Starting phenix.real_space_refine (version: dev) on Wed Apr 6 01:16:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dkf_7952/04_2022/6dkf_7952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dkf_7952/04_2022/6dkf_7952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dkf_7952/04_2022/6dkf_7952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dkf_7952/04_2022/6dkf_7952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dkf_7952/04_2022/6dkf_7952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dkf_7952/04_2022/6dkf_7952.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.131 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 152": "NH1" <-> "NH2" Residue "D ARG 152": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "K ARG 152": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "L ARG 152": "NH1" <-> "NH2" Residue "M ARG 152": "NH1" <-> "NH2" Residue "N ARG 152": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 17060 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "C" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 829 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 621 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 249 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "G" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1276 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Chain: "I" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 829 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 621 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 249 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "N" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1276 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Time building chain proxies: 9.99, per 1000 atoms: 0.59 Number of scatterers: 17060 At special positions: 0 Unit cell: (119.78, 130.38, 113.42, 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 72 16.00 O 3330 8.00 N 2950 7.00 C 10708 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: 7.93 Conformation dependent library (CDL) restraints added in 2.9 seconds 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 28 sheets defined 54.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'B' and resid 20 through 27 removed outlier: 3.683A pdb=" N LEU B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.781A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 184 Processing helix chain 'D' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.765A pdb=" N ILE D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 147 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 150 " --> pdb=" O THR D 146 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 150 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.670A pdb=" N ASN A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'E' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 Processing helix chain 'E' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.512A pdb=" N PHE E 102 " --> pdb=" O SER E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 159 removed outlier: 3.929A pdb=" N ASN E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 150 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 153 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP F 27 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 55 Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN F 141 " --> pdb=" O GLU F 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 147 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 150 " --> pdb=" O THR F 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE F 153 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG F 157 " --> pdb=" O ILE F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 184 Processing helix chain 'G' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP G 27 " --> pdb=" O ARG G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.765A pdb=" N ILE G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 159 removed outlier: 3.931A pdb=" N ASN G 141 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG G 147 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG G 157 " --> pdb=" O ILE G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 184 Processing helix chain 'I' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP I 27 " --> pdb=" O ARG I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 70 through 84 removed outlier: 3.763A pdb=" N ILE I 77 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE I 102 " --> pdb=" O SER I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG I 147 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 150 " --> pdb=" O THR I 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE I 153 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG I 157 " --> pdb=" O ILE I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.781A pdb=" N LYS I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 184 Processing helix chain 'K' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 70 through 84 removed outlier: 3.765A pdb=" N ILE K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 159 removed outlier: 3.931A pdb=" N ASN K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG K 147 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 150 " --> pdb=" O THR K 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE K 153 " --> pdb=" O LYS K 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG K 157 " --> pdb=" O ILE K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 184 Processing helix chain 'J' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 55 Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 159 removed outlier: 3.929A pdb=" N ASN J 141 " --> pdb=" O GLU J 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU J 150 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE J 153 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG J 157 " --> pdb=" O ILE J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 169 removed outlier: 3.781A pdb=" N LYS J 167 " --> pdb=" O GLU J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 184 Processing helix chain 'H' and resid 21 through 26 Processing helix chain 'H' and resid 37 through 55 Processing helix chain 'H' and resid 70 through 84 Processing helix chain 'H' and resid 98 through 106 Processing helix chain 'H' and resid 134 through 145 removed outlier: 3.670A pdb=" N ASN H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 Processing helix chain 'H' and resid 161 through 170 Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'L' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP L 27 " --> pdb=" O ARG L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 55 Processing helix chain 'L' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE L 77 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 105 removed outlier: 3.512A pdb=" N PHE L 102 " --> pdb=" O SER L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN L 141 " --> pdb=" O GLU L 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG L 147 " --> pdb=" O ILE L 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU L 150 " --> pdb=" O THR L 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE L 153 " --> pdb=" O LYS L 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 157 " --> pdb=" O ILE L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS L 167 " --> pdb=" O GLU L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 184 Processing helix chain 'M' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP M 27 " --> pdb=" O ARG M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 70 through 84 removed outlier: 3.765A pdb=" N ILE M 77 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE M 102 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 159 removed outlier: 3.931A pdb=" N ASN M 141 " --> pdb=" O GLU M 137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG M 147 " --> pdb=" O ILE M 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 150 " --> pdb=" O THR M 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE M 153 " --> pdb=" O LYS M 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG M 157 " --> pdb=" O ILE M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS M 167 " --> pdb=" O GLU M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 184 Processing helix chain 'N' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 55 Processing helix chain 'N' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE N 77 " --> pdb=" O ALA N 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN N 141 " --> pdb=" O GLU N 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU N 150 " --> pdb=" O THR N 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE N 153 " --> pdb=" O LYS N 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG N 157 " --> pdb=" O ILE N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS N 167 " --> pdb=" O GLU N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 184 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE B 30 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN B 65 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 32 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER B 66 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET B 95 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE B 113 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 90 " --> pdb=" O PHE B 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 114 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA3, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE D 30 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN D 65 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU D 32 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER D 66 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET D 95 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE D 113 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR D 90 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 114 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE C 30 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN C 65 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU C 32 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER C 66 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET C 95 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE C 113 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR C 90 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 114 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.350A pdb=" N ILE A 60 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 91 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 62 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 93 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 64 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET A 95 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU A 119 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A 94 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET A 121 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA A 96 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.350A pdb=" N ILE A 60 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 91 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 62 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 93 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 64 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET A 95 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE A 113 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR A 90 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.417A pdb=" N ILE E 30 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN E 65 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU E 32 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER E 66 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET E 95 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE E 113 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR E 90 " --> pdb=" O PHE E 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA E 114 " --> pdb=" O GLU E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AB2, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.416A pdb=" N ILE F 30 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN F 65 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU F 32 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER F 66 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET F 95 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE F 113 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR F 90 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 114 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AB4, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE G 30 " --> pdb=" O TYR G 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN G 65 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU G 32 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER G 66 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET G 95 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE G 113 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR G 90 " --> pdb=" O PHE G 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 114 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 119 through 121 Processing sheet with id=AB6, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE I 30 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN I 65 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU I 32 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER I 66 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE I 113 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR I 90 " --> pdb=" O PHE I 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 114 " --> pdb=" O GLU I 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 119 through 121 Processing sheet with id=AB8, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.417A pdb=" N ILE K 30 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN K 65 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU K 32 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N SER K 66 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE K 113 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR K 90 " --> pdb=" O PHE K 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA K 114 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 119 through 121 Processing sheet with id=AC1, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER J 66 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE J 113 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR J 90 " --> pdb=" O PHE J 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA J 114 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 119 through 121 Processing sheet with id=AC3, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.350A pdb=" N ILE H 60 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE H 91 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU H 62 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE H 93 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE H 64 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET H 95 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU H 119 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY H 94 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET H 121 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA H 96 " --> pdb=" O MET H 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.350A pdb=" N ILE H 60 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE H 91 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU H 62 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE H 93 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE H 64 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET H 95 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N PHE H 113 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR H 90 " --> pdb=" O PHE H 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE L 30 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN L 65 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU L 32 " --> pdb=" O ASN L 65 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER L 66 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE L 113 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR L 90 " --> pdb=" O PHE L 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA L 114 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 119 through 121 Processing sheet with id=AC7, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.417A pdb=" N ILE M 30 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN M 65 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU M 32 " --> pdb=" O ASN M 65 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER M 66 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE M 113 " --> pdb=" O VAL M 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR M 90 " --> pdb=" O PHE M 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA M 114 " --> pdb=" O GLU M 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 119 through 121 Processing sheet with id=AC9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER N 66 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE N 113 " --> pdb=" O VAL N 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR N 90 " --> pdb=" O PHE N 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 114 " --> pdb=" O GLU N 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 119 through 121 856 hydrogen bonds defined for protein. 2568 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: 5.19 Time building geometry restraints manager: 8.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5815 1.34 - 1.45: 1793 1.45 - 1.57: 9508 1.57 - 1.68: 0 1.68 - 1.80: 132 Bond restraints: 17248 Sorted by residual: bond pdb=" CA LEU A 150 " pdb=" C LEU A 150 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.27e-02 6.20e+03 7.09e+00 bond pdb=" CA LEU H 150 " pdb=" C LEU H 150 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.27e-02 6.20e+03 7.09e+00 bond pdb=" CA THR A 146 " pdb=" C THR A 146 " ideal model delta sigma weight residual 1.523 1.492 0.032 1.30e-02 5.92e+03 5.97e+00 bond pdb=" N THR H 146 " pdb=" CA THR H 146 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.21e-02 6.83e+03 5.67e+00 bond pdb=" CA THR H 146 " pdb=" C THR H 146 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.30e-02 5.92e+03 5.61e+00 ... (remaining 17243 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.10: 305 106.10 - 112.44: 9277 112.44 - 118.78: 4589 118.78 - 125.12: 9029 125.12 - 131.46: 108 Bond angle restraints: 23308 Sorted by residual: angle pdb=" N ILE H 143 " pdb=" CA ILE H 143 " pdb=" C ILE H 143 " ideal model delta sigma weight residual 110.62 102.83 7.79 1.02e+00 9.61e-01 5.83e+01 angle pdb=" N HIS H 142 " pdb=" CA HIS H 142 " pdb=" C HIS H 142 " ideal model delta sigma weight residual 111.28 102.96 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N HIS A 142 " pdb=" CA HIS A 142 " pdb=" C HIS A 142 " ideal model delta sigma weight residual 111.28 102.96 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N ILE A 143 " pdb=" CA ILE A 143 " pdb=" C ILE A 143 " ideal model delta sigma weight residual 110.62 102.87 7.75 1.02e+00 9.61e-01 5.77e+01 angle pdb=" N GLU H 137 " pdb=" CA GLU H 137 " pdb=" C GLU H 137 " ideal model delta sigma weight residual 111.28 103.97 7.31 1.09e+00 8.42e-01 4.50e+01 ... (remaining 23303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.27: 10267 15.27 - 30.54: 269 30.54 - 45.81: 36 45.81 - 61.08: 12 61.08 - 76.36: 12 Dihedral angle restraints: 10596 sinusoidal: 3906 harmonic: 6690 Sorted by residual: dihedral pdb=" CA ILE H 64 " pdb=" C ILE H 64 " pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ILE A 64 " pdb=" C ILE A 64 " pdb=" N ASN A 65 " pdb=" CA ASN A 65 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ILE K 64 " pdb=" C ILE K 64 " pdb=" N ASN K 65 " pdb=" CA ASN K 65 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 10593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2166 0.061 - 0.123: 546 0.123 - 0.184: 42 0.184 - 0.245: 4 0.245 - 0.307: 2 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CA ILE H 143 " pdb=" N ILE H 143 " pdb=" C ILE H 143 " pdb=" CB ILE H 143 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE A 143 " pdb=" N ILE A 143 " pdb=" C ILE A 143 " pdb=" CB ILE A 143 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLU H 137 " pdb=" N GLU H 137 " pdb=" C GLU H 137 " pdb=" CB GLU H 137 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 2757 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN M 124 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO M 125 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO M 125 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO M 125 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 124 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 125 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 125 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 125 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN I 124 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO I 125 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO I 125 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 125 " -0.019 5.00e-02 4.00e+02 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 90 2.50 - 3.10: 14663 3.10 - 3.70: 24623 3.70 - 4.30: 36947 4.30 - 4.90: 59314 Nonbonded interactions: 135637 Sorted by model distance: nonbonded pdb=" OD1 ASP C 170 " pdb=" N GLU M 135 " model vdw 1.898 2.520 nonbonded pdb=" OD1 ASP F 170 " pdb=" N GLU J 135 " model vdw 1.904 2.520 nonbonded pdb=" OD1 ASP G 170 " pdb=" N GLU I 135 " model vdw 1.906 2.520 nonbonded pdb=" N GLU C 135 " pdb=" OD1 ASP M 170 " model vdw 1.923 2.520 nonbonded pdb=" N GLU B 135 " pdb=" OD1 ASP N 170 " model vdw 1.935 2.520 ... (remaining 135632 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 20 through 125 or resid 135 through 192)) selection = (chain 'B' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 20 through 125 or resid 135 through 192)) selection = (chain 'I' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'N' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10708 2.51 5 N 2950 2.21 5 O 3330 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 3.180 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.140 Process input model: 46.480 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.010 0.051 17248 Z= 0.642 Angle : 0.880 8.678 23308 Z= 0.489 Chirality : 0.053 0.307 2760 Planarity : 0.005 0.035 3052 Dihedral : 8.963 76.356 6252 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.00 % 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: -5.10 (0.10), residues: 2258 helix: -3.85 (0.09), residues: 1190 sheet: -2.27 (0.30), residues: 168 loop : -2.66 (0.11), residues: 900 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 867 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 867 average time/residue: 0.2889 time to fit residues: 367.0686 Evaluate side-chains 623 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 623 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 175 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 83 HIS D 42 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN C 142 HIS C 173 ASN E 54 GLN E 117 ASN F 39 ASN F 42 ASN F 52 GLN F 89 GLN F 141 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS I 82 GLN I 83 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN L 54 GLN M 42 ASN M 52 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN N 54 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 17248 Z= 0.305 Angle : 0.671 8.437 23308 Z= 0.349 Chirality : 0.046 0.160 2760 Planarity : 0.005 0.071 3052 Dihedral : 5.029 16.878 2430 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 6.79 % 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 (0.15), residues: 2258 helix: -1.08 (0.13), residues: 1284 sheet: -2.33 (0.31), residues: 168 loop : -1.86 (0.16), residues: 806 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 710 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 72 residues processed: 764 average time/residue: 0.2709 time to fit residues: 311.6090 Evaluate side-chains 678 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 606 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.1538 time to fit residues: 24.2392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 169 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 ASN B 83 HIS B 123 HIS D 39 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 HIS E 42 ASN E 83 HIS F 52 GLN G 39 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 ASN I 83 HIS ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 HIS J 42 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN L 42 ASN L 83 HIS L 166 GLN M 42 ASN M 52 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 17248 Z= 0.259 Angle : 0.599 6.847 23308 Z= 0.310 Chirality : 0.044 0.177 2760 Planarity : 0.005 0.116 3052 Dihedral : 4.615 19.575 2430 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 3.69 % 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: -1.09 (0.17), residues: 2258 helix: -0.05 (0.14), residues: 1284 sheet: -2.08 (0.30), residues: 198 loop : -1.29 (0.19), residues: 776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 688 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 24 residues processed: 715 average time/residue: 0.2830 time to fit residues: 300.6216 Evaluate side-chains 644 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 620 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1458 time to fit residues: 9.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 58 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS D 42 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN F 52 GLN F 117 ASN G 54 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 142 HIS J 173 ASN M 42 ASN M 52 GLN ** M 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN N 89 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 17248 Z= 0.370 Angle : 0.664 7.180 23308 Z= 0.342 Chirality : 0.047 0.201 2760 Planarity : 0.005 0.086 3052 Dihedral : 4.834 20.724 2430 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 6.02 % 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: -0.91 (0.17), residues: 2258 helix: 0.07 (0.15), residues: 1278 sheet: -1.60 (0.35), residues: 168 loop : -1.32 (0.20), residues: 812 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 676 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 63 residues processed: 712 average time/residue: 0.2747 time to fit residues: 292.6343 Evaluate side-chains 683 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 620 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.1575 time to fit residues: 20.8803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 54 optimal weight: 40.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 39 ASN B 83 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN E 42 ASN E 142 HIS F 52 GLN F 117 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS K 42 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 HIS J 173 ASN L 42 ASN M 42 ASN M 52 GLN M 117 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17248 Z= 0.288 Angle : 0.622 10.492 23308 Z= 0.320 Chirality : 0.046 0.281 2760 Planarity : 0.005 0.087 3052 Dihedral : 4.631 19.906 2430 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 3.75 % 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: -0.61 (0.17), residues: 2258 helix: 0.31 (0.15), residues: 1278 sheet: -1.46 (0.35), residues: 180 loop : -1.17 (0.21), residues: 800 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 675 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 24 residues processed: 696 average time/residue: 0.2812 time to fit residues: 294.8653 Evaluate side-chains 647 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 623 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1544 time to fit residues: 9.7843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 113 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 83 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN I 83 HIS J 42 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 17248 Z= 0.334 Angle : 0.654 8.429 23308 Z= 0.337 Chirality : 0.046 0.245 2760 Planarity : 0.005 0.070 3052 Dihedral : 4.740 20.807 2430 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 4.35 % 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: -0.67 (0.18), residues: 2258 helix: 0.29 (0.15), residues: 1276 sheet: -1.75 (0.35), residues: 178 loop : -1.19 (0.21), residues: 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 670 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 52 residues processed: 700 average time/residue: 0.2763 time to fit residues: 289.2635 Evaluate side-chains 673 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 621 time to evaluate : 2.125 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.1579 time to fit residues: 18.3386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 182 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS B 166 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN F 52 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN L 42 ASN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 17248 Z= 0.234 Angle : 0.609 8.025 23308 Z= 0.315 Chirality : 0.044 0.257 2760 Planarity : 0.005 0.090 3052 Dihedral : 4.460 21.132 2430 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.79 % 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: -0.27 (0.18), residues: 2258 helix: 0.57 (0.15), residues: 1278 sheet: -1.56 (0.35), residues: 190 loop : -0.91 (0.22), residues: 790 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 648 time to evaluate : 1.939 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 658 average time/residue: 0.2726 time to fit residues: 267.2023 Evaluate side-chains 640 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 622 time to evaluate : 2.024 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1455 time to fit residues: 7.6572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 169 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS C 42 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS I 83 HIS ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 ASN L 117 ASN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN M 117 ASN ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** N 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 17248 Z= 0.375 Angle : 0.704 9.546 23308 Z= 0.365 Chirality : 0.047 0.308 2760 Planarity : 0.006 0.080 3052 Dihedral : 4.776 20.379 2430 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 2.80 % 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: -0.59 (0.18), residues: 2258 helix: 0.37 (0.15), residues: 1272 sheet: -1.49 (0.36), residues: 180 loop : -1.22 (0.22), residues: 806 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 654 time to evaluate : 2.193 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 31 residues processed: 668 average time/residue: 0.2790 time to fit residues: 278.7613 Evaluate side-chains 659 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 628 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1503 time to fit residues: 11.4844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 61 optimal weight: 50.0000 chunk 181 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS F 47 GLN F 52 GLN F 89 GLN F 117 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 ASN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN N 89 GLN ** N 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 17248 Z= 0.197 Angle : 0.621 8.576 23308 Z= 0.321 Chirality : 0.044 0.295 2760 Planarity : 0.004 0.076 3052 Dihedral : 4.381 21.164 2430 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.19 % 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: -0.04 (0.18), residues: 2258 helix: 0.73 (0.15), residues: 1278 sheet: -1.07 (0.33), residues: 260 loop : -0.82 (0.24), residues: 720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 635 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 641 average time/residue: 0.2810 time to fit residues: 268.0599 Evaluate side-chains 619 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 606 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1546 time to fit residues: 6.7052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 108 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS D 42 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN E 47 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 ASN J 142 HIS J 173 ASN L 42 ASN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN M 52 GLN M 123 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 17248 Z= 0.340 Angle : 0.705 10.584 23308 Z= 0.366 Chirality : 0.047 0.290 2760 Planarity : 0.005 0.072 3052 Dihedral : 4.667 20.538 2430 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.49 % 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: -0.50 (0.18), residues: 2258 helix: 0.44 (0.15), residues: 1292 sheet: -1.13 (0.33), residues: 262 loop : -1.28 (0.23), residues: 704 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 636 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 646 average time/residue: 0.2832 time to fit residues: 273.3499 Evaluate side-chains 633 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 619 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1572 time to fit residues: 6.9189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 40.0000 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 182 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS D 42 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN C 65 ASN E 42 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN F 52 GLN G 82 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS K 42 ASN ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS J 42 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN M 47 GLN M 52 GLN M 166 GLN N 47 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129838 restraints weight = 25262.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132819 restraints weight = 13416.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134670 restraints weight = 8474.770| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 17248 Z= 0.223 Angle : 0.663 9.550 23308 Z= 0.344 Chirality : 0.045 0.314 2760 Planarity : 0.004 0.075 3052 Dihedral : 4.466 24.690 2430 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.66 % 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: -0.05 (0.18), residues: 2258 helix: 0.75 (0.15), residues: 1272 sheet: -0.98 (0.33), residues: 262 loop : -0.92 (0.23), residues: 724 =============================================================================== Job complete usr+sys time: 4749.89 seconds wall clock time: 85 minutes 43.86 seconds (5143.86 seconds total)