarity : 0.003 0.031 2910 Dihedral : 4.219 30.200 2287 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.11 % Allowed : 11.23 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.18), residues: 2028 helix: 2.39 (0.18), residues: 786 sheet: 1.89 (0.23), residues: 424 loop : 0.65 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 84 HIS 0.005 0.001 HIS D 86 PHE 0.011 0.002 PHE F 110 TYR 0.024 0.003 TYR F 36 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 278 time to evaluate : 2.203 Fit side-chains REVERT: A 130 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 196 LEU cc_start: 0.8263 (mm) cc_final: 0.8008 (mt) REVERT: B 41 LYS cc_start: 0.9006 (mttp) cc_final: 0.8495 (mppt) REVERT: B 194 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6565 (pp30) REVERT: C 194 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6825 (pp30) REVERT: C 196 LEU cc_start: 0.8226 (mt) cc_final: 0.7670 (mm) REVERT: C 206 ASN cc_start: 0.8579 (m-40) cc_final: 0.8267 (m-40) REVERT: D 56 MET cc_start: 0.7765 (tpp) cc_final: 0.7521 (tpp) REVERT: D 181 GLN cc_start: 0.5819 (OUTLIER) cc_final: 0.5106 (mt0) REVERT: F 56 MET cc_start: 0.7490 (tpp) cc_final: 0.7197 (mmm) REVERT: F 192 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.5658 (tptt) REVERT: G 56 MET cc_start: 0.7540 (mmm) cc_final: 0.7124 (tpp) REVERT: H 56 MET cc_start: 0.7603 (tpp) cc_final: 0.7200 (tpp) REVERT: H 175 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8801 (mm) REVERT: H 196 LEU cc_start: 0.8227 (mt) cc_final: 0.7861 (mm) REVERT: I 192 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7573 (tttm) REVERT: I 194 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6362 (pp30) REVERT: J 56 MET cc_start: 0.7704 (tpp) cc_final: 0.7452 (tpp) REVERT: J 192 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6465 (tttt) REVERT: K 56 MET cc_start: 0.7468 (tpp) cc_final: 0.7051 (tpp) REVERT: K 196 LEU cc_start: 0.8368 (mt) cc_final: 0.8090 (mm) outliers start: 36 outliers final: 11 residues processed: 293 average time/residue: 1.4074 time to fit residues: 454.5228 Evaluate side-chains 289 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 269 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 190 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 28 GLN D 90 GLN E 90 GLN E 176 ASN F 45 GLN F 176 ASN G 100 ASN G 194 GLN H 90 GLN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 28 GLN K 194 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16421 Z= 0.338 Angle : 0.576 10.342 22074 Z= 0.312 Chirality : 0.043 0.128 2347 Planarity : 0.004 0.038 2910 Dihedral : 4.379 30.785 2287 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.46 % Allowed : 11.29 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.18), residues: 2028 helix: 2.25 (0.18), residues: 783 sheet: 1.85 (0.22), residues: 424 loop : 0.62 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 84 HIS 0.006 0.002 HIS G 86 PHE 0.012 0.003 PHE K 110 TYR 0.027 0.003 TYR F 36 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 275 time to evaluate : 1.975 Fit side-chains REVERT: A 130 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: A 196 LEU cc_start: 0.8273 (mm) cc_final: 0.8018 (mt) REVERT: B 41 LYS cc_start: 0.9010 (mttp) cc_final: 0.8480 (mppt) REVERT: B 130 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: B 194 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6579 (pp30) REVERT: B 201 GLU cc_start: 0.8121 (tp30) cc_final: 0.7321 (mm-30) REVERT: C 194 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6799 (pp30) REVERT: C 196 LEU cc_start: 0.8243 (mt) cc_final: 0.7689 (mm) REVERT: C 206 ASN cc_start: 0.8609 (m-40) cc_final: 0.8310 (m-40) REVERT: D 56 MET cc_start: 0.7787 (tpp) cc_final: 0.7441 (tpp) REVERT: D 181 GLN cc_start: 0.5864 (OUTLIER) cc_final: 0.5060 (mt0) REVERT: F 56 MET cc_start: 0.7587 (tpp) cc_final: 0.6337 (tpt) REVERT: F 192 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.5623 (tptt) REVERT: G 56 MET cc_start: 0.7595 (mmm) cc_final: 0.7190 (tpp) REVERT: H 56 MET cc_start: 0.7648 (tpp) cc_final: 0.7278 (tpp) REVERT: H 175 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8793 (mm) REVERT: H 196 LEU cc_start: 0.8224 (mt) cc_final: 0.7832 (mm) REVERT: I 192 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7564 (tttm) REVERT: I 194 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6348 (pp30) REVERT: J 56 MET cc_start: 0.7758 (tpp) cc_final: 0.7501 (tpp) REVERT: J 192 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6467 (tttt) REVERT: K 56 MET cc_start: 0.7468 (tpp) cc_final: 0.6973 (tpp) REVERT: K 92 ASN cc_start: 0.8700 (t0) cc_final: 0.8463 (t0) outliers start: 42 outliers final: 12 residues processed: 296 average time/residue: 1.4224 time to fit residues: 463.3270 Evaluate side-chains 290 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 90 GLN E 90 GLN E 176 ASN F 176 ASN G 100 ASN G 194 GLN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16421 Z= 0.202 Angle : 0.509 11.305 22074 Z= 0.271 Chirality : 0.039 0.124 2347 Planarity : 0.003 0.025 2910 Dihedral : 4.124 29.569 2287 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.22 % Allowed : 11.64 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.45 (0.18), residues: 2028 helix: 2.48 (0.18), residues: 786 sheet: 1.96 (0.23), residues: 421 loop : 0.68 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 84 HIS 0.004 0.001 HIS D 86 PHE 0.010 0.002 PHE F 110 TYR 0.022 0.002 TYR F 36 ARG 0.002 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 275 time to evaluate : 2.166 Fit side-chains REVERT: A 130 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: A 196 LEU cc_start: 0.8271 (mm) cc_final: 0.8023 (mt) REVERT: B 194 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6854 (pp30) REVERT: B 201 GLU cc_start: 0.8091 (tp30) cc_final: 0.7309 (mm-30) REVERT: C 55 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7435 (mtm-85) REVERT: C 194 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6792 (pp30) REVERT: C 196 LEU cc_start: 0.8188 (mt) cc_final: 0.7625 (mm) REVERT: C 206 ASN cc_start: 0.8614 (m-40) cc_final: 0.8299 (m-40) REVERT: D 56 MET cc_start: 0.7792 (tpp) cc_final: 0.7435 (tpp) REVERT: D 181 GLN cc_start: 0.5879 (OUTLIER) cc_final: 0.5055 (mt0) REVERT: F 56 MET cc_start: 0.7492 (tpp) cc_final: 0.7198 (mmm) REVERT: F 192 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.5642 (tptt) REVERT: G 56 MET cc_start: 0.7504 (mmm) cc_final: 0.7052 (tpp) REVERT: H 56 MET cc_start: 0.7585 (tpp) cc_final: 0.7215 (tpp) REVERT: H 175 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8815 (mm) REVERT: H 196 LEU cc_start: 0.8233 (mt) cc_final: 0.7884 (mm) REVERT: I 194 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6575 (pp30) REVERT: J 56 MET cc_start: 0.7663 (tpp) cc_final: 0.7397 (tpp) REVERT: J 192 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6454 (tttt) REVERT: K 56 MET cc_start: 0.7474 (tpp) cc_final: 0.6996 (tpp) outliers start: 38 outliers final: 10 residues processed: 291 average time/residue: 1.4014 time to fit residues: 449.8412 Evaluate side-chains 291 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 273 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 107 optimal weight: 0.0040 chunk 77 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 168 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 90 GLN B 176 ASN C 28 GLN C 37 GLN C 176 ASN D 90 GLN E 30 GLN E 45 GLN E 90 GLN E 176 ASN F 45 GLN F 176 ASN G 100 ASN G 194 GLN H 90 GLN H 176 ASN I 30 GLN I 90 GLN J 30 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16421 Z= 0.290 Angle : 0.563 12.129 22074 Z= 0.301 Chirality : 0.042 0.126 2347 Planarity : 0.004 0.032 2910 Dihedral : 4.277 30.282 2287 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.99 % Allowed : 12.17 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.31 (0.18), residues: 2028 helix: 2.35 (0.18), residues: 786 sheet: 1.90 (0.23), residues: 424 loop : 0.60 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 84 HIS 0.005 0.002 HIS D 86 PHE 0.011 0.002 PHE F 110 TYR 0.026 0.003 TYR F 36 ARG 0.003 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 267 time to evaluate : 2.072 Fit side-chains REVERT: A 130 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: A 196 LEU cc_start: 0.8284 (mm) cc_final: 0.8027 (mt) REVERT: B 194 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6799 (pp30) REVERT: B 201 GLU cc_start: 0.8095 (tp30) cc_final: 0.7308 (mm-30) REVERT: C 194 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6792 (pp30) REVERT: C 196 LEU cc_start: 0.8231 (mt) cc_final: 0.7675 (mm) REVERT: C 206 ASN cc_start: 0.8629 (m-40) cc_final: 0.8297 (m-40) REVERT: D 56 MET cc_start: 0.7805 (tpp) cc_final: 0.7438 (tpp) REVERT: D 181 GLN cc_start: 0.5822 (OUTLIER) cc_final: 0.5002 (mt0) REVERT: D 192 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8167 (tttm) REVERT: F 56 MET cc_start: 0.7556 (tpp) cc_final: 0.6387 (tpt) REVERT: F 192 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.5626 (tptt) REVERT: G 56 MET cc_start: 0.7550 (mmm) cc_final: 0.7089 (tpp) REVERT: H 56 MET cc_start: 0.7654 (tpp) cc_final: 0.7275 (tpp) REVERT: H 175 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8808 (mm) REVERT: H 196 LEU cc_start: 0.8230 (mt) cc_final: 0.7843 (mm) REVERT: I 194 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6529 (pp30) REVERT: J 56 MET cc_start: 0.7707 (tpp) cc_final: 0.7434 (tpp) REVERT: J 192 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6461 (tttt) REVERT: K 55 ARG cc_start: 0.7137 (ptp90) cc_final: 0.6873 (ptp90) REVERT: K 56 MET cc_start: 0.7480 (tpp) cc_final: 0.7004 (tpp) REVERT: K 92 ASN cc_start: 0.8672 (t0) cc_final: 0.8443 (t0) outliers start: 34 outliers final: 11 residues processed: 284 average time/residue: 1.4059 time to fit residues: 440.1107 Evaluate side-chains 283 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 263 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 197 optimal weight: 0.0770 chunk 181 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 28 GLN D 90 GLN E 90 GLN E 176 ASN F 176 ASN G 100 ASN G 194 GLN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16421 Z= 0.162 Angle : 0.502 12.534 22074 Z= 0.262 Chirality : 0.038 0.123 2347 Planarity : 0.003 0.025 2910 Dihedral : 3.965 29.280 2287 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.70 % Allowed : 12.70 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.59 (0.19), residues: 2028 helix: 2.60 (0.18), residues: 787 sheet: 2.03 (0.23), residues: 421 loop : 0.74 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 84 HIS 0.003 0.001 HIS D 69 PHE 0.008 0.001 PHE F 110 TYR 0.018 0.002 TYR F 36 ARG 0.002 0.000 ARG F 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 285 time to evaluate : 2.022 Fit side-chains REVERT: A 130 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 196 LEU cc_start: 0.8248 (mm) cc_final: 0.7997 (mt) REVERT: B 194 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6691 (pp30) REVERT: B 201 GLU cc_start: 0.8097 (tp30) cc_final: 0.7252 (mm-30) REVERT: B 202 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7034 (mm-30) REVERT: C 55 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7424 (mtm-85) REVERT: C 194 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6783 (pp30) REVERT: C 196 LEU cc_start: 0.8143 (mt) cc_final: 0.7574 (mm) REVERT: D 56 MET cc_start: 0.7739 (tpp) cc_final: 0.7395 (tpp) REVERT: D 192 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8193 (tttm) REVERT: F 56 MET cc_start: 0.7394 (tpp) cc_final: 0.7111 (mmm) REVERT: F 192 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.5646 (tptt) REVERT: G 56 MET cc_start: 0.7417 (mmm) cc_final: 0.7022 (tpp) REVERT: H 56 MET cc_start: 0.7577 (tpp) cc_final: 0.7184 (tpp) REVERT: H 175 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8816 (mm) REVERT: H 196 LEU cc_start: 0.8227 (mt) cc_final: 0.7908 (mm) REVERT: I 194 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6503 (pp30) REVERT: J 56 MET cc_start: 0.7612 (tpp) cc_final: 0.7341 (tpp) REVERT: J 192 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6459 (tttt) REVERT: K 55 ARG cc_start: 0.7078 (ptp90) cc_final: 0.6797 (ptp90) REVERT: K 56 MET cc_start: 0.7404 (tpp) cc_final: 0.7003 (tpp) REVERT: K 133 LYS cc_start: 0.8056 (mppt) cc_final: 0.7810 (mmtp) outliers start: 29 outliers final: 8 residues processed: 299 average time/residue: 1.4931 time to fit residues: 490.1217 Evaluate side-chains 292 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 276 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 176 ASN C 28 GLN C 176 ASN D 90 GLN E 90 GLN E 176 ASN F 45 GLN F 90 GLN F 176 ASN G 28 GLN G 100 ASN H 90 GLN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 90 GLN K 176 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.149990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114847 restraints weight = 17146.905| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.48 r_work: 0.3116 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16421 Z= 0.185 Angle : 0.520 12.675 22074 Z= 0.271 Chirality : 0.039 0.123 2347 Planarity : 0.003 0.025 2910 Dihedral : 3.985 29.471 2287 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.46 % Allowed : 12.93 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.58 (0.18), residues: 2028 helix: 2.58 (0.18), residues: 787 sheet: 2.03 (0.23), residues: 421 loop : 0.75 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 84 HIS 0.003 0.001 HIS D 86 PHE 0.009 0.001 PHE F 110 TYR 0.020 0.002 TYR F 36 ARG 0.004 0.000 ARG A 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7295.73 seconds wall clock time: 127 minutes 56.35 seconds (7676.35 seconds total)