Starting phenix.real_space_refine on Mon Dec 11 04:22:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/12_2023/8bjm_16089.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/12_2023/8bjm_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_16089/12_2023/8bjm_16089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/12_2023/8bjm_16089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/12_2023/8bjm_16089.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjm_16089/12_2023/8bjm_16089.pdb" } 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 Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 8.90, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 7.16 Conformation dependent library (CDL) restraints added in 2.9 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: 1.66 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: 4.59 Time building geometry restraints manager: 7.04 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: 100.39 - 107.11: 271 107.11 - 113.83: 8864 113.83 - 120.55: 6740 120.55 - 127.27: 6100 127.27 - 133.99: 99 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 2.440 nonbonded pdb=" OD2 ASP B 123 " pdb=" O HOH B 501 " model vdw 2.211 2.440 nonbonded pdb=" O LEU B 47 " pdb=" OH TYR B 171 " model vdw 2.213 2.440 nonbonded pdb=" OD2 ASP E 123 " pdb=" O HOH E 501 " model vdw 2.214 2.440 nonbonded pdb=" OE1 GLU B 35 " pdb=" O HOH B 502 " model vdw 2.218 2.440 ... (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 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: 0.460 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: 2.880 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 43.720 Find NCS groups from input model: 1.320 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.480 ------------------------------------------------------------------------------- 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 : 1.914 Fit side-chains outliers start: 20 outliers final: 2 residues processed: 299 average time/residue: 1.5203 time to fit residues: 498.7316 Evaluate side-chains 253 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 251 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.2092 time to fit residues: 3.1526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 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 28 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: 0.8642 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16421 Z= 0.270 Angle : 0.521 4.896 22074 Z= 0.287 Chirality : 0.042 0.129 2347 Planarity : 0.004 0.035 2910 Dihedral : 4.285 14.486 2285 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.64 % Allowed : 9.36 % Favored : 89.00 % 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: 2.19 (0.18), residues: 2028 helix: 2.18 (0.18), residues: 783 sheet: 1.83 (0.23), residues: 424 loop : 0.61 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 84 HIS 0.005 0.002 HIS D 86 PHE 0.012 0.002 PHE F 110 TYR 0.023 0.003 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 293 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 265 time to evaluate : 2.130 Fit side-chains outliers start: 28 outliers final: 8 residues processed: 276 average time/residue: 1.5058 time to fit residues: 458.4328 Evaluate side-chains 267 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 259 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 6 average time/residue: 0.4388 time to fit residues: 6.1085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 178 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 A 164 ASN B 30 GLN B 90 GLN B 176 ASN C 90 GLN C 176 ASN D 28 GLN D 90 GLN D 194 GLN E 90 GLN E 176 ASN F 28 GLN F 176 ASN G 28 GLN G 90 GLN G 100 ASN G 194 GLN H 28 GLN H 90 GLN H 99 ASN H 206 ASN I 30 GLN I 90 GLN J 28 GLN J 30 GLN J 90 GLN K 176 ASN K 194 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16421 Z= 0.409 Angle : 0.599 5.790 22074 Z= 0.329 Chirality : 0.045 0.129 2347 Planarity : 0.005 0.051 2910 Dihedral : 4.520 14.789 2285 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.17 % Allowed : 9.77 % Favored : 88.06 % 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: 2.00 (0.18), residues: 2028 helix: 2.07 (0.18), residues: 783 sheet: 1.68 (0.22), residues: 430 loop : 0.48 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 84 HIS 0.007 0.002 HIS D 86 PHE 0.014 0.003 PHE K 110 TYR 0.028 0.003 TYR F 36 ARG 0.004 0.001 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 285 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 248 time to evaluate : 1.799 Fit side-chains outliers start: 37 outliers final: 9 residues processed: 267 average time/residue: 1.4679 time to fit residues: 431.5556 Evaluate side-chains 254 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 245 time to evaluate : 1.931 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 6 average time/residue: 0.2274 time to fit residues: 4.9273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 D 194 GLN E 90 GLN E 176 ASN F 176 ASN G 100 ASN G 194 GLN H 28 GLN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 28 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: 0.8584 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16421 Z= 0.113 Angle : 0.427 7.640 22074 Z= 0.228 Chirality : 0.038 0.122 2347 Planarity : 0.002 0.022 2910 Dihedral : 3.838 13.362 2285 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.64 % Allowed : 11.00 % Favored : 87.36 % 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: 2.51 (0.18), residues: 2028 helix: 2.59 (0.18), residues: 793 sheet: 2.00 (0.24), residues: 424 loop : 0.59 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 84 HIS 0.002 0.001 HIS C 69 PHE 0.007 0.001 PHE B 110 TYR 0.013 0.001 TYR B 36 ARG 0.003 0.000 ARG F 55 *********************** 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 326 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 298 time to evaluate : 1.862 Fit side-chains outliers start: 28 outliers final: 7 residues processed: 309 average time/residue: 1.3912 time to fit residues: 475.3111 Evaluate side-chains 285 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 278 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1997 time to fit residues: 3.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 142 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 176 ASN C 37 GLN C 90 GLN C 99 ASN C 176 ASN D 90 GLN D 176 ASN E 90 GLN E 176 ASN F 176 ASN G 28 GLN G 100 ASN G 194 GLN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN J 206 ASN K 90 GLN K 99 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16421 Z= 0.293 Angle : 0.536 8.240 22074 Z= 0.290 Chirality : 0.042 0.127 2347 Planarity : 0.004 0.036 2910 Dihedral : 4.206 14.207 2285 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.81 % Allowed : 11.88 % Favored : 86.31 % 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: 2.39 (0.18), residues: 2028 helix: 2.45 (0.18), residues: 786 sheet: 1.88 (0.23), residues: 424 loop : 0.63 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 84 HIS 0.006 0.002 HIS F 86 PHE 0.012 0.002 PHE K 110 TYR 0.025 0.003 TYR F 36 ARG 0.003 0.000 ARG A 156 *********************** 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 290 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 259 time to evaluate : 1.812 Fit side-chains outliers start: 31 outliers final: 10 residues processed: 275 average time/residue: 1.3993 time to fit residues: 425.7851 Evaluate side-chains 268 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.2037 time to fit residues: 3.6745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 40.0000 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 30 GLN A 90 GLN B 30 GLN B 176 ASN C 99 ASN C 176 ASN D 28 GLN D 90 GLN E 90 GLN E 176 ASN F 176 ASN G 69 HIS G 100 ASN G 194 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 99 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1284 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= 0.199 Angle : 0.495 9.398 22074 Z= 0.262 Chirality : 0.039 0.124 2347 Planarity : 0.003 0.025 2910 Dihedral : 4.039 13.997 2285 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.40 % Allowed : 12.58 % Favored : 86.02 % 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: 2.50 (0.18), residues: 2028 helix: 2.57 (0.18), residues: 786 sheet: 1.92 (0.23), residues: 424 loop : 0.70 (0.22), residues: 818 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 0.020 0.002 TYR F 36 ARG 0.002 0.000 ARG F 112 *********************** 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 297 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 273 time to evaluate : 2.006 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 285 average time/residue: 1.4239 time to fit residues: 448.7145 Evaluate side-chains 276 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 267 time to evaluate : 1.967 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.2059 time to fit residues: 3.6472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.1325 > 50: distance: 83 - 220: 10.251 distance: 96 - 208: 16.158 distance: 99 - 205: 14.463 distance: 106 - 197: 28.867 distance: 109 - 194: 31.463 distance: 117 - 181: 8.622 distance: 133 - 166: 22.140 distance: 136 - 163: 3.387 distance: 155 - 156: 5.618 distance: 155 - 158: 3.015 distance: 156 - 163: 5.736 distance: 158 - 159: 5.430 distance: 159 - 160: 3.323 distance: 160 - 161: 5.516 distance: 160 - 162: 3.333 distance: 163 - 164: 5.943 distance: 164 - 165: 6.093 distance: 164 - 167: 4.764 distance: 165 - 166: 15.404 distance: 165 - 171: 4.810 distance: 167 - 168: 8.636 distance: 168 - 169: 7.493 distance: 168 - 170: 11.624 distance: 172 - 173: 5.109 distance: 172 - 175: 5.886 distance: 173 - 174: 6.175 distance: 173 - 178: 4.628 distance: 175 - 176: 10.287 distance: 175 - 177: 14.010 distance: 178 - 179: 6.108 distance: 179 - 180: 6.769 distance: 180 - 181: 13.755 distance: 180 - 182: 9.944 distance: 182 - 183: 10.020 distance: 183 - 184: 6.266 distance: 183 - 186: 6.775 distance: 184 - 185: 27.977 distance: 184 - 194: 34.576 distance: 186 - 187: 5.105 distance: 187 - 188: 4.155 distance: 187 - 189: 3.011 distance: 190 - 192: 3.172 distance: 191 - 192: 3.631 distance: 192 - 193: 3.962 distance: 194 - 195: 54.584 distance: 195 - 196: 13.913 distance: 196 - 197: 22.621 distance: 196 - 198: 24.065 distance: 198 - 199: 5.889 distance: 199 - 200: 7.672 distance: 199 - 202: 4.563 distance: 200 - 201: 12.883 distance: 202 - 203: 3.979 distance: 202 - 204: 6.818 distance: 206 - 209: 6.481 distance: 207 - 208: 3.252 distance: 209 - 210: 5.157 distance: 212 - 213: 3.422 distance: 213 - 214: 8.013 distance: 216 - 217: 5.995 distance: 217 - 218: 7.204 distance: 217 - 219: 14.129 distance: 221 - 222: 6.878 distance: 222 - 223: 13.312 distance: 222 - 224: 7.485